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2021 2020 2019 2016 2006 1996 1986

Publications 2021


J337. Chen F, Shi Q, Pei F, Vogt A, Porritt RA, Garcia G, Gomez AC, Cheng MH, Schurdak ME, Chan SY, Arumugaswami V, Stern AM, Taylor DL, Arditi M, Bahar I. (2021) A Systems-level Study Reveals Host-targeted Repurposable Drugs Against SARS-CoV2 Infection. Molecular Systems Biol [Online ahead of print]. PMID: 34339582

J336. Kaynak BT, Zhang S, Bahar I, Doruker P (2021) ClustENMD: Efficient sampling of biomolecular conformational space at atomic resolution. Bioinformatics. Jul 8. PMID: 34240100

J335. Zhang Y, Zhang S, Xing J, Bahar I (2021) Normal mode analysis of membrane protein dynamics using the vibrational subsystem analysis. J Chem Phys 154, 195102 PMID: 34240914 PMCID: PMC8131107

J334. Mikulska-Ruminska K, Anthonymuthu TS, Levkina A, Shrivastava IH, Kapralov AA, Bayir H, Kagan VE, Bahar I. (2021) NO● Represses the Oxygenation of Arachidonoyl PE by 15LOX/PEBP1: Mechanism and Role in Ferroptosis. Int J Mol Sci. 22(10): 5253. PMID: 34067535 PMCID: PMC8156958

J333. Aggarwal J, Cheng MH, Salvino JM, Bahar I, Mortensen OV. (2021) Functional Characterization of the Dopaminergic Psychostimulant Sydnocarb as an Allosteric Modulator of the Human Dopamine Transporter. Biomedicines, 9(6), 634; PMID: 34199621 PMCID: PMC8227285

J332. Aguilar JI, Cheng MH, Font J, Schwartz AC, Ledwitch K, Duran A, Mabry SJ, Belovich AN, Zhu Y, Carter AM, Shi L, Kurian MA, Fenollar-Ferrer C, Meiler J, Ryan RM, Mchaourab HS, Bahar I, Matthies HJG, Galli A. (2021) Psychomotor impairments and therapeutic implications revealed by a mutation associated with infantile Parkinsonism-Dystonia. ELife, 10, e68039 PMID: 34002696 PMCID: PMC8131106

J331. Cheng MH, Porritt RA, Rivas MN, Krieger JM, Ozdemir AB, Garcia G Jr, Arumugaswami V, Fries BC, Arditi M, Bahar I. (2021) A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry in vitro. Structure [Online ahead of print]. PMID: 33269352 PMCID: PMC7709177

J330. Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I. (2021) ProDy 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python. Bioinformatics [Online ahead of print]. PMID: 33822884

J329. Pei F, Shi Q, Zhang H, Bahar I (2021) Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. J Chem Inf Model 61:1670-1682. PMID: 33831302 PMCID: PMC8253547

J328. Porritt RA, Paschold L, Noval Rivas M, Cheng MH, Yonker LM, Chandnani H, Lopez M, Simnica D, Schultheiß C, Santiskulvong C, van Eyk J, McCormick JK, Fasano A, Bahar I, Binder M, Arditi M (2021) HLA class I-associated expansion of TRBV11-2 T cells in Multisystem Inflammatory Syndrome in Children. J Clin Invest. 131(10). PMID: 33705359 PMCID: PMC8121516 Link to article /commentary

J327. Sorkina T, Cheng MH, Bagalkot TR, Wallace C, Watkins SC, Bahar I, Sorkin A. (2021) Direct coupling of oligomerization and oligomerization-driven endocytosis of the dopamine transporter to its conformational mechanics and activity. J Biol Chem. Feb 18:100430. PMID: 33610553 PMCID: PMC8010718

J326. Wang H, Pei F, Vanyukov MM, Bahar I, Wu W, Xing EP. (2021) Coupled mixed model for joint genetic analysis of complex disorders with two independently collected data sets. BMC Bioinformatics 22(1):50. PMID: 33546598 PMCID: PMC7866684

J325. Sun WY, Tyurin VA, Mikulska-Ruminska K, Shrivastava IH, Anthonymuthu TS, Zhai YJ, Pan MH, Gong HB, Lu DH, Sun J, Duan WJ, Korolev S, Abramov AY, Angelova PR, Miller I, Beharier O, Mao GW, Dar HH, Kapralov AA, Amoscato AA, Hastings TG, Greenamyre TJ, Chu CT, Sadovsky Y, Bahar I, Bayir H, Tyurina YY, He RR, Kagan VE. (2021) Phospholipase iPLA2ß averts ferroptosis by eliminating a redox lipid death signal. Nat Chem Biol Feb 4(8). PMID: 33542532 PMCID: PMC8152680

J324. Meirovitch H, Bahar I. (2021) Harold A. Scheraga (10/18/1921—8/1/2020): A pioneering scientist who laid the foundations of protein science in the 20th century. Proc Natl Acad Sci USA 118(8) PMID: 33547253 PMCID: PMC7923550.

J323. Cheng MH, Krieger JM, Kaynak B, Arditi M, Bahar I. (2021) Impact of South African 501.V2 Variant on SARS-CoV-2 Spike Infectivity and Neutralization: A Structure-based Computational Assessment. BioRxiv [Online ahead of print].

J322. Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T (2021) HiDeF: Identifying Persistent Structures in Multiscale 'Omics Data. Genome Biol. 22: 21. PMID: 33413539 PMCID: PMC7789082

J321. Dagvadorj J, Mikulska-Ruminska K, Tumurkhuu G, Ratsimandresy RA, Carriere J, Andres AM, Marek-Iannucci S, Song Y, Chen S, Lane M, Dorfleutner A, Gottlieb RA, Stehlik C, Cassel S, Sutterwala FS, Bahar I, Crother TR, Arditi M (2021) Recruitment of pro-IL-1a to Mitochondrial Cardiolipin, via Shared LC3 Binding Domain, Inhibits Mitophagy and Drives Maximal NLRP3 Activation. Proc Natl Acad Sci USA 118 PMID: 33361152 PMCID: PMC7817159

J320. Rivas MN, Porritt RA, Cheng MH, Bahar I, Arditi M. (2021) COVID-19 Associated Multisystem Inflammatory Syndrome in Children (MIS-C): A Novel Disease that Mimics Toxic Shock Syndrome. The Superantigen Hypothesis. J Allergy Clin Immunol. 147: 57-59. PMID: 33075409 PMCID: PMC7564502

J319. Anthonymuthu TS, Tyurina YY, Sun WY, Mikulska-Ruminska K, Shrivastava IH, Tyurin VA, Cinemre FB, Dar HH, VanDemark AP, Holman TR, Sadovsky YS, Stockwell BR, He RR, Bahar I, Bayir H, Kagan VE. (2021) Resolving the Paradox of Ferroptotic Cell Death: Ferrostatin-1 Binds to 15LOX/PEBP1 Complex, Suppresses Generation of Peroxidized ETE-PE, and Protects against Ferroptosis. Redox Biol. 38: 101744 PMID: 33126055 PMCID: PMC7596334 .

Publications 2020

J318. Wingert B, Krieger JM, Li H, Bahar I (2020) Adaptability and Specificity: How Do Proteins Balance Opposing Needs to Achieve Function? Curr Opin Struct Biol 67:25-32. PMID: 33053463

J317. Porritt RA, Paschold L, Rivas MN, Cheng MH, Yonker LM, Chandnani H, Lopez M, Simnica D, Schulthei C, Santiskulvong C, Van Eyk J, Fasano A, Bahar I, Binder M, Arditi M. (2020) Identification of a Unique TCR Repertoire, Consistent with a Superantigen Selection Process in Children with Multi-system Inflammatory Syndrome. BioRxiv doi:

J316. Cheng MH, Porritt RA, Rivas MN, Krieger JM, Ozdemir AB, Garcia G, Arumugaswami V, Fries BC, Arditi M, Bahar I. (2020) A Monoclonal Antibody Against Staphylococcal Enterotoxin B Superantigen Inhibits SARS-CoV-2 entry in vitro. BioRxiv doi:

J315. Zhou Z, Huang F, Shrivastava IH, Zhu R, Luo A, Hottiger M, Bahar I, Liu Z, Cristofanilli M, Wan Y (2020) New Insight into the Significance of KLF4 PARylation in Genome Stability, Carcinogenesis, and Therapy. EMBO Molecular Medicine, e12391. [Online ahead of print].

J314. Song X, Zhou Z, Li H, Xue Y, Lu X, Bahar I, Kepp O, Hung MC, Kroemer G, Wan Y (2020) Pharmacological Suppression of B7-H4 Glycosylation Restores Antitumor Immunity in Immune-Cold Breast Cancers. Cancer Discov 10:1872-1893. doi: 10.1158/2159-8290.CD-20-0402. [Online ahead of print]. PMID: 32938586 PMCID: 7710601

J313. Cheng MH, Zhang S, Porritt RA, Rivas MN, Paschold L, Willscher E, Binder M, Arditi M*, Bahar I* (2020) Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. Proc Natl Acad Sci USA 117: 25254-25262 PMID: 32989130 PMCID: PMC7568239

J312. Zhang Y, Krieger JM, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, Xing J, Bahar I (2020) State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. Prog Biophys Mol Biol S0079-6107(20)30082-1. PMID: 32866476

J311. Clark LJ, Krieger J, White AD, Bondarenko V, Lei S, Fang F, Lee JY, Doruker P, Bttke T, Jean-Alphonse F, Tang P, Gardella TJ, Xiao K, Sutkeviciute I, Coin I, Bahar I, Vilardaga JP (2020) Allosteric interactions in the parathyroid hormone GPCR-arrestin complex formation. Nat Chem Biol 16(10):1096-1104 PMID: 32632293 PMCID: PMC7502484 (available on 2021-01-06)

J310. Kaynak BT,* Bahar I,* Doruker P. (2020) Essential Site Scanning Analysis: a new approach for detecting sites that modulate the dispersion of protein global motions. Comp Struct Biotech J 18:1577-1586. PMID: 32637054 PMCID: PMC7330491

J309. Krieger JM, Doruker P, Scott AL, Perahia D, Bahar I. (2020) Towards Gaining Sight of Multiscale Events: Utilizing Network Models and Normal Modes in Hybrid Methods. Curr Opin Struct Biol 64:34-41. PMID: 32622329 PMCID: PMC7666066 (available on 2021-10-01)

J308. Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T. (2020) Decoding of persistent multiscale structures in complex biological networks. bioRxiv. PMID: 32587977 PMCID: PMC7310637

J307. Zhao J, Dar HH, Deng Y, St. Croix CM, Li Z, Minami Y, Shrivastava IH, Tyurina YY, Etling E, Rosenbaum JC, Nagasaki T, Trudeau JB, Watkins SC, Bahar I, Bayir H, VanDemark AP, Kagan VE, Wenzel SE. (2020) PEBP1 Acts as a Rheostat Between Prosurvival Autophagy and Ferroptotic Death in Asthmatic Epithelial Cells. Proc Natl Acad Sci (USA) 117:14376-14385. PMID: 32513718 PMCID: PMC7321965

