Boston 2023

Description

The 2023 Workshop on Free Energy Methods in Drug Design, which took place from May 10-12, 2023, at the Novartis Institutes for BioMedical Research in Cambridge, MA, brought together experts from both the pharmaceutical industry and academia. The workshop’s objective was to discuss challenges and future directions for free energy techniques in drug design. The workshop was organized in partnership with Boston Area Group for Informatics and Modeling (BAGIM).

Group Photo

A photo of 140 attendees.

Organization Committee

Keynote Speaker: Derek Lowe

Institution: Director in Chemical Biology Therapeutics at Novartis Institutes for BioMedical Research (NIBR); Blogger
Trade Blog: In The Pipeline
Title: “FEP and Drug Discovery: Where We’ve Been and Where We’d Like to Go”

Schedule

May 10th, 2023 (Day 1)

Time (EST)	Speaker	Title
8:45	ARRIVAL
9:00	Jose Duca	Welcome to NIBR
9:05	Kira + Hannah	Opening remarks
	Session Chair	David Huggins
9:10	Michael Shirts	Free energies: What we’ve learned about how to estimate them
9:35	Sereina Riniker	10+ Years with (RE-)EDS: Efficient Free-Energy Calculations with a Multistate Method
10:00	Huafeng Xu	Adaptive optimization of binding free energy networks and integration of experimental data
10:25	BREAK
Session Chair: Rafal Wiewiora
10:40	Bill Jorgensen	Free Energy Calculations from Butane to COVID-19
11:05	Jonathan Essex	Enhancing protein and ligand sampling in molecular simulations by fully adaptive simulated tempering
11:30	Derek Lowe (KEYNOTE)	FEP and Drug Discovery: Where We’ve Been and Where We’d Like to Go
12:15	LUNCH
1:30	Zoe Cournia	Welcome back
Session Chair: Matthew Hurley
1:35	Jonah Vilseck	Rapid and Accurate Free Energies of Binding from λ-Dynamics with Bias Updated Gibbs Sampling
2:00	David Mobley	Separated Topologies: A flexible approach for relative binding free energy calculations
2:25	Christopher Bayly	Making Binding Free Energies Practical in a Massively Parallel Universe
2:50	BREAK
Session Chair: Ernest Awoonor-Williams
3:05	Ana Silveira	On the use of high-throughput binding free energy simulations in design cycles for drug discovery
3:30	Katharina Meier	Free Energy Calculations in Pharmaceutical and Crop Science R&D at Bayer
3:55	POSTER SESSION

May 11th, 2023 (Day 2)

Time (EST)	Speaker	Title
9:00	Sereina + Camilo	Welcome + Opening remarks
Session Chair: Yutong Zhao
9:10	Chia-en Chang	Ligand Binding Kinetics: Pathways, Transient States and Unbinding Free Energy Profile
9:35	Alex Dickson	Learning and sampling complex ligand binding pathways with weighted ensemble techniques
10:00	Josh Fass	A local resampling trick for focused molecular dynamics
10:25	BREAK
Session Chair: Phillip Hudson
10:40	Robert Abel	Accelerating drug discovery with ultra-large scale collaborative deployment of predictive modeling
11:05	Marco De Vivo	Pushing the boundaries: FEP for protein-protein and protein-nucleic acids interaction
11:30	Xin (Cindy) Yan	Promises and Limitations: Free Energy Methods in Drug Discovery Projects
11:55	LUNCH
Session Chair: Antonia Mey
1:15	Zoe Cournia	Welcome back + Poster prize announcement
1:20	Julien Michel	Engineering FEP science in the open
1:45	Jay Ponder	Accuracy of the AMOEBA Force Field in Binding Free Energy Simulations
2:10	Lance M. Westerhoff	Fast, absolute binding free energy calculations using MovableType: the impact of different global sampling regimes on predictive performance
2:35	BREAK
Session Chair: Zoe Cournia
2:50	Emilio Galliachio	AToM-OpenMM: An Open-Source Software Package for Relative Binding Free Energy Estimation in Drug Discovery
3:15	Francesca Deflorian	Expanding the Realm of FEP and GPCR Drug Design
3:40	John Chodera	Teaching free energy calculations to learn
4:05	BREAK
Session Chair: Ryan Hayes
4:25	Gianni De Fabritiis	Relative binding affinity calculations towards accuracy and scalability
4:50	Lingle Wang	Beyond Small Molecule Binding: Free Energy Calculations for Antibody Affinity, pH Sensing, Small Molecule Solubility and More
5:15	David Hahn	Impacting drug discovery with open source free energy calculation tools

May 12th, 2023 (Day 3)

Time (EST)	Speaker	Title
9:00	Kira + Jonah	Welcome + Opening remarks
Session Chair: Jonah Vilseck
9:10	Darrin York	Enhancing Precision and Accuracy in Alchemical Free Energy Simulations
9:35	David Pearlman	Free Energy Perturbation calculations incorporating a quantum representation of the ligand binding site
10:00	Mark Mackey	Improving efficiency of free energy calculations with adaptive lambda schedules
10:25	BREAK
Session Chair: Sepehr Dehghanighahnaviyeh
10:40	Hugo Gutierrez de Teran	QFEP: combining ligand SAR and in silico mutagenesis for ligand design
11:05	Andrey Frolov	Dealing with high flexibility of crosslinked peptides in FEP calculation
11:30	ROUND TABLE DISCUSSION
11:55	LUNCH
Session Chair: Alisha Caliman
1:15	Zoe Cournia	Welcome back
1:20	Michael Schnieders	An Alchemical Pipeline for Polymorph Discovery and Optimization
1:45	David Minh	Binding pose prediction using absolute binding free energy calculations
2:10	Lucy Colwell	Machine learning to predict protein function from sequence with therapeutic applications
2:35	Kira + Hannah	Closing remarks