The Future of Principles-Based Drug Discovery
Laufer Center, Stony Brook University –
Icahn School of Medicine, Mount Sinai
Academic Affiliation Workshop
April 14 – 15, 2019
Workshop components include the structure-based forcefield MD
simulations world; and cell physics, molecular mechanisms of drug
resistance and evolution, fluctuations in gene expression, etc.
Located at
Laufer Center, Stony Brook University
(April 14) and
Hilton Garden Inn on Stony Brook’s campus
(April 15)
Sunday, April 14 — 12:30 PM – 9:00 PM
12:30 – 1:20 Workshop check-in and Lunch (Laufer Center Hub room 110)
Afternoon Session 1:30 – 5:30 (Laufer lecture hall room 101)
Dr. Ken A. Dill, Director, Laufer Center - Welcome and Opening Remarks
1:30 – 2:00 Jin Wang, Professor Chemistry and Physics, SBU
Specificity Quantification, Scoring Function Optimization and Drug Lead Explorations
2:00 – 2:30 Emiliano Brini, Postdoc (Ken Dill lab), Laufer Center, SBU
Seeking the mechanisms of cystic fibrosis mutations
2:30 - 3:15 Jeremiah Faith, Assistant Professor Genetics and Genomic Sciences, ISMMS
Strain-Level Variation in Gut Microbiome Composition Drives Complex Disease Risk
Coffee Break 3:15 – 3:45 (Laufer Hub 110)
3:45 – 4:15 Arjun Singh Yadaw, Postdoc (Ravi Iyengar lab), ISMMS
Dynamical model of neurite outgrowth and it’s applicability in systems therapeutic for axonal regeneration
4:15 – 4:45 Vageli Coutsias, Professor, Applied Math and Statistics, SBU
Conformational sampling of Macrocycles
4:45 – 5:30 Justin Kinney, Asst Professor, Simons Center for Quantitative Biology, Cold Spring Harbor Lab
Measuring cis-regulatory energetics in living cells using allelic manifolds
6:00 –9:00 Dinner Banquet at Hilton Garden Inn
Monday, April 15 — 8:00 AM – 6:00 PM
Hilton Garden Inn – University Room B & C (poster session and reception in University Room A)
Continental Breakfast, 8:00 – 9:00
Morning Session 9:00 – 12:15
9:00 - 9:30 Carlos Simmerling, Professor of Chemistry, Laufer Center, SBU
Improving the accuracy of biomolecular simulation models
9:30 - 10:00 Rob Rizzo, Professor Applied Math and Statistics, SBU
Computational approaches for drug-lead discovery
10:00 – 10:30 Jingqi Gong, Grad student (adviser Eric Sobie), ISMMS
Mechanistic modeling combined with quantitative physiology translates cardiac myocyte drug responses to multiple populations
Coffee Break 10:30 – 11:00
11:00 – 11:45 Eirini Papapetrou, MD, PhD, Associate Professor, ISMMS
Modeling human leukemia with induced pluripotent stem cells
11:45 - 12:15 Tyler Guinn, Grad student (adviser Gabor Balazsi) Laufer Center, SBU
Optogenetic Gene Circuits for Unraveling Potential Drug Targets through Precision Gene Expression Control
Lunch and Poster Setup 12:15 - 1:30
Afternoon Session 1:30 - 3:30
1:30 – 2:15 Davide Provasi, Associate Professor Pharmacological Sciences, ISMMS
Thermodynamics and Kinetics of G Protein-Coupled Receptor Activation Using Metadynamics and Maximum Caliber
2:15 – 2:45 Rayees Rahman, Grad student, Biophysics & Systems Pharma (adviser Avner Schlessinger), ISMMS
Redefining the Protein Kinase Conformational Space with Machine Learning
2:45 – 3:15 Tom MacCarthy, Assistant Professor Applied Math and Statistics, SBU
Computational approaches to herpesvirus evolution under the effect of AID/APOBEC mutagenesis
3:15 – 3:45 Josh Rest, Associate Professor Ecology and Evolution, SBU
Thinking about drug interactions and epistasis in light of standing genetic variation
Reception & Poster Session 4:00 – 6:00. (Presenters should be available to answer questions.) Recognition of top posters 5:30
6:30 - HGI shuttle to Stony Brook LIRR station to get the 6:49 PM train to NYC (Meet in hotel lobby by reception desk.)