J306. Kim Y, Jun I, Shin DH, Yoon JG, Piao H, Jung J, Park HW, Cheng MH, Bahar I, Whitcomb DC, Lee MG (2020) Regulation of CFTR Bicarbonate Channel Activity by WNK1: Implications for Pancreatitis and CFTR-Related Disorders. Cell Mol Gastroenterol Hepatol 9:71-103. PMID: 31561038 PMCID: PMC6889609

J305. Shi Q, Pei F, Silverman GA, Pak SC, Perlmutter DH, Liu B*, Bahar I*. (2020) Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis. Int. J. Mol. Sci 21:2855. PMID: 32325894 PMCID: PMC7215584

J304. Ponzoni L, Nguyen NH, Bahar I*, Brodsky JL*. (2020) Complementary Computational and Experimental Evaluation of Missense Variants in the ROMK Potassium Channel. PLOS Comp Biol 16, e1007749. PMID: 32251469 PMCID: PMC7162551

J303. Li H, Doruker P, Hu G, Bahar I. (2020) Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding. Biophys J 118: 1782-1794. PMID: 32130874 PMCID: 7136436

J302. Li H, Pei F, Taylor DL, Bahar I. (2020) QuartataWeb: Integrated Chemical-protein-pathway Mapping for Polypharmacology and Chemogenomics. Bioinformatics 36:3935-3937. PMID: 32221612 PMCID: PMC7320630

J301. Zhou Z, Zhou H, Ponzoni L, Luo A, Zhu R, He M, Huang Y, Guan KL, Bahar I, Liu Z, Wan Y. (2020) EIF3H Orchestrates Hippo Pathway-mediated Oncogenesis Through an Unexpected Catalytic Control of YAP Stability. Cancer Res 80:2550-2563. PMID: 32269044 PMCID: PMC7316131

J300. Cheng MH, Zhang S, Porritt RA, Arditi M, Bahar I. (2020) An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations. BioRxiv. 2020 May 21:2020.05.21.109272. PMID: 32511374 PMCID: PMC7263503

J299. Thermozier S, Hou W, Zhang X, Shields D, Fisher R, Bayir H, Kagan V, Yu J, Liu B, Bahar I, Epperly MW, Wipf P, Wang H, Huq MS, and Greenberger JS. (2020) Anti-Ferroptosis Drug Enhances Total-Body Irradiation Mitigation by Drugs that Block Apoptosis and Necroptosis. Radiat Res 193:435-450. PMID: 32134361 PMCID: PMC7299160

J298. Ponzoni L, Penaherrera DA, Oltvai ZN, and Bahar I (2020) Rhapsody: Predicting the pathogenicity of human missense variants. Bioinformatics 36:3084-3092.PMID: 32101277 PMCID: PMC7214033

J297. Kapralov AA, Yang Q, Dar HH, Tyurina YY, Anthonymuthu TS?, Kim R, St. Croix CM, Mikulska-Ruminska K, Liu B, Shrivastava IH, Tyurin VA, Ting HC, Wu YL, Gao Y, Shurin GV, Artyukhova MA, Ponomareva LA, Timashev8 PS, Domingues RM, Stoyanovsky DA, Greenberger JS, Mallampalli RK, Bahar I, Gabrilovich DI, Bayir H, Kagan VE. (2020) Redox Lipid Reprogramming Commands Susceptibility of Macrophages and Microglia to Ferroptotic Death. Nat Chem Biol 16:278-290. PMID: 32080625 PMCID: PMC7233108

B18. Shrivastava IH, Liu C, Dutta A, Bakan A, Bahar I. (2020) Allostery as Structure-Encoded Collective Dynamics: Significance in Drug Design. Structural Biology in Drug Discovery: Methods, Techniques, and Practices. Eds Jean-Paul Renaud. Chapter 6, p125-141, John Wiley & Sons, NY.

J296. Lee JY, Krieger JM, Li H, Bahar I. (2020) Pharmmaker: Pharmacophore Modeling and Hit Identification Based on Druggability Simulations. Protein Sci 29:76-86 PMID: 31576621 PMCID: 6933858

J295. Zhang S, Chen F, Bahar I. (2020) Differences in the Intrinsic Spatial Dynamics of the Chromatin Contribute to Cell Differentiation. Nucleic Acids Res 48, 1131-1145. PMID: 31828312 PMCID: 7026660

J294. Zhang Y, Doruker P, Kaynak B, Zhang S, Krieger JM, Li H, Bahar I. (2020) Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior. Curr Opin Struct Biol 62:14-21. PMID: 31785465 PMCID: PMC7250723

Publications 2019

J293. Belovich AN, Aguilar JI, Mabry SJ, Cheng MH, Zanella D, Hamilton PJ, Stanislowski DJ, Shekar A, Foster JD, Bahar I, Matthies HJG, Galli A. (2019) A network of phosphatidylinositol (4, 5)-bisphosphate (PIP 2) binding sites on the dopamine transporter regulates amphetamine behavior in Drosophila Melanogaster. Molec. Psychiatry. pp 1-14.

J292. Chi J, Li H, Zhou Z, Izquierdo-Ferrer J, Xue Y, Wavelet CM, Schiltz GE, Zhang B, Cristofanilli M, Lu X, Bahar I, Wan Y. (2019) A Novel Strategy to Block Mitotic Progression for Targeted Therapy. EBioMedicine 49:40-54 PMID:31669221 PMCID: 6945239

J291. Cheng MH, Bahar I. (2019) Monoamine transporters: structure, intrinsic dynamics and allosteric regulation. Nat Struct. & Molec. Biol 26: 545556. PMID: 31270469 PMCID: 6712983

J290. Thermozier S, Zhang X, Hou W, Fisher R, Epperly MW, Liu B, Bahar I, Wang H, Greenberger JS. (2019) Radioresistance of Serpinb3a-/- Mice and Derived Hematopoietic and Marrow Stromal Cell Lines. Radiat Res. 192: 267-281. PMID: 31295086 PMCID: 6759811

B18. Taylor DL, Gough A, Schurdak ME, Vernetti L, Chennubhotla CS, Lefever D, Pei F, Faeder JR, Lezon TR, Stern AM, Bahar I. (2019) Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology in Handb Exp Pharmacol, 260:327-367 PMID: 31201557 PMCID: 6911651

J289. Cheng MH, Ponzoni L, Sorkina T, Lee JY, Zhang S, Sorkin A, Bahar I. (2019) Trimerization of Dopamine Transporter Triggered by AIM-100 Binding: Molecular Mechanisms and Effect of Mutations. Neuropharmacology 161:107676 PMID: 31228486 PMCID: 6917874 DOI: 10.1016/j.neuropharm.2019.107676

J288. Zhou Z, Feng Z, Hu D, Yang P, Gur M, Bahar I, Cristofanilli M, Gradishar WJ, Xie XQ, Wan Y. (2019) ) A novel small-molecule antagonizes PRMT5-mediated KLF4 methylation for targeted therapy. EBioMedicine 44: 98-111. PMID: 31101597 PMCID: 6604046

J287. Zhang S, Li H, Krieger JM, Bahar I. (2019) Shared signature dynamics tempered by local fluctuations enables fold adaptability and specificity. Mol Biol Evol 36: 2053-2068. PMID: 31028708 PMCID: 6736388

J286. Pei F, Li H, Liu, B, Bahar I. (2019) Quantitative systems pharmacological analysis of drugs of abuse reveals the pleiotropy of their targets and the effector role of mTORC1. Front Pharmacol 10: 191. PMID: 30906261 PMCID: 6418047

J285. Mikulska-Ruminska K, Shrivastava IH, Krieger JM, Zhang S, Li H, Bayir H, Wenzel SE, VanDemark AP, Kagan VE, Bahar I. (2019) Characterization of differential dynamics, specificity, and allostery of lipoxygenase family members. J Chem Inf Model 59: 2496-2508. PMID: 30762363 PMCID: 6541894

J284. Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux J, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai C, Jang H, Padhorny D, Kozakov D, McLeish T (2019) Allostery in Its Many Disguises: From Theory to Applications Structure 27(4): 566-578. PMID: 30744993 PMCID: 6688844

J283. Wang Y, Cobanoglu MC, Li J, Hidvegi T, Hale P, Ewing M, Chu AS, Gong Z, Muzumdar R, Pak SC, Silverman GA, Bahar I, Perlmutter DH (2019) An analog of glibenclamide selectively enhances autophagic degradation of misfolded α1-antitrypsin Z PloS One 14: e0209748. PMID: 30673724 PMCID: 6343872

J282. COS Sorzano, A Jimnez, J Mota, JL Vilas, D Maluenda, M Martnez, E Ramrez-Aportela, T Majtner, J Segura, R Snchez-Garca, Y Rancel, L del Cao, P Conesa, R Melero, S Jonic, J Vargas, F Cazals, Z Freyberg, J Krieger, I Bahar, R Marabini, JM Carazo (2019) Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy. Acta Crystallog F Struct Biol Commun 75: 19-32. PMID: 30605122 PMCID: 6317454

J281. Lee JY, Krieger J, Herguedas B, Garca-Nafra J, Dutta A, Shaikh SA, Greger IH, Bahar I. (2019) Druggability Simulations and X-ray Crystallography Reveal a Ligand-binding Site in the GluA3 AMPA Receptor N-terminal Domain. Structure 27: 241-252. PMID: 30528594 PMCID: 6365164

J280. Stoyanovsky D, Shrivastava I, Tyurina Y, Bahar I, Tyurin U, Protchenko O, Jadhav S, Bolevich S, Kozlov A, Vladimirov Y, Shvedova A, Philpott C, Bayir H, Kagan V. (2019) Iron catalysis of lipid peroxidation in ferroptosis: Regulated enzymatic or random free radical reaction? Free Radic Biol Med, 133: 153-161. PMID: 30217775 PMCID: 6555767

J279. Krieger J, Lee JY, Greger IH, Bahar I. (2019) Activation and Desensitization of Ionotropic Glutamate Receptors by Selectively Triggering Pre-existing Motions. Neurosci Lett 700: 22-29 PMID: 29481851 PMCID: 6107436

Publications 2018

J278. Anthonymuthu T, Kenny E, Shrivastava I, Tyurina YY, Hier Z, Ting H-C, Dar H, Tyurin V, Nesterova A, Amoscato A, Mikulska-Ruminska K, Rosenbaum J, Mao G, Jinming Z, Conrad M, Kellum J, Wenzel S, VanDemark A, Bahar I, Kagan V, Bayir H (2018) Empowerment of 15-lipoxygenase catalytic competence in selective oxidation of membrane ETE-PE to ferroptotic death signals, HpETE-PE. J Am Chem Soc 140: 17835-17839. PMID: 30525572 PMCID: 6622169

J277. Wang K, Steer E, Otero PA, Bateman N, Cheng MH, Scott A, Wu C, Bahar I, Shih Y-T, Hsueh Y-P, Chu C (2018) PINK1 Interacts with VCP/p97 and Activates PKA to Promote NSFL1C/p47 Phosphorylation and Dendritic Arborization in Neurons. eNeuro 5(6) ENEURO.0466-18.2018 eCollec PMID: 30783609 PMCID: 6377406

J276. Van Dijk L, Giladi M, Refaeli B, Hiller R, Cheng MH, Bahar I, Khananshvili D. (2018) Key residues controlling bidirectional ion movements in Na+/Ca2+ exchanger. Cell Calcium 76: 10-22. PMID: 30248574 PMCID: 6688843

