Gaussian Network Model:


"Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential",
I. Bahar, A. R. Atilgan, and B. Erman, Folding & Design, 2, 173-181, (1997) 

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

"Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability,"
Bahar, I., Atilgan, A. R., Demirel, M. C. and Erman B., Phys. Rev. Lett., 80 (1998)

"Correlation between native state hydrogen exchange and cooperative residue fluctuations from a simple model"
I. Bahar, A. Wallqvist, D. G. Covell, & R.L. Jernigan, Biochemistry 37, 1067-1075, (1998)

"Identification of Kinetically Hot Residues in Proteins,"
Demirel, M. C., Atilgan, A. R., Jernigan, R. L., Erman, B. and Bahar I., submitted to Protein Science, (1998)

"Vibrational dynamics of transfer RNAs. Comparison of the free and enzyme-bound forms."
I. Bahar & R. L. Jernigan, J. Mol. Biol. 281, 871-884 (1998)

"Collective dynamics of HIV-1 reverse transcriptase: Examination of Flexibility and Enzyme Function"
I. Bahar, B. Erman, R. L. Jernigan, A. R. Atilgan, & D. Covell J. Mol. Biol. 285, 1023-1037, (1999)

"Cooperative fluctuations and subunit communication in tryptophan synthase"
I. Bahar & R.L. Jernigan Biochemistry 38, 3478-3490, (1999)
Full paper (PDF)

"Relating structure to function through the dominant modes of motion of DNA topoisomerase II"
R.L. Jernigan, M. C. Demirel & I. Bahar Int.J. Quantum Chem. 75, 301-312, (1999). 
Full paper (.pdf)

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

"Proteins with similar architecture exhibit similar large-scale dynamic behavior. Specificity resides in local differences"
O. Keskin, R. L. Jernigan & I. Bahar, Biophysical Journal 78, 2093-2106, (2000).
 Full paper (PDF)

"Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure"
O. Keskin, I. Bahar, R.L.Jernigan, T.G.Myers, J.A.Beutler, R.H.Shoemaker, E.A.Sausville, D.G.Covell Anticancer Drug Design 15, 79-98, (2000). 
Full paper (.pdf)

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

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

"Relating the structure of HIV-1 reverse transcriptase to its processing step"
 R.L.Jernigan, I. Bahar, D.G.Covell, A.R.Atilgan, B. Erman & D. Flatow, J. Biomol. Structure & Dynamics, 1, 49-55, (2000).

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

"Collective motions of neutral and low pH forms of incluenza virus hemagglutinin"
Isin, B., Bahar, I. & Doruker, P. Biochemistry 40 (29), (2001). 

"Large functional motions of proteins"
O. Keskin, Bahar I, Covell D, Atilgan AR, Durell S, Jernigan RL, Biophys. J. 80 (661), 2001. 

"Dynamics of large proteins through hierarchical levels of coarse-grained structures".
Doruker P, Jernigan RL, Bahar I. J Comp Chem 23:119-127,(2002).
Full paper (.pdf)

"Functional motions of influenza virus hemagglutinin: A structure-based analytical approach"
Isin B, Doruker P, Bahar I.  Biophys J. 82:569-581, (2002).
Full paper (.pdf)

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

"Relating molecular flexibility to function: A case study of tubulin"
Keskin O, Durell SR, Bahar I, Jernigan RL, Covell, DG.  Biophys J. 83, 663-680, (2002). 
Full paper (.pdf)

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


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