Virtual 2020
Description
The 2020 Workshop on Free Energy Methods in Drug Design turned out to become a virtual conference held from June 15-17, 2021. The workshop focused on the application of free energy methods in drug design, with a particular emphasis on celebrating the 10th anniversary of the first free energy workshop.
Organization Committee
Schedule
June 15th, 2021 (Day 1)
| Time (EST) |
Speaker |
Title |
| 11:15 |
INTRODUCTION |
|
| Session Chair: Antonia Mey |
|
|
| 11:30 |
Julien Michel |
Adaptive absolute binding free energy calculations for lead compounds and flexible proteins |
| 11:55 |
Hannah Baumann |
Binding free energy calculations: Sampling challenges, nonequilibrium switching, and alternate approaches |
| 12:20 |
Emilio Gallicchio |
The Alchemical Transfer Method: a Streamlined Approach to Absolute and Relative Binding Free Energy Calculations |
| 12:45 |
RREAK |
|
| Session Chair: Sereina Riniker |
|
|
| 1:00 |
Christopher Bayly |
Non-Equilibrium Switching in Orion |
| 1:25 |
Michael Shirts |
Learning Free Energy Surfaces |
| 1:50 |
POSTERS |
|
| Session Chair: Jonah Vilseck |
|
|
| 2:15 |
David Minh |
Large-scale Free Energy Calculations with Implicit Ligand Theory |
| 2:40 |
Cindy Yan |
Binding affinity predictions in small-molecule drug discovery: Is balancing accuracy and efficiency possible? |
| 3:05 |
Matteo Aldeghi |
Structure-based predictions of kinase inhibitor resistance: a prospective evaluation |
June 16th, 2021 (Day 2)
| Time (EST) |
Speaker |
Title |
| 11:15 |
INTRODUCTION |
|
| Session Chair: Richard Lonsdale |
|
|
| 11:30 |
Benjamin Ries |
Relative binding free energies with scaffold-hopping type transformations using RE-EDS |
| 11:55 |
Jonathan Essex |
Combining grand canonical and nonequilibrium candidate Monte Carlo to enhance sampling |
| 12:20 |
Wonpil Im |
What can CHARMM-GUI do for you? |
| 12:45 |
RREAK |
|
| Session Chair: Zoe Cournia |
|
|
| 1:00 |
Jonah Vilseck |
Multisite Sampling with Discrete Gibbs Sampler-Based Lambda-Dynamics |
| 1:25 |
William Jorgensen |
40 Years of Free-Energy Calculations from Solvent Effects to SARS-CoV-2 Inhibitors |
| 1:50 |
POSTERS |
|
| Session Chair: Emilia Pecora de Barros |
|
|
| 2:40 |
Yutong Zhao |
Improved Orientational Restraints for Binding Free Energies |
| 3:05 |
Lyna Luo |
Understand and optimize reversible covalent inhibitors and allosteric agonists |
June 17th, 2021 (Day 2)
| Time (EST) |
Speaker |
Title |
| 11:15 |
INTRODUCTION |
|
| Session Chair: Camilo Velez-Vega |
|
|
| 11:30 |
Niels Hansen |
Exploring a correlation between Soret and partition coefficient by means of free-energy calculations |
| 11:55 |
Robert Abel |
Models to Medicines: The impact of large scale physics-based design on clinical candidate discovery |
| 12:20 |
Vytautas Gapsys |
Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design |
| 12:45 |
RREAK |
|
| Session Chair: Kira Armacost |
|
|
| 1:00 |
Joy Yang |
Optimal Designs for Pairwise Calculation: An Application to FEP in Minimizing Prediction Variability |
| 1:25 |
Brian Radak |
Advancing Drug Discovery with a Practical Approach to Free Energy Simulations |
| 1:50 |
POSTERS |
|
| Session Chair: Zhuyan Guo |
|
|
| 2:40 |
Dave Thompson & Kira Armacost |
Free Energy Methods in Drug Discovery : “It will be the most important field in computational chemistry.” |
| 3:05 |
Gary Tresadern |
NA |
Online Poster Session
June 15th, 2021 (Day 1)
| Presenter |
Title |
| Michael Gillhofer |
Importance of water molecules for alchemical free-energy calculations |
| Oriol Gracia i Carmona |
Evaluating Accelerated Enveloping Distribution Sampling (AEDS) for Efficient Free Energy Calculations in the T4 L99A Lysozyme System |
| Jonathan Barnes |
Analysis of Software Methods for Estimation of Protein-Protein Relative Binding Affinity |
| Anthony Hazel |
Rapid and accurate estimation of protein–ligand relative binding affinities using site-identification by ligand competitive saturation |
| Sheenam Khuttan |
Relative Binding Free Energy Calculations for the GDCC SAMPL8 Blinded Challenge using the Alchemical Transfer Method |
June 16th, 2021 (Day 2)
| Presenter |
Title |
| Jenke Scheen |
FEP-Space: Towards Data-driven estimation of optimal perturbation networks in relative alchemical free energy calculations |
| Ivy Zhang |
Predicting the impact of circulating SARS-CoV-2 variants using relative binding free energy calculations |
| Sofia Bariami |
Implementation and Validation of the QUBE Forcefield in Sire MD Framework |
| Adam Green |
Application of Multi-Site Lambda Dynamics in BIOVIA Pipeline Pilot and Discovery Studio |
| João Morado |
Parameterization Made Easy With ParaMol |
| Martin Reinhardt |
Calculating Free Energy Differences Through Variationally-derived Intermediates |
| Nitin Singh |
Understanding the Helical Stability of Charged Peptides |
| Salomé Rieder |
Using GAFF topologies and RE-EDS to calculate relative hydration free energies in GROMOS |
| Drazen Petrov |
Perturbation free-energy toolkit: automated alchemical topology builder and adaptive simulation update scheme |
| David Zierke |
Prediction of Factor Xa - Inhibitor Binding Affinities using Multisite Lambda Dynamics |
June 17th, 2021 (Day 3)
| Presenter |
Title |
| Mateusz K. Bieniek |
TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing |
| Yunhui Ge |
Enhancing sampling of water rearrangements on ligand binding: A comparison of techniques |
| Esteban Vohringer |
Environment Specific D-MBIS Atomic Charges Improve Binding Free Energy Predictions of SAMPL5 Host-Guest Systems |
| Ernest Williams |
Modelling the Binding Free Energy of Peptidomimetic inhibitors of SARS CoV-2 Main Protease |
| Germano Heinzelmann |
Automated tools for absolute binding free energy calculations |
| Krystel El Hage |
Inhibiting RNA : Protein Interactions using an Integrative Computational and Experimental Approach: Application to YB1 |
| Himanshu Goel |
Capturing Water Networks During Ligand Binding with the Site-Identification by Ligand Competitive Saturation Approach |