J275. Dar HH, Tyurina YY, Mikulska-Ruminska K, Shrivastava I, Ting HC, Tyurin VA, Krieger J, St Croix CM, Watkins S, Bayir E, Mao G, Ambruster C, Kapralov A, Wang H, Parsek MH, Anthonymuthu TS, Ogunsola AF, Flitter BA, Freedman CJ, Gaston JR, Holman TR, Pilewski JM, Greenberger JS, Mallampalli RK, Doi Y, Lee JS, Bahar I, Bomberger JM, Bayir H, Kagan VE. (2018) Pseudomonas aeruginosa utilizes host polyunsaturated phosphatidylethanolamines to trigger theft-ferroptosis in bronchial epithelium. J Clin Invest. 128: 4639-4653 PMID: 3018910 PMCID: 6159971

J274. Ponzoni L, Zhang S, Cheng MH, Bahar I. (2018) Shared dynamics of LeuT superfamily members and allosteric differentiation by structural irregularities and multimerization. Philos Trans R Soc Lond B Biol Sci 373: pii: 20170177 PMID: 29735731 PMCID: 5941172

J273. Ponzoni L, Bahar I. (2018) Structural dynamics is a determinant of the functional significance of missense variants. Proc Natl Acad Sci USA 115: 4164-4169 PMID: 29610305 PMCID: 5910821

J272. Kaya C, Cheng MH, Block ER, Bartol TM, Sejnowski TJ, Sorkin A, Faeder JR, Bahar I. (2018) Heterogeneities in Axonal Structure and Transporter Distribution Lower Dopamine Reuptake Efficiency eNeuro 5: ENEURO.0298-17.2017 PMID: 29430519 PMCID: 5804147

J271. Cheng MH, Kaya C, Bahar I. (2018) A Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine Transporter. J Phys Chem B 122: 5336-5346 PMID: 29232131 PMCID: 5991911

J270. Steinman J, Epperly M, Hou W, Willis J, Wang H, Fisher R, Liu B, Bahar I, McCaw T, Kagan V, Bayir H, Yu J, Wipf P, Li S, Huq MS, Greenberger JS. (2018) Improved Total-Body Irradiation Survival by Delivery of Two Radiation Mitigators that Target Distinct Cell Death Pathways. Radiat Res. J 189: 68-83 PMID: 29140165 PMCID: 5808408

J269. Tyurina YY, Shrivastava I, Tyurin VA, Mao G, Dar HH, Watkins S, Epperly M, Bahar I, Shvedova AA, Pitt B, Wenzel SE, Mallampalli RK, Sadovsky Y, Gabrilovich D, Greenberger JS, Bayir H, Kagan VE. (2018) "Only a life lived for others is worth living:" Redox Signaling by Oxygenated Phospholipids in Cell Fate Decisions. Antioxid Redox Signal 29: 1333-1358 PMID: 28835115 PMCID: 6157439

Publications 2017

J268. Lee JY, Feng Z, Xie XQ, Bahar I. (2017) Allosteric Modulation of Intact γ-Secretase Structural Dynamics. Biophys J 113: 2634-2649 PMID: 29262358 PMCID: 5770568

J267. Pei F, Li H, Henderson MJ, Titus SA, Jadhav A, Simeonov A, Cobanoglu MC, Mousavi SH, Shun T, McDermott L, Iyer P, Fioravanti M, Carlisle D, Friedlander RM, Bahar I, Taylor DL, Lezon TR, Stern AM, Schurdak ME. (2017) Connecting Neuronal Cell Protective Pathways and Drug Combinations in a Huntington's Disease Model through the Application of Quantitative Systems Pharmacology. Sci Rep 7: 17803 PMID: 29259176 PMCID:5736652

J266. Liu B, Oltvai ZN, Bayir H, Silverman GA, Pak SC, Perlmutter DH, Bahar I. (2017) Quantitative assessment of cell fate decision between autophagy and apoptosis. Sci Rep 7: 17605 PMID: 29242632 PMCID: 5730598

J265. Wenzel SE, Tyurina YY, Zhao J, St Croix CM, Dar HH, Mao G, Tyurin VA, Anthonymuthu TS, Kapralov AA, Amoscato AA, Mikulska-Ruminska K, Shrivastava IH, Kenny EM, Yang Q, Rosenbaum JC, Sparvero LJ, Emlet DR, Wen X, Minami Y, Qu F, Watkins SC, Holman TR, VanDemark AP, Kellum JA, Bahar I, Bayir H, Kagan VE. (2017) PEBP1 Wardens Ferroptosis by Enabling Lipoxygenase Generation of Lipid Death Signals. Cell 171: 628-641 PMID: 29053969 PMCID: 5683852

J264. Mikulska-Ruminska K, Kulik AJ, Benadiba C, Bahar I, Dietler G, Nowak W. (2017) Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD. Sci Rep 7: 8852 PMID: 28821864 PMCID: 5562865

J263. Ma S, Cheng MH, Guthrie DA, Newman AH, Bahar I, Sorkin A. (2017) Targeting of dopamine transporter to filopodia requires an outward-facing conformation of the transporter. Sci Rep 7: 5399 PMID: 28710426 PMCID: 5511133

J262. Li H, Sharma N, General IJ, Schreiber G, Bahar I. (2017) Dynamic Modulation of Binding Affinity as a Mechanism for Regulating Interferon Signaling. J Mol Biol 429: 2571-2589 PMID: 28648616 PMCID: 5545807

J261. Cheng MH, Garcia-Olivares J, Wasserman S, DiPietro J, Bahar I. (2017) Allosteric Modulation of Human Dopamine Transporter Activity under Conditions Promoting its Dimerization. J Biol Chem 292: 12471-12482 PMID: 28584050 PMCID: 5535022

J260. Cheng MH, Torres-Salazar D, Gonzalez-Suarez AD, Amara SG, Bahar I. (2017) Substrate transport and anion permeation proceed through distinct pathways in glutamate transporters. ELife 6: pii: e25850 PMID: 28569666 PMCID: 5472439

J259. Li H, Chang YY, Lee JY, Bahar I, Yang LW. (2017) DynOmics: dynamics of structural proteome and beyond Nucleic Acids Res 45(W1): W374-W380 PMID: 28472330 PMCID: 5793847

J258. Sauerwald N, Zhang S, Kingsford C, Bahar I. (2017) Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings Nucleic Acids Res 45: 3663-3673 PMID: 28334818 PMCID: 5397156

J257. Gur M, Cheng MH, Zomot E, Bahar I. (2017) Effect of Dimerization on the Dynamics of Neurotransmitter:Sodium Symporters J Phys Chem B 121: 3657-3666 PMID: 28118712 PMCID: 5402697

T1. Bahar I, Jernigan R, Dill K. (2017) Protein Actions: Principles & Modeling. New York, NY: Garland Science, Taylor & Francis Group ISBN: 9780815341772

J256. Zhou Z, Luo A, Shrivastava I, He M, Huang Y, Bahar I, Liu Z, Wan Y. (2017) Regulation of XIAP Turnover Reveals a Role for USP11 in Promotion of Tumorigenesis EBioMedicine 15: 48-61 PMID: 28040451 PMCID: 5233825

J255. Kagan VE, Mao G, Qu F, Angeli JP, Doll S, Croix CS, Dar HH, Liu B, Tyurin VA, Ritov VB, Kapralov AA, Amoscato AA, Jiang J, Anthonymuthu T, Mohammadyani D, Yang Q, Proneth B, Klein-Seetharaman J, Watkins S, Bahar I, Greenberger J, Mallampalli RK, Stockwell BR, Tyurina YY, Conrad M, Bayir H (2017) Oxidized Arachidonic and Adrenic Phosphatidylethanolamines Navigate Cells to Ferroptosis Nature Chem Biol 13: 81-90 PMID: 27842066 PMCID: 5506843

Publications 2016

J254. Kurkcuoglu Z, Bahar I, Doruker P (2016) ClustENM: ENM-based sampling of essential conformational space at full atomic resolution J Chem Theory Comput 12: 4549-62 PMID: 27494295 PMCID: 5088496

J253. Liu B, Liu Q, Yang L, Palaniappan SK, Bahar I, Thiagarajan PS, Ding JL (2016) Innate immune memory and homeostasis may be conferred through crosstalk between the TLR3 and TLR7 pathways Sci Signal 9: ra70 PMID: 27405980 PMCID: 5087126

J252. Stern AM, Schurdak ME, Bahar I, Berg JM, Taylor DL (2016) A perspective on implementing a quantitative systems pharmacology platform for drug discovery and the advancement of personalized medicine J of Biomolecular Screening 21: 521-34 PMID: 26962875, PMC4917453

J251. Li H, Chang YY, Yang LW, Bahar I (2016) iGNM 2.0: the Gaussian network model database for bimolecular structural dynamics Nucleic Acids Res 44: D415-422 PMID: 26582920; PMC4702874

J250. Jun I, Cheng MH, Sim E, Jung J, Suh BL, Kim Y, Son H, Park K, Kim CH, Yoon J-H, Whitcomb DC, Bahar I, Lee MG (2016) Pore Dilation Increases the Bicarbonate Permeability of CFTR, ANO1, and Glycine Receptor Anion Channels J of Physiology 594: 2929-55 PMID:26663196 PMCID: 4887682

Publications 2015

J249. Gur M, Zomot E, Cheng MH, Bahar I (2015) Energy landscape of LeuT from molecular simulations J Chem Phys 143: 243134 PMID: 26723619; PMC4662675

J248. Cheng MH, Bahar I (2015) Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter Structure 23: 2171-81PMID: 26481814; PMC4635030

J247. Hu D, Gur M, Zhou Z, Gamper A, Hung MC, Fujita N, Lan L, Bahar I, Wan Y (2015) Interplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis Nat Commun 6: 8419PMID: 26420673; PMC4598737

J246. Keskin O, Dyson HJ, Bahar I (2015) Biomolecular Systems Interactions, Dynamics, and Allostery: Reflections and New Directions Biophys J 109: E01-2PMID: 26377787; PMC4576319

J245. Krieger J, Bahar I, Greger IH (2015) Structure, Dynamics, and Allosteric Potential of Ionotropic Glutamate Receptor N-Terminal Domains Biophys J 109: 1136-48PMID: 26255587; PMC4576161

J244. Dutta A, Krieger J, Lee JY, Garcia-Nafria J, Greger IH, Bahar I (2015) Cooperative Dynamics of Intact AMPA and NMDA Glutamate Receptors: Similarities and Subfamily-Specific Differences Structure 23: 1692-1704PMID: 26256538; PMC4558295

J243. Haliloglu, T, Bahar I (2015) Adaptability of protein structures to enable functional interactions and evolutionary implications Curr Opin in Struct Biol 35: 17-23PMID: 26254902; PMC4688206

J242. Bahar I, Cheng MH, Lee JY, Kaya C, Zhang S (2015) Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions Biophys J 109: 1101-9PMID: 26143655; PMC4576147

J241. Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Glymour C, Jacobson RC, Kienholz M, Lee AV, Lu X, Scheines R, the Center for Causal Discovery team (2015) Center for Causal Discovery of Biomedical Knowledge from Big Data J Am Med Inform Assoc 22: 1132-6PMID: 26138794 PMCID: 5009908

