Boston 2025

Description

The 2025 Free Energy Workshop, hosted by the Alchemistry Organization Committee and the OMSF, took place from May 6-8th at the Merck Research Laboratories in Boston, Massachusetts. The workshop focuses on free energy methods in computational chemistry and drug design and welcomed around 240 researchers from around the globe.

Group Photo

A photo of 240 attendees.

Organization Committee

Jonah Vilseck, PhD
Heidi Koldsø, PhD
George Giambasu, PhD
Cesar Mendoza Martinez, PhD
Dmitry Lupyan, PhD
Aakankschit Nandkeolyar (AK)
Cristian Gabellini
Zachary