Poster Presentations
Poster # 1 “Amber ff14SB Force Field Parameters for Phosphorylated Amino Acids”
Lauren Raguette
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Carlos Simmerling
Poster # 2 “Characterization of Novel Positive Allosteric Modulators of the µ-Opioid Receptor for The Development of Safer Drugs”
Abhijeet Kapoor
Postdoc, ISMMS
Adviser: Marta Filizola
Poster # 3 “Thermodynamics and Kinetics of The Divalent and Monovalent Cation Competition for Binding Sites at the Μ-Opioid Receptor”
Xiaohu Hu
Postdoc, ISMMS
Adviser: Marta Filizola
Poster # 4 “A GPU Implemented Genetic Algorithm for Optimizing Torsion Parameters”
Kellon Belfon
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Carlos Simmerling
Poster # 5 “Protein Evolution Speed Depends on Stability, Abundance and Chaperone Concentrations”
Luca Agozzino
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Ken Dill
Poster # 6 “Reservoir REMD: A Faster and More Efficient Way to Do REMD”
Koushik Kasavajhala
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Carlos Simmerling
Poster # 7 “Redefining the Protein Kinase Conformational Space with Machine Learning”
Rayees Rahman
Grad Student/PhD Candidate, ISMMS
Adviser: Avner Schlessinger
Poster # 8 “The Biological Catch Bond Suppresses Fluctuations in Nonequilibrium Systems”
Jason Wagoner
Postdoc, Laufer Center, SBU
Adviser: Ken Dill
Poster # 9 “Optimizing sampling methods for RNA simulation”
Kenneth Lam
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Carlos Simmerling
Poster # 10 “H-Bond Pattern in SSE’s & Restricted Sampling: A Geometrical Analysis”
Mosavverul Hassan
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Evangelos Coutsias
Poster # 11 “Synthetic Control of Mitotic Exit for Studying Multicellular Drug Resistance in Yeast”
Oleksandra Romanyshyn
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Gabor Balazsi
Poster # 12 “Transcriptomics Based Mechanistic Modeling Elucidates Patient Specific Dynamics of Tyrosine Kinase Inhibitor Induced Excitation Coupling Abnormalities”
Eric Sobie
PI, ISMMS
Poster # 13 “Role of Network-Mediated Stochasticity in Mammalian Drug Resistance”
Kevin Farquhar
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Gabor Balazsi
Poster # 14 “Computational Modelling and Virtual Screening Campaign Targeting Glycoprotein E in Zika Virus”
Stephen Telehany
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Robert Rizzo
Poster # 15 “Protein Docking on Rotational Manifolds”
Dzmitry Padhorny
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Dima Kozakov
Poster # 16 “ClusPro FMFT-SAXS: Ultra-Fast Filtering Using Small Angle X-ray Scattering Data in Protein Docking”
Mikhail Ignatov
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Dima Kozakov
Poster # 17 “Monte Carlo Minimization for Pose Prediction of Protein-Ligand Complexes”
Andrey Alekseenko
Postdoc, Laufer Center, SBU
Adviser: Dima Kozakov
Poster # 18 “Template-Based Pose Prediction of Protein-Ligand Complexes: 2018 D3R Grand Challenge”
Sergei Kotelnikov
Grad Student/PhD Candidate, Applied Mathematics and Statistics, SBU
Adviser: Dima Kozakov
Poster # 19 “Exploring the Trade-off Between Brain Function and Metabolic Cost: Insights from fMRI”
Corey Weistuch
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Ken Dill
Poster # 20 “Protein Structure and Contact Geometry”
Bihua Yu
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Evangelos Coutsias
Poster # 21 “MELD: Predicting Drug Binding Pose Using Physics”
Cong Liu
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Ken Dill
Poster # 22 “De Novo Design Approaches to Drug Discovery Targeting Tsg101 and nSMase2”
Lauren Prentis
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Robert Rizzo
Poster # 23 “Microfluidic Platform for Multifaceted Single-Cell Analysis of Rare and Low-Cell-Number Samples”
Rafał Krzysztoń
Postdoc, Department of Biomedical Engineering,SBU
Adviser: Eric Brouzes
Poster # 24 “ff19SB: Amino-acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energies in Solution”
Chuan Tian
Grad Student/PhD Candidate, Laufer Center, SBU
Adviser: Carlos Simmerling
Congratulations to the Top Poster Presentations
#1 Lauren Prentis
Grad Student/PhD Candidate, Laufer Center, SBU, Adviser: Robert Rizzo
De Novo Design Approaches to Drug Discovery Targeting Tsg101 and nSMase2
#2 Kevin Farquhar
Grad Student/PhD Candidate, Laufer Center, SBU, Adviser: Gabor Balazsi
Role of Network-Mediated Stochasticity in Mammalian Drug Resistance
#3 Dima Padhorny
Grad Student/PhD Candidate, Laufer Center, SBU, Adviser: Dima Kozakov
Protein Docking on Rotational Manifolds
Lauren Prentis, Dima Padhorny,
Kevin Farquhar (pictured left to right)
Thank you to everyone who presented posters at the workshop! It wouldn’t have been the same without your participation.
And a special thanks to the judges—Jeremiah Faith, Icahn School of Medicine, Mt Sinai; Justin Kinney, Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory; and John Van Drie, Van Drie Research, LLC. They took the time to visit all the posters and listen to the presenters. It was a difficult decision, and we truly appreciate your commitment to the task. Thank you!