J240. Cheng MH, Block E, Hu F, Cobanoglu MC, Sorkin A, Bahar I (2015) Insights into the modulation of dopamine transporter function by amphetamine, orphenadrine, and cocaine binding Front Neurol 6: 134PMID: 26106364; PMC4460958

J239. Bakan A, Kapralov AA, Bayir H, Hu F, Kagan VE, Bahar I (2015) Inhibition of Peroxidase Activity of Cytochrome c: De Novo Compound Discovery and Validation Mol Pharmacol 88: 421-7PMID: 26078313; PMC: 4551054

J238. Mao W, Kaya C, Dutta A, Horovitz A, Bahar I (2015) Comparative Study of the Effectiveness and Limitations of Current Methods for Detecting Sequence Coevolution Bioinformatics 31: 1929-37 PMID: 25697822; PMC4481699

J237. Eyal E, Lum G, Bahar I (2015) The Anisotropic Network Model web server at 2015 (ANM 2.0) Bioinformatics 31: 1487-9 PMID: 25568280; PMC4410662

J236. Zomot E, Gur M, Bahar I (2015) Microseconds Simulations Reveal a New Sodium-Binding Site and the Mechanism of Sodium-Coupled Substrate Uptake by LeuT J Biol Chem 290: 544-55 PMID: 25381247; PMC4281755

J235. Cobanoglu MC, Oltvai ZN, Taylor DL, Bahar I (2015) BalestraWeb: Efficient, online evaluation of drug-target interactions Bioinformatics 31:131-3 PMID: 25192741; PMC4271144

Publications 2014

J234. Cheng MH, Bahar I (2014) Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle PLoS Comput Biol 10: e1003879 PMID: 25299050; PMC4191883

J233. Liu B, Bhatt D, Oltvai ZN, Greenberger JS, Bahar I (2014) Significance of p53 dynamics in regulating apoptosis in response to ionizing radiation, and polypharmacological strategies Sci Rep 4: 6245 PMID: 25175563; PMC4150106

J232. Bahar I (2014) Coupling between Neurotransmitter Translocation and Protonation State of a Titratable Residue during Na(+)-Coupled Transport Biophys J 106: 2547-8 PMID: 24940770; PMC4070272

J231. Bakan A,* Dutta A,* Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I (2014) Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics Bioinformatics 30: 2681-3 PMID: 24849577; PMC4155247

J230. O'Reilly LP,* Long OS,* Cobanoglu MC,* Benson JA, Luke CJ, Miedel MT, Hale P, Perlmutter DH, Bahar I, Silverman GA, Pak SC (2014) A genome-wide RNAi screen identifies potential drug targets in a C. elegans model of α1-antitrypsin deficiency Hum Mol Genet 23: 5123-32 PMID: 24838285; PMC4159156

J229. LaRusch J, Jung J, General IJ, Lewis MD, Park HW, Brand RE, Gelrud A, Anderson MA, Banks PA, Conwell D, Lawrence C, Romagnuolo J, Baillie J, Alkaade S, Cote' G, Gardner TB, Amann ST, Slivka A, Sandhu B, Aloe A, Kienholz ML, Yadav D, Barmada MM, Bahar I, Lee MG, Whitcomb DC, North American Pancreatitis Study Group (2014) Mechanisms of CFTR functional variants that impair regulated bicarbonate permeation and increase risk for pancreatitis but not for cystic fibrosis PLoS Genetics 10: e1004376 PMID: 25033378; PMC4102440

J228. General IJ, Liu Y, Blackburn M, Mao W, Gierasch LM, Bahar I (2014) ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones PLoS Comp Bio 10: e1003624 PMID: 24831085; PMC4022485

J227. Korotchenko VN, Saydmohammed M, Vollmer LL, Bakan A, Sheetz K, Debiec KT, Greene KA, Agliori CS, Bahar I, Day BW, Vogt A, Tsang M (2014) In Vivo Structure-Activity Relationship Studies Support Allosteric Targeting of a Dual Specificity Phosphatase ChemBioChem 15: 1436-1445 PMID: 24909879; PMC4118675

J226. Das A, Gur M,* Cheng MH,* Jo S, Bahar I, Roux B (2014) Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model PLoS Comput Biol 10: e1003521 PMID: 24699246; PMC3974643

J225. Jiang J, Bakan A, Kapralov AA, Ishara Silva KI, Huang Z, Amoscato AA, Peterson J, Krishna Garapati VK, Saxena S, Bayir H, Atkinson J, Bahar I, Kagan VE (2014) Designing inhibitors of cytochrome c/cardiolipin peroxidase complexes: mitochondria-targeted imidazole-substituted fatty acids Free Radic Biol Med 71C: 221-230 PMID: 24631490; PMC4216591

J224. Lui VW, Peyser ND, Ng PK, Hritz J, Zeng Y, Lu Y, Li H, Wang L, Gilbert BR, General IJ, Bahar I, Ju Z, Wang Z, Pendleton KP, Xiao X, Du Y, Vries JK, Hammerman PS, Garraway LA, Mills GB, Johnson DE, Grandis JR (2014) Frequent mutation of receptor protein tyrosine phosphatases provides a mechanism for STAT3 hyperactivation in head and neck cancer Proc Natl Acad Sci USA 111: 1114-9 PMID: 24395800; PMC3903220

Publications 2013

J223. Cobanoglu MC, Liu C, Hu F, Oltvai ZN, Bahar I (2013) Predicting drug-target interactions using probabilistic matrix factorization J Chem Inf Model 53: 3399-409 PMID: 24289468; PMC3871285

J222. Chu CT, Ji J, Dagda RK, Jiang JF, Tyurina YY, Kapralov AA, Tyurin VA, Yanamala N, Shrivastava IH, Mohammadyani D, Qiang Wang KZ, Zhu J, Klein-Seetharaman J, Balasubramanian K, Amoscato AA, Borisenko G, Huang Z, Gusdon AM, Cheikhi A, Steer EK, Wang R, Baty C, Watkins S, Bahar I, Bayir H, Kagan VE (2013) Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells Nature Cell Biology 15: 1197-1205 PMID: 24036476; PMC3806088

J221. Gur M, Madura JD, Bahar I (2013) Global transitions of proteins explored by a multiscale hybrid methodology: Application to adenylate kinase Biophys J 105: 1643-1652 PMID: 24094405; PMC3791301

J220. Gur M, Zomot E, Bahar I (2013) Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions J Chem Phys 139: 121912. PMID: 24089724; PMC3739829

J219. Cheng MH, Bahar I (2013) Coupled global and local changes direct substrate translocation by neurotransmitter-sodium symporter ortholog LeuT Biophys J 105: 630-639. PMID: 23931311; PMC3736663

J218. Zomot E, Bahar I (2013) Intracellular gating in an inward-facing state of aspartate transporter GltPh is regulated by the movements of the helical hairpin HP2 J Biol Chem 288: 8231-8237. PMID: 23386619; PMC3605641

Publications 2012

J217. Perez A, Yang Z, Bahar I, Dill KA, MacCallum JL (2012) FlexE: Using elastic network models to compare models of protein structure J Chem Theor Comp 8: 3985-3991. PMID: 25530735 PMCID: PMC4269272

J216. Kurkcuoglu Z, Bakan A, Kocaman D, Bahar I, Doruker P (2012) Coupling between catalytic loop motions and enzyme global dynamics PLoS Comput Biol 8: e1002705. PMID: 23028297; PMC3459879

J215. Bhatt D, Bahar I (2012) An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates J Chem Phys 137: 104101. PMID: 22979844; PMC3460967

J214. Dutta A, Shrivastava IH, Sukumaran M, Greger IH, Bahar I (2012) Comparative dynamics of NMDA- and AMPA-Glutamate receptor N-terminal domains Structure 20: 1838-49. PMID: 22959625; PMC3496038

J213. Isin B, Tirupula KC, Oltvai ZN, Klein-Seetharaman J, Bahar I (2012) Identification of motions in membrane proteins by elastic network models and their experimental validation Methods Mol Biol 914: 285-317. PMID: 22976035

J212. Zomot E, Bahar I (2012) A conformational switch in a partially unwound helix selectively determines the pathway for substrate release from the carnitine/-butyrobetaine antiporter CaiT J Biol Chem 287: 31823-32. PMID: 22843728; PMC3442516

J211. Bakan A, Nevins N, Lakdawala AS, Bahar I (2012) Druggability assessment of allosteric proteins by dynamics simulations in the presence of probe molecules J Chem Theory Comput 8: 2435-2447. PMID: 22798729; PMC3392909

J210. Liu Y, Bahar I (2012) Sequence evolution correlates with structural dynamics Mol Biol Evol 29: 2253-63.PMID: 22427707; PMC3424413

J209. Lezon TR, Bahar I (2012) Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh Biophys J 102: 1331-40. PMID: 22455916; PMC3309413

J208. Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjolander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S (2012) The interface of protein structure, protein biophysics, and molecular evolution Protein Science 21: 769-85. PMID: 22528593; PMC3403413

B17. Doruker P, Liu Y, Yang Z, Bahar I. (2012) In Silico Coarse-Grained Approaches to Structural Dynamics and Function of Proteins and their Assemblies in Comprehensive Biophysics. Editor-in-Chief: EH Egelman, vol 9, chapter 9.3, pp 27-52, Academic Press, Elsevier.

J207. Liu L, Byeon IJ, Bahar I, Gronenborn AM (2012) Domain swapping proceeds via complete unfolding: A 19F- and 1H- NMR study of the cyanovirin-N protein J Am Chem Soc 134: 4229-35. PMID: 22296296; PMC3326405

Publications 2011

B16. Zomot E, Bakan A, Shrivastava IH, DeChancie J, Lezon TR, Bahar I. (2011) Sodium-coupled secondary transporters: Insights from Stucture-based computations in Molecular Machines. Edited by Benoit Roux World Scientific, NY.

J206. Liu L, Gronenborn AM, Bahar I (2011) Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion Proteins 80: 616-625. PMID: 22105881; PMC3290687

J205. Marcos E, Crehuet R, Bahar I (2011) Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members PLoS Comput Biol 9: e1002201. PMID: 21980279; PMC3182869

J204. Jiang J, Shrivastava IH, Watts SD, Bahar I, Amara SG (2011) Large collective motions regulate the functional properties of glutamate transporter trimers Proc Natl Acad Sci USA 108: 15141-6. PMID: 21876140; PMC3174670

J203. Meireles L, Gur M, Bakan A, Bahar I (2011) Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins Protein Science 20: 1645-58. PMID: 21826755; PMC3218357

J202. Morel PA, Srinivas M, Turner MS, Fuschiotti P, Munshi R, Bahar I, Feili-Hariri M, Ahrens ET (2011) Gene expression analysis of dendritic cells that prevent diabetes in NOD mice: analysis of chemokines and costimulatory molecules J Leukoc Biol 90: 539-50. PMID: 21628331; PMC3157898

J201. Eyal E, Dutta A, Bahar I (2011) Cooperative dynamics of proteins unraveled by network models WIREs Computational Molecular Science 1: 426-439.

J200. Zomot E, Bahar I (2011) Protonation of glutamate-208 induces the release of agmatine in an outward-facing conformation of arginine/agmatine antiporter J Biol Chem 286: 19693-701. PMID: 21487006; PMC3103348

J199. Bakan A, Meireles LM, Bahar I (2011) ProDy: Protein dynamics inferred from theory and experiments Bioinformatics 27: 1575-1577. PMID: 21471012; PMC3102222

J198. Sukumaran M, Rossmann M, Shrivastava I, Dutta A, Bahar I, Greger IH (2011) Dynamics and allosteric potential of the AMPA receptor N-terminal domain EMBO J 30: 972-82. PMID: 21317871; PMC3049213

J197. DeChancie J, Shrivastava IH, Bahar I (2011) Mechanism of substrate release by the aspartate transporter GltPh: Insights from simulations Mol. BioSyst 7:832-842. PMID: 21161089; PMC3227142

J196. Bakan A, Bahar I (2011) Computational generation inhibitor-bound conformers of p38 map kinase and comparison with experiments Pac Symp Biocomput 2011: 181-92. PMID: 21121046

J195. Mustata G, Li M, Zevola N, Bakan A, Zhang L, Epperly M, Greenberger JS, Yu J, Bahar I (2011) Development of small-molecule PUMA inhibitors for mitigating radiation-induced cell death Curr Top Med Chem 11: 281-90. PMID: 21320058; PMC3086011

Publications 2010

J194. Liu Y, Gierasch LM, Bahar I (2010) Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs PLoS Comput Biol 6: e1000931. PMID: 20862304; PMC2940730

J193. Dutta A, Bahar I (2010) Metal-binding sites are designed to achieve optimal mechanical and signaling properties Structure 18: 1140-8. PMID: 20826340; PMC2937013

J192. Lezon TR, Bahar I (2010) Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology PLoS Comput Biol 6: e:1000816. PMID: 20585542; PMC2887458

J191. Bahar I (2010) On the functional significance of soft modes predicted by coarse-grained models for membrane proteins J Gen Physiol 135: 563-73. PMID: 20513758; PMC2888054

J190. Zomot E, Bahar I (2010) The sodium/galactose symporter crystal structure is a dynamic, not so occluded state Mol Biosyst 6: 1040 -1046. PMID: 20358053; PMC2938171

J189. Marcos E, Crehuet R, Bahar I (2010) On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm PLoS Comput Biol 6: e1000738. PMID: 20386738; PMC2851564

J188. Bahar I, Lezon TR, Yang LW, Eyal E (2010) Global Dynamics of Proteins: Bridging Between Structure and Function Annu Rev Biophys 39: 23-42. PMID: 20192781; PMC2938190

J187. Liu Y, Bahar I (2010) Toward understanding allosteric signaling mechanisms in the ATPase domain of molecular chaperones Pac Symp Biocomput 2010: 269-80. PMID: 19908379; PMC2938181

J186. Bahar I, Lezon T, Bakan A, Shrivastava IH (2010) Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins Chem Rev 110: 1463-1497. PMID: 19785456; PMC2836427

Publications 2009

B15. Lezon TR, Shrivastava IH, Yang Z, Bahar I. in Handbook on Biological Networks. Edited by Boccaletti S, Latora V, Moreno Y (2009) Elastic network models for biomolecular dynamics: Theory and application to membrane proteins and viruses World Scientific.

J185. Yang Z, Bahar I, Widom M (2009) Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity Biophys J 96: 4438-48. PMID: 19486668; PMC2711457

J184. Molina G,* Vogt A,* Bakan A,* Dai W, Queiroz de Oliveira P, Znosko W, Smithgall TE, Bahar I, Lazo JS, Day BW, Tsang M (2009) Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages Nature Chem Biol 5: 680-7. PMID: 19578332; PMC2771339

J183. Liu L, Koharudin LM, Gronenborn AM, Bahar I (2009) A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations Proteins 77: 927-939. PMID: 19688820; PMC2767477

J182. Lezon TR, Sali A, Bahar I (2009) Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models PLoS Comput Biol 9: e1000496. PMID: 19730674; PMC2725293

J181. Bakan A, Bahar I (2009) The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor bindingProc Natl Acad Sci USA 106: 14349-14354. PMID: 19706521; PMC2728110

J180. Yang Z, Majek P, Bahar I (2009) Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL  PLoS Comput Biol 5: e1000360. PMID: 19381265; PMC2664929

J179. Yang LW, Eyal E, Bahar I, Kitao A (2009) Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics  Bioinformatics 25: 606-614. PMID: 19147661; PMC2647834

J178. Mustata G, Follis AV, Hammoudeh DI, Metallo SJ, Wang H, Prochownik EV, Lazo JS, Bahar I (2009) Discovery of Novel Myc-Max Heterodimer Disruptors with a Three-Dimensional Pharmacophore Model J Med Chem 52: 1247-1250. PMID: 19215087; PMC2765518

J177. Gu Y, Shrivastava IH, Amara SG, Bahar I (2009) Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter Proc Natl Acad Sci U S A 106: 2589-94. PMID: 19202063; PMC2637273

Publications 2008

J176. Bakan A, Lazo JS, Wipf P, Brummond KM, Bahar I (2008) Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening Curr Med Chem 15: 2536-44. PMID: 18855677; PMC2764859

J175. Shrivastava IH, Jiang J, Amara SG, Bahar I (2008) Time-resolved mechanism of extracellular gate opening and substrate binding in glutamate transporter J Biol Chem 283: 28680-28690. PMID: 18678877; PMC2568915  (Supplementary Material)

J174. Engen JR, Wales TE, Hochrein JM, Meyn MA III, Ozkan SB, Bahar I, Smithgall TE (2008) Structure and dynamic regulation of Src-family kinases Cell Mol Life Sci 65: 3058-73.

J173. Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout B, Bahar I (2008) Computational Insights on the Competing Effects of Nitric Oxide in Regulating Apoptosis PLoS ONE 3: e2249. PMID: 18509469; PMC2386238

J172. Isin B, Schulten K, Tajkhorshid E, Bahar I (2008) Mechanism of Signal Propagation upon Retinal Isomerization: Insights from Molecular Dynamics Simulations of Rhodopsin Restrained by Normal Modes Biophysical J 95: 789-803.  PMID: 18390613; PMC2440475

J171. Liu Y, Eyal E, Bahar I (2008) Analysis of correlated mutations in HIV-1 protease using spectral clustering Bioinformatics 24: 1243-50. PMID: 18375964

J170. Chennubhotla C, Yang Z, Bahar I (2008) Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL Mol. BioSyst 4: 287-292. PMID: 18354781

J169. Eyal E, Bahar I (2008) Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models Biophys J 94: 3424-35. PMID: 18223005; PMC2292382

Publications 2007

J168. Bahar I, Chennubhotla C, Tobi D (2007) Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation Curr Opin Struct Biol 17: 633-40. PMID: 18024008; PMC2197162

J167. Chennubhotla C, Bahar I (2007) Signal propagation in proteins and relation to equilibrium fluctuations PLoS Comput Biol 3, 17: 16-26. PMID: 17892319; PMC1988854

J166. Chennubhotla C, Bahar I (2007) Markov methods for hierarchical coarse-graining of large protein dynamics J Comput Biol 14: 765-76. PMID: 17691893

J165. Tobi D, Bahar I (2007) Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity?   BMC Bioinformatics  8: 226. PMID: 17598909

J164. Eyal E, Chennubhotla C, Yang L-W, Bahar I (2007) Anisotropic Fluctuations of Amino Acids in Protein Structures: Insights from X-Ray Crystallography and Elastic Network Models Bioinformatics 23: i175-i184. PMID: 17646294 (Supplementary Materials)

J163.Eyal E, Pietrokovski S, Bahar I (2007) Rapid Assessment of Correlated Amino Acids from Pair-to-Pair (P2P) Substitution Matrices   Bioinformatics 23: 1837-1839. PMID: 17496318

J162. Yang L-W, Eyal E, Chennubhotla C, JunGoo J, Gronenborn AM, Bahar I (2007) Insights into Equilibrium Dynamics of Proteins from Comparison of NMR and X-ray Data with Computational Predictions   Structure 15: 741-749. PMID: 17562320; PMC2760440

J161. Lazo JS, Skoko JJ, Werner S, Mitasev B, Bakan A, Koizumi F, Yellow-Duke A, Bahar I, Brummond KM (2007) Structurally Unique Inhibitors of Human Mitogen-activated Protein Kinase Phosphatase-1 Identified in a Pyrrole Carboxamide Library J Pharmacol Exp Ther 322: 940-947. PMID: 17538006

J160. Vries JK, Liu X, Bahar I (2007) The relationship between N-gram patterns and protein secondary structure Proteins 68: 830-838. PMID: 17523186

J159. Iyer, AK, Tran KT, Borysenko CW, Cascio M, Camacho CJ, Blair HC, Bahar I, Wells AJ (2007) Tenascin cytotactin epidermal growth factor-like repeat binds epidermal growth factor receptor with low affinity J Cell Physiol  211: 748-58. PMID: 17311283

B13. Chennubhotla C, Bahar I (2007) Markov Methods for Hierarchical Coarse-Graining of Large Protein Dynamics Lect Notes in Comp Sci 3909: 379-393.

Publications 2006

E1. Normal Mode Analysis. Theory and Applications to Biological and Chemical Systems, Eds Cui Q, Bahar I (2006) Math & Comp Biology Series, Chapman & Hall CRC Press, Taylor & Francis.

J158. Eyal E, Yang LW, Bahar I (2006) Anisotropic network model: systematic evaluation and a new web interface Bioinformatics 22: 2619-27. PMID: 16928735

J157. Isin B, Rader AJ, Dhiman HK, Klein-Seetharaman J, Bahar I (2006) Predisposition of the dark state of rhodopsin to functional changes in structure Proteins 65: 970-83. PMID: 17009319

J156. Farkas IJ, Wu C, Chennubhotla C, Bahar I, Oltvai ZN (2006) Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae BMC Bioinformatics 7: 478. PMID: 17069658; PMC1643839

J155. Chennubhotla C, Bahar I (2006) Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES Mol Syst Biol 2: 36. PMID: 16820777; PMC1681507

J154. Yang LW, Rader AJ, X Liu, CJ Jursa, SC Chen, HA Karimi, Bahar I (2006) oGNM: online computation of structural dynamics using the Gaussian Network Model Nucleic Acids Res 34: W24-31. PMID: 16845002; 16845002

J153. Shrivastava IH, Bahar I (2006) Common Mechanism of Pore Opening Shared by Five Different Potassium Channels Biophys J 90: 3929-3940. PMID: 16533848; PMC1459499

B14. Rader AJ, Chennubhotla C, Yang L-W, Bahar I Eds Cui Q, Bahar I (2006) The Gaussian Network Model: Theory and Applications in Normal Mode Analysis. Theory and Applications to Biological and Chemical Systems Math & Comp Biology Series, Chapman & Hall CRC Press, Taylor & Francis Group, 41-64.

J152. Munshi R, Coalson RD, Ermentrout GB, Madura JD, Meirovitch H, Stiles JR, Bahar I (2006) An Introduction to Simulation and Visualization of Biological Systems at Multiple Scales: A Summer Training Program for Interdisciplinary Research Biotechnology Progress 22: 179-185. PMID: 16454509

J151. Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout GB, Bahar I (2006) Bistability in Apoptosis: Roles of Bax, Bcl-2, and Mitochondrial Permeability Transition Pores Biophys J 90: 1546-1559.

J150. Tobi D, Bahar I (2006) Optimal Design of Protein Docking Potentials: Efficiency and Limitations Proteins: Structure, Function, and Bioinformatics 62: 970-981. PMID: 16385562

Publications 2005

J149. Chennubhotla C, Rader AJ, Yang L-W, Bahar I (2005) Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies CPhysical Biology 2: S173-S180. PMID: 16280623

J148. Tobi D, Bahar I (2005) Structural Changes Involved in Protein Binding Correlate with intrinsic Motions of Proteins in the Unbound State Proc Natl Acad Sci (USA) 102: 18908-18913. PMID: 16354836; PMC1323175

J147. Bahar I, Rader AJ (2005) Coarse-grained normal mode analysis in structural biology Curr Opin Struct Biology 15: 1-7. PMID: 16143512; PMC1482533

J146. Yang L-W, Liu X, Jursa CJ, Holliman M, Rader AJ, Karimi H, Bahar I (2005) iGNM: A Database of Protein Functional Motions Based on Gaussian Network Model Bioinformatics 21: 2978 - 2987. PMID: 15860562; PMC1752228

J145. Yang L-W, Bahar I (2005) Coupling between Catalytic Site and Collective Dynamics: A requirement for Mechanochemical Activity of Enzymes Structure 13: 893-904. PMID: 15939021; PMC1489920

J144. Berberich J, Yang L-W, Madura J, Bahar I, Russell AJ (2005) A stable three enzyme creatinine biosensor. 1. Impact of structure, function and environment on PEGylated and immobilized sarcosine oxidase ACTA Biomaterialia 1(2): 173-181. PMID: 16701794

J143. Berberich J, Yang L-W, Bahar I, Russell AJ (2005) A stable three enzyme creatinine biosensor. 2. Analysis of the impact of silver ions on creatine amidinohydrolase ACTA Biomaterialia 1(2): 183-191. PMID: 16701795

J142. Ramaswamy A, Bahar I, Ioshikhes I (2005) Structural Dynamics of Nucleosome Core Particle: Comparison with Nucleosomes Containing Histone Variants Proteins: Structure, Function and Bioinformatics 58: 683-696. PMID: 15624215

J141. Rader AJ, Vlad D, Bahar I (2005) Maturation Dynamics of Bacteriophage HK97 Capsid RStructure  13: 413-21. PMID: 15766543

Publications 2004

J140. Vodovotz Y, Kim P, Bagci EZ, Ermentrout GB, Chow CC, Bahar I, Billiar TR (2004) Inflammatory Modulation of Hepatocyte Apoptosis by Nitric Oxide: In Vivo, In Vitro, and In Silico Studies Current Molecular Medicine 4: 753-762. PMID: 15579022

J139. Rader AJ, Bahar I (2004) Folding Core Predictions from Network Models of Proteins Polymer 45: 659-668.

B11. Liu X, Karimi H, Yang L-W, Bahar I (2004) Protein Functional Motion Query and Visualization IEEE Proceedings, 28th Annual International Computer Software and Applications Conference - (COMPSAC'04).

J138. Seki M, Masutani C, Yang L-W, Schuffert A, Iwai S, Bahar I, Wood RD (2004) High efficiency bypass of DNA damage by a single human DNA polymerase EMBO J 10: 4484-94. PMID: 15496986; PMC526458

J137. Vries JK, Munshi R, Tobi D, Klein-Seetharaman J, Benos PV, Bahar I (2004)A Sequence Alignment-Independent Method For Protein Classification Applied Bioinformatics 3: 137-48. PMID: 15693739

J136. Brisson M, Nguyen T, Vogt A, Yalowich J, Giorgianni A, Tobi D, Bahar I, Stephenson CRJ, Wipf P, Lazo JS (2004) Discovery and characterization of novel small molecule inhibitors of human Cdc25B dual specificity phosphatase Mol Pharmacology 66: 824-833. PMID: 15231869

J135. Sluis-Cremer N, Temiz NA, Bahar I (2004)Conformational changes in HIV-1 reverse transcriptase induced by nonnucleoside reverse transcriptase inhibitor binding Current HIV Research 2: 323-32. PMID: 15544453; PMC1298242

J134. Temiz NA, Meirovitch E, Bahar I (2004) Escherichia coli Adenylate Kinase Dynamics: Comparison of Elastic Network Model Modes with Mode-Coupling 15N-NMR Relaxation Data Proteins, Structure, Function and Bioinformatics 57: 468-480. PMID: 15382240; PMC1752299

J133. Chen S-C, Bahar I (2004) Mining frequent patterns in proteins: A study of serine proteinases Bioinformatics 20: i77-i85. PMID: 15262784

J132. Rader AJ, Anderson G, Isin B, Khorana HG, Bahar I, Klein-Seetharaman J (2004) Identification of core amino acids stabilizing rhodopsin Proc Natl Acad Sci USA 101: 7246-7251. PMID: 15123809; PMC409904

J131. Wang Y, Rader AJ, Bahar I, Jernigan RL (2004) Global Ribosome Motions Revealed with Elastic Network Model J Struct Biol 147: 302-314. PMID: 15450299

Publications 2003

J130. Bagci Z, Kloczkowski A, Jernigan RL, Bahar I (2003) The Origin and Extent of Coarse-Grained Regularities in Protein Internal Packing Proteins: Structure, Function and Genetics 53: 56-67. PMID: 12945049

J129. Xu C, Tobi D, Bahar I (2003) Allosteric Changes in Protein Structure Computed by a Simple Mechanical Model: Hemoglobin T --> R2 Transition J Mol Biol 333: 153-168.

J128. Ozkan SB, Dill KA, Bahar I (2003) Computing the Transition State Populations in Simple Protein Models Biopolymers 68: 35-46. PMID: 12579578

Publications 2002

J127. Temiz NA, Bahar I (2002) Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase Proteins: Structure, Function and Genetics 49: 61-70.

J126. Keskin O, Durell SR, Bahar I, Jernigan RL, Covell DG (2002) Relating molecular flexibility to function: A case study of tubulin Biophys J 83: 663-680. PMID: 12124255; PMC1302177

J125. Bagci Z, Jernigan RL, Bahar I (2002) Residue packing in proteins: Uniform distribution on a coarse-grained scale J Chem Physics 116: 2269-2276. (selected for the February 1, 2002 issue of the Virtual Journal of Biological Physics Research in

J124. Keskin O, Bahar I, Flatow D, Covell DG, Jernigan RL (2002) Molecular mechanisms of chaperonin GroEL/GroES function Biochemistry 41: 491-501.

J123. Bagci Z, Jernigan RL, Bahar I (2002) Residue coordination in proteins conforms to the closest packing of spheres Polymer 43: 451-459.

J122. Isin B, Doruker P, Bahar I (2002) Functional motions of influenza virus hemagglutinin: A structure-based analytical approach Biophys J 82: 569-581. PMID: 11806902; PMC1301869

J121. Doruker P, Bahar I, Baysal C, Erman B (2002) Collective deformations in proteins determined by a mode analysis of molecular dynamics trajectories Polymer 43: 431-439.

J120. Ozkan SB, Dill KA, Bahar I (2002) Fast-folding protein kinetics, hidden intermediates and the sequential stabilization model OProtein Science 11: 1958-1970. PMID: 12142450; PMC2373683

J119. Doruker P, Jernigan RL, Bahar I (2002) Dynamics of large proteins through hierarchical levels of coarse-grained structures J Comp Chem 23: 119-12. PMID: 11913377


Publications 2001

P1. (Patent 1) Erman B, Mark JE, Paterson BZ, Bahar I, Kloczkowski A (2001) High Performance of Biodegradable Materials from Oriented Starch Derivatives US Patent #6,218,532 B1.

J118. Ozkan B, Bahar I, Dill KA (2001) Transition states and the meaning of F-values in protein folding kinetics Nature Struct Biol 8: 765-769.

J117. Konuklar FAS, Aviyente V, Sen TZ, Bahar I (2001)Modeling the deamidation of asparagine residues via succinimide intermediates J Mol Model 7: 147-160.

J116. Atilgan AR, Durrell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model Biophys J 80: 505-515.

Publications 2000

J115. Jernigan RL, Bahar I, Covell DG, Atilgan AR, Erman B, Flatow D (2000) Relating the structure of HIV-1 reverse transcriptase to its processing step J Biomol Structure & Dynamics 1: 49-55.

J114. Doruker P, Atilgan AR, Bahar I (2000) Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to a-amylase inhibitor Proteins: Structure, Function & Genetics 40: 512-524.

J113. Duman G, Keskin O, Bahar I, Robinson JR (2000) Stabilization of the molten globule state of hen egg white lysozyme with solutions containing polyvinyl pyrrolidone J Controlled Release 64: 331-333.

J112. Haliloglu T, Bahar I, Jernigan RL (2000) Collective dynamics of class I MHC/peptide complexes and binding to T cell receptors Biophys J 78: 34A.

J111. Keskin O, Bahar I, Jernigan RL, Myers TG, Beutler JA, Shoemaker RH, Sausville EA, Covell DG (2000) Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure Anticancer Drug Design 15: 79-98. PMID: 10901296

J110. Keskin O, Jernigan RL, Bahar I (2000) Proteins with similar architecture exhibit similar large-scale dynamic behavior. Specificity resides in local differences Biophysical Journal 78: 2093-2106.

Publications 1999

J109. Bahar I (1999) Dynamics of proteins and biomolecular complexes. Inferring functional motions from structure Reviews in Chemical Engineering 15: 319-349.

B10. Jernigan RL, Bahar I (1999) Geometric Regularities among bonded and nonbonded residues in proteins In Perspectives in Structural Biology (GN Ramachandran Volume) Vijayan M, Yathindra N, Kolaskar AS Eds., Indian Academy of Sciences, Universities Press, Hyderabad, pp 209-225.

J108. Haliloglu T, Bahar I (1999) Structure-based analysis of protein dynamics. Comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data Proteins: Structure, Function & Genetics 37: 654-667.

J107. Jernigan RL, Demirel MC, Bahar I (1999) Relating structure to function through the dominant slow modes of motion of DNA topoisomerase II Int J Quantum Chem 75: 301-312.

J106. Bahar I, Jernigan RL (1999) Cooperative fluctuations and subunit communication in tryptophan synthase Biochemistry 38: 3478-3490.

J105. Sen TZ, Bahar I, Erman B, Laupretre F, Monnerie L (1999) Local dynamics of cis-polybutadiene and cis-polyisoprene. A comparative study based on cooperative kinematics theory and NMR experiments Macromolecules 32: 3017-3024.

J104. Bahar I, Erman B, Jernigan RL, Atilgan AR, Covell D (1999) Collective motions of HIV-1 reverse transcriptase. Examination of Flexibility and Enzyme Function J Mol Biol 285: 1023-1037.

Publications 1998

B9. Erman B, Bahar I Eds Inan E, Markov KZ (1998) Simulation of polymeric systems in Continuum Models and Discrete Systems, pp 297-303, World Scientific Publishing.

J103. Keskin O, Bahar I, Badredtinov A, Ptitsyn O, Jernigan RL (1998) Empirical solvent-mediated potentials hold for both intramolecular and inter-molecular inter-residue interactions Protein Science 7: 2578-2586.

J102. Erman B, Bahar I (1998) Local chain dynamics and glass transition Makromolekulare Chem Makromol Symp. 133: 33-46.

J101. Lustig B, Bahar I, Jernigan RL (1998) RNA bulge entropies are correlated with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access Nucleic Acids Res 26: 5212-5217.

J100. Demirel MC, Atilgan AR, Jernigan RL, Erman B, Bahar I (1998) Identification of kinetically hot residues in proteins Protein Science 7: 2522-2532.

J99. Keskin O, Bahar I (1998) Packing of sidechains in low resolution models for proteins Folding & Design 3: 469-479.

J98. Bahar I, Atilgan AR, Demirel MC, Erman B (1998)Vibrational dynamics of folded proteins: Significance of slow and fast motions in relation to function and stability Phys. Rev Lett 80: 2733-2736.

J97. Erdal S, Bahar I, Erman B (1998) Swelling of sodium chloride filled polybutadiene networks in aqueous environment Polymer 39, 2035-2041.

J96. Atilgan AR, Haliloglu T, Bahar I, & Erman B (1998) Correlated fluctuations in polymer networks Comput Theor Polym Sci 8: 55-59.

J95. Bahar I, Jernigan RL (1998) Vibrational dynamics of transfer RNAs. Comparison of the free and enzyme-bound forms J Mol Biol 281: 871-884.

J94. Ozkan B, Bahar I (1998) Recognition of native structure from complete enumeration of low resolution models with constraints Proteins: Structure, Function and Genetics 32: 211-222.

J93. Haliloglu T, Bahar I (1998) Coarse-grained simulations of conformational dynamics of proteins Application to apomyoglobin Proteins: Structure, Function and Genetics 3: 271-281.

B8. Jernigan RL, Bahar I Eds Schleyer P vR, Allinger NL, Clark T, Gasteiger J, Kollman PA, Schaefer III HF, Schreiner PR (1998) Coarse Grained Searches over Protein Conformations Encyclopedia of Computational Chemistry &Sons: Chichester.

J92. Bahar I, Wallqvist A, Covell DG, Jernigan RL (1998) Correlation between native state hydrogen exchange and cooperative residue fluctuations from a simple model Biochemistry 37: 1067-1075.

Publications 1997

J91. Bahar I, Erman B, Haliloglu T, Jernigan RL (1997) Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations Biochemistry 36: 13512-13523.

J90. Baysal C, Erman B, Bahar I, Laupretre L, Monnerie L (1997) Local dynamics of bulk polybutadiene of various microstructures: Comparison of Theory with NMR Measurements Macromolecules 30: 2058-2066.

J89. Haliloglu T, Bahar I, Erman B (1997) Gaussian dynamics of folded proteins Phys. Rev. Lett. 79: 3090-3093.

J88. Bahar I (1997) Local relaxation in dense media: cooperative kinematics theory and applications Macromol Theory & Simulations 6: 881-906.

J87. Bahar I, Kaplan M, Jernigan RL (1997) Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches Proteins 29: 292-308.

J86. Bahar I, Atilgan AR, Jernigan RL, Erman B (1997) Understanding the recognition of protein structural classes by amino acid composition Proteins 29: 172-185. PMID: 9329082

J85. Erman B, Bahar I, Jernigan RL (1997) Equilibrium states of rigid bodies with multiple interaction sites. Application to protein helices J Chem Phys 107: 2046-2059.

J84. Fakirov S, Sarac Z, Anbar T, Boz B, Bahar I, Evstatiev M, Apostolov A, Mark JE, Kloczkowski A (1997) Mechanical properties and transition temperatures of crosslinked-oriented gelatin: II. Effect of orientation and water content on transition temperatures Colloid Polym Sci 275: 307-314.

J83. Bahar I, Cho J, Doruker P, Erman B, Haliloglu T, Kim E-G, Mattice WL, Monnerie L, Rapold RF (1997) Three approaches that permit more efficient simulation of the dynamics of atomistic models of polymers Trends in Polymer Science 5: 155-160.

J82. Doruker P, Bahar I (1997) Role of water on unfolding kinetics of polypeptides studied by molecular dynamics simulations Biophys J 72: 2445-2456. (Abstract)

J81. Bahar I, Atilgan AR, Erman B (1997) Direct evaluation of thermal fluctuations in protein Folding & Design 2: 173-181.

J80. Bahar I, Jernigan RL (1997) Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separations J Mol Biol 266: 195-214.

Publications 1996

J79. Zhao WY, Kloczkowski A, Mark JE, Erman B, Bahar I (1996) Make tough plastic films from gelatin Chemtech 26: 32-38.

J78. Haliloglu T, Bahar I, Erman B, Mattice WL (1996) Relative contributions of coupled rotations and small amplitude torsions to conformational relaxation in polymers Macromolecules 29: 8942-8947.

J77. Bahar I, Jernigan RL (1996) Coordination geometry of non-bonded residues in globular proteins Folding & Design 1: 357-370.

J76. Haliloglu T, Bahar I, Erman B (1996) The Response of a Single Grafted Chain to Shear Flow. A Brownian Dynamics Simulation Study J Chemical Physics 105: 2919-2926.

J75. Zhao WV, Kloczkowski A, Mark JE, Erman B, Bahar I (1996) Main-Chain Lyotropic Liquid-Crystalline Elastomers. 2. Orientation and Mechanical Properties of Polyisocyanate Films" Macromolecules 29: 2805-2812.

J74. Zhao WV, Kloczkowski A, Mark JE, Erman B, Bahar I (1996) Main-Chain Lyotropic Liquid-Crystalline Elastomers. 1. Syntheses of Cross-Linked Polyisocyanate Gels Acquiring Liquid-Crystalline Behavior in the Swollen State Macromolecules 29: 2796-2804.

J73. Haliloglu T, Bahar I, Erman B, Mattice WL (1996) Mechanisms of the Exchange of Diblock Copolymers between Micelles at Dynamic Equilibrium Macromolecules 29: 4764-4771.

J72. Baysal C, Erman B, Bahar I, Monnerie L (1996) Kinematics of Polymer Chains in Dense Medium. 4. Effect of Backbone Geometry and Application to Polybutadiene Macromolecules 29: 2980-2988.

B7. Bahar I, Erman B Ed Fakirov S (1996) Segmental Orientation in Deformed Rubbery Networks Oriented Polymer Materials Huthig & Webf Verlag, Oxford, p467-481.

J71. Baysal C, Atilgan AR, Erman B, Bahar I (1996) A Molecular Dynamics Analysis of Coupling between Librational Motions and Isomeric Jumps in Chain Molecules Macromolecules 29: 2510-2514.

J70. Jernigan RL, Bahar I (1996) Structure-Derived Potentials and Protein Simulations Current Opinion in Structural Biology 6: 195-209.

J69. Zhao WV, Kloczkowski A, Mark JE, Erman B, Bahar I (1996) Oriented Gelatin- A New Source for High-Performance Macromol Sci Pure Appl ChemA33, 525-540.

J68. Haliloglu T, Bahar I, Erman B, Kim EG, Mattice WL (1996) A Dynamic Rotational Isomeric State Approach for Extension of the Time Scale of the Local Dynamics Observed in Fully Atomistic Molecular Dynamics Simulations J Chem Phys 104: 4828-4834.

Publications 1995

J67. Baysal C, Atilgan AR, Erman B, Bahar I (1995) Coupling Between Different Modes in Local Chain Dynamics: A Modal Correlation Analysis J Chem Soc Faraday Trans 91: 2483-2490.

J66. Haliloglu T, Bahar I, Erman B (1995) Dependence of Segmental Orientation on Polymer Conformational Characteristics Polymer 36: 4131-4134.

J65. Sarac Z, Erman B, Bahar I (1995) Segmental Orientation in Deformed Networks. 2. Molecular Theory of Biaxial Deformation Macromolecules 28: 582-588.

J64. Bahar I, Baysal N, Erman B, Monnerie L (1995) Kinematics of Polymer Chains in Dense Medium. 3. Influence of Intramolecular Conformational Potentials Macromolecules 28: 1038-1048.

J63. Serhatkulu T, Erman B, Bahar I, Fakirov S, Evstatiev M, Sapundjieva D (1995) Dynamic-Mechanical Study of Amorphous Phases in Poly(ethylene terephtalate)/Nylon-6 Blends Polymer 36, 2371-2377.

J62. Besbes S, Bokobza L, Monnerie L, Bahar I, Erman B (1995) Molecular Orientation in Deformed Bimodal Networks. 2. Fourier Transform Infrared Measurements on PDMS Networks and Comparison with Theory Macromolecules 28: 231-235.

J61. Bahar I, Erman B, Bokobza L, Monnerie L (1995) Molecular Orientation in Deformed Bimodal Networks. 1. Theory Macromolecules 28: 225-230.

Publications 1994

J60. Mark JE, Yang Y, Kloczkowski A, Erman B, Bahar I (1994) A Novel Orientation Technique for Semi-rigid Polymers. 2. Mechanical Properties of the Cellulose Acetate and Hydroxypropyl cellulose Films Colloid & Polym Sci 272: 393.

J59. Bahar I, Erman B, Fytas G, Steffen W (1994) Intramolecular Contributions to Stretched Exponential Relaxation Behavior in Polymers Macromolecules 27: 5200-5205.

J58. Baysal C, Erman B, Bahar I (1994) Contribution of Bond Rotational Interdependence to Local Chain Dynamics: A Brownian Dynamics Study Macromolecules 27, 3650-2657.

J57. Jernigan RL, Raghunathan G, Bahar I (1994) Characterization of Interactions and Metal Ion Binding Sites in Proteins Current Opinion in Structural Biology 4: 256-263.

J56. Apostolov AA, Fakirov S, Sezen B, Bahar I, Kloczkowski A (1994) Structural and Mechanical Studies of a Blend of Poly(butylene terephtalate) and Poly(ether ester) Based on Poly(butylene terephtalate) and Poly(ethylene glycol) Polymer 35: 5247-5256.

J55. Yang Y, Kloczkowski A, Mark JE, Erman B, Bahar I (1994) A Novel Orientation Technique for Semi-Rigid Polymers. 1. Preparation of Cross-linked Cellulose Acetate and Hydroxypropylcellulose Films Having Permanent Anisotropy in the Swollen State Colloid & Polym Sci 272: 284.

J54. Bahar I, Haliloglu T, Erman B (1994) Role of Structural Heterogeneities on Segmental Orientation in Deformed Chains: Application to Alternating Copolymers Macromolecules 27: 1703.

J53. Bahar I, Erman B, Monnerie L (1994) Effect of Molecular Structures on Local Chain Dynamics: Analytical Approaches and Computational Methods Adv Polymer Sciences 116: 145-206, Springer-Verlag Berlin Heidelberg.

J52. Sakrak G, Bahar I, Erman B (1994) Computer Simulation of Two-Dimensional Trifunctional Bimodal Networks Macromol Theory Simul 3: 151.

J51. Bahar I, Jernigan RL (1994) Cooperative Structural Reorganizations Induced by Nonhomogeneous Intramolecular Interactions in Compact Globular Proteins Biophysical Journal 66: 467. (Abstract)

J50. Bahar I, Jernigan RL (1994) Stabilization of Intermediate Density States in Globular Proteins by Homogeneous Intramolecular Attractive Interactions Biophysical Journal 66: 454. (Abstract)

Publications 1993

J49. Kanberoglu C, Bahar I, Erman B (1993) Stress-Strain-Molecular Orientation in Highly Cross-Linked cis- Polyisoprene Networks Polymer 34: 4997.

J48. Doruker P, Bahar I (1993) Effect of Intrachain Constraints and Polymer-Solvent Interactions on Chain Statistics and Dynamics Comp Polymer Science 3: 87.

J47. Bahar I, Badur B, Doruker P (1993) Solvent Effect on Translational Diffusivity and Segmental Orientational Mobility of Polymers in Dilute Solution: A Molecular Dynamics Study J Chem Phys 99: 2235.

J46. Erman B, Bahar I, Besbes S, Bokobza L, Monnerie L (1993) Interpretation of Segmental Orientation in Deformed Networks in Terms of Constrained Junction Model of Rubber Elasticity Polymer 34: 1858.

J45. Haliloglu T, Erman B, Bahar I (1993) Orientational Mobility of Uniaxially Deformed Polymer Chains: A Brownian Dynamics Simulation Study Polymer Communications 34: 440.

J44. Besbes S, Bokobza I, Monnerie L, Bahar I, Erman B (1993) An Infrared Dichroism Investigation of Segmental Orientation in Dry and Swollen Poly(dimethyl siloxane) Networks Polymer 34: 1179.

J43. Bahar I, Erman B, Kremer F, Fischer EW (1993) Dynamic Rotational Isomeric State Approach for Segmental Motions of cis-Polyisoprene in the Bulk State Colloid Polym Sci 91: 1.

J42. Erman B, Bahar I (1993) Local Dynamics of Freely Rotating Chains in Dense Systems Colloid Polym Sci 91: 16.

Publications 1992

B6. Erman B, Bahar I, Kloczkowski A, Mark JE Ed Aharoni SM (1992) Networks with Semi-Flexible Chains, in Synthesis, Characterization, and Theory of Polymeric Networks and Gels Plenum Press, New York, p.113-126.

B5. Kloczkowski A, Mark JE, Erman B, Bahar I Eds Noda I, Rubingh DN (1992) Isotropic-Nematic Phase Transitions in Polymer Networks Deformed in the Dry and Swollen States in Polymer Solution, Blends and Interfaces Elsevier Science Publishers B V, p 221.

B4. Erman B, Bahar I, Yang Y, Kloczkowski A, Mark JE Eds Noda I, Rubingh DN (1992) Novel Orientation Techniques for the Preparation of High- Performance Materials from Semi-Flexible Polymers such as Cellulosics in Polymer Solution, Blends and Interfaces, Elsevier Science Publishers B V, p 209.

B3. Erman B, Bahar I Eds Noda I, Rubingh DN (1992) Local Dynamics of Polymers in Restrictive Environment in Polymer Solution, Blends and Interfaces, Elsevier Science Publishers B. V., p 197.

J41. Bahar I, Erman B, Monnerie L (1992) Kinematics of Polymer Chains with Freely Rotating Bonds in Restrictive Environment. 2. Conformational and Orientational Correlations Macromolecules 25: 6315.

J40. Bahar I, Erman B, Monnerie L (1992) Kinematics of Polymer Chains with Freely Rotating Bonds in Restrictive Environment. 1. Theory Macromolecules 25: 6309.

J39. Akcasu AZ, Bahar I, Erman B, Feng Y, Han C (1992) Theoretical and Experimental Study of Dissolution of Inhomogeneities Formed During Spinodal Decomposition in Polymer Mixtures J Chem Phys 97: 5782.

J38. Akcasu AZ, Erman B, Bahar I (1992) Nonlinear Kinetics of Spinodal Decomposition and Dissolution of Inhomogeneities formed by Spinodal Decomposition in Polymer Blends Makromolekulare Chemie Makromol Symp 62: 43.

J37. Haliloglu T, Erman B, Bahar I (1992) Time-Dependent Probability Distribution Functions for Orientational Motions of Segments in Polymer Chains J Chem Phys 97: 4438.

J36. Haliloglu T, Bahar I, Erman B (1992) Orientational and Conformational Correlations in Deformed Polymer Chains with Fixed End-to-End Separation: A Brownian Dynamics Simulation Study J Chem Phys 97: 4428.

J35. Bahar I, Neuburger N, Mattice WL (1992) Mechanism of Local Conformational Transitions in Poly(dialkyl Siloxanes). Molecular Dynamics Simulation and Dynamic Rotational Isomeric State Approach Macromolecules 25: 4619.

J34. Neuburger N, Bahar I, Mattice WL (1992) Molecular Dynamics Simulations of Poly (dialkylsiloxanes). Equilibrium Statistics and Unperturbed Chain Dimensions Macromolecules 25: 2447.

J33. Besbes S, Cermelli I, Bokobza L, Monnerie L, Bahar I, Erman B, Herz J (1992) Segmental Orientation in Model Networks of Poly(dimethyl siloxane): Fourier Transform Infrared Dichroism Measurements and Theoretical Interpretation Macromolecules 25: 1949.

B2. Erman B, Bahar I, Kloczkowski A, Mark JE Eds Mark JE, Erman B (1992) Stresss-Strain and Segmental Orientation in Networks with Semirigid Chains in Elastomeric Polymer Networks Prentice Hall Polymer Science and Engineering Series Prentice Hall, Inc. New Jersey, p142.

J32. Bahar I, Erman B, Kremer F, Fischer EW (1992) Segmental Motions of cis-Polyisoprene in the Bulk State: Interpretation of Dielectric Relaxation Data Macromolecules 25: 816.

Publications 1991

J31. Zuniga I, Bahar I, Dodge R, Mattice WL (1991) Molecular Dynamics Analysis of Transitions Between Rotational Isomers in Polymethylene with Discrete Hydrogen Atoms J Chem Phys 95: 5348.

J30. Haliloglu T, Bahar I, Erman B (1991) Segmental Orientation in Poly(oxyethylene) Networks Comp Polymer Science 1, 151.

J29. Bahar I, Erman B, Monnerie L (1991) A Stochastic Treatment of Conformational Transitions of Polymer Chains in the Sub-Rouse Regime Macromolecules 24: 3618.

J28. Bahar I, Dodge R, Zuniga I, Mattice WL (1991) Configurational Statistics of Poly(dimethyl siloxane). II. A New Rotational Isomeric State Approach Macromolecules 24: 2993,.

J27. Bahar I, Zuniga I, Dodge R, Mattice WL (1991) Conformational Statistics of Poly (dimethyl siloxane). I. Probability Distribution of Rotational Isomers from Molecular Dynamics Simulations Macromolecules 24: 2986.

J26. Mattice WL, Zuniga I, Dodge R, Bahar I (1991) Use of Molecular Dynamics Trajectories for the Formulation of Statistical Weight Matrices for Chains with Symmetric Threefold Rotation Potentials Comp Polymer Science 1, 35: .

J25. Bahar I, Mattice WL (1991) Bimodal Distribution of Relaxational Modes for the Helix-Coil Transition in Poly(oxymethylene) Macromolecules 24: 877.

J24. Erman B, Haliloglu T, Bahar I, Mark JE (1991) Segmental Orientation in Uniaxially Deformed Networks: A Higher Order Approximation for Finite Chains at Large Deformations Macromolecules 24: 901.

Publications 1990

J23. Bahar I, Erman B, Kloczkowski A, Mark JE (1990) A Lattice Model for Segmental Orientation in Deformed Polymeric Networks.2. Effect of Chain Stiffness and Thermotropic Interactions Macromolecules 23: 5341.

J22. Erman B, Bahar I, Kloczkowski A, Mark JE (1990) A Lattice Model for Segmental Orientation in Deformed Polymeric Networks.1. Contribution of Intermolecular Correlations Macromolecules 23: 5335.

J21. Kuntman A, Baysal B, Bahar I (1990) Conformational Characteristics of Poly(ethyl methacrylate). Dipole Moment Measurements and Calculations Macromolecules 23: 4959.

J20. Bahar I, Erman B, Monnerie L (1990) Effect of Surrounding Medium on Intramolecular Conformational Changes in Probe Molecules Macromolecules 23: 3805.

J19. Bahar I, Mattice WL (1990) Efficient Calculation of the Intramolecular Contribution to Orientational Autocorrelation Functions Using Dynamic Rotational Isomeric State Theory Macromolecules 23: 2719.

J18. Bahar I, Erman B, Monnerie L (1990) Local Orientational Motions in Flexible Polymeric Chains Macromolecules 23: 1174.

J17. Kloczkowski A, Mark JE, Bahar I, Erman B (1990) A Closed Form Solution for the Internal Dynamics of Polymer Chains: I. Bonds with Independent Rotational Potentials J Chem Phys 92: 4513.

Publications 1989

J16. Bahar I, Mattice WL (1989) Dynamics of Conformational Transitions to Isomeric States Favoring Intramolecular Excimer Formation in Aromatic Polyesters with Methylene or Oxyethylene Spacers\ J Chem Phys 90: 6783.

J15. Bahar I, Mattice WL (1989) Dynamics of Conformational Transitions to Isomeric States Favoring Intramolecular Excimer Formation in Polymeric Chains: Application to Dimer Models of Polystyrene J Chem Phys 90: 6775.

J14. Bahar I, Erman B, Monnerie L (1989) Application of the Dynamic Isomeric States Model to Poly(ethylene oxide) and Comparison with Nuclear Magnetic Relaxation Data Macromolecules 22: 2396.

J13. Erman B, Bahar I, Navard P (1989) Rheology of Solutions of Rodlike Polymers: Theory and Comparison with Experiments Macromolecules 22: 358.

J12. Bahar I (1989) Stochastics of Rotational Isomeric Transitions in Polymer Chains J Chem Phys 91: 6525.

J11. Bahar I, Erman B, Monnerie L (1989) Comparison of Dynamic Rotational Isomeric State Results with Previous Expressions for Local Chain Motion Macromolecules 22: 431.

Publications 1988

J10. Bahar I, Erman B, Monnerie L (1988) A New Approach to the Relationship Between Chemical Structure and Local Dynamics Nuclear Magnetic Resonance Measurements in Dilute Polymer Solutions Polymer Commun 29: 349.

J9. Bahar I, Erman B (1988) Anisotropy of Static and Dynamic Orientational Correlations in n- Alkanes J Chem Phys 88: 1228.

J8. Bahar I, Mattice WL (1988) The Configurational Contribution to the Segmental Orientation in Network Chains Subject to Excluded Volume Effect J Chem Phys 89: 1153.

J7. Erman B, Bahar I (1988)Effects of Chain Structure and Network Constitution on Segmental Orientation in Deformed Amorphous Polymeric Networks Macromolecules 2l: 452.

Publications 1987

Publications 1986

J2. Bahar I, Baysal B, Erman B (1986) Local Solvent Effects on the Configurational Characteristics of Polymer Chains: Poly (p-chlorostyrene) in Benzene Macromolecules 19: 1703.

J1. Bahar I, Erman B (1986) Effect of Flow on Solutions of Rodlike Molecules J Polym Sci Polymer Phys Ed 24: l36l.

Publications 1985

B1. Bahar I. (1985) Thermodynamics of Compatibility in Binary Polymeric Mixtures in Polymer Blends and Mixtures, NATO ASI Series E: 89, Martinus Nijhoff Publishers, Dordrecht, p.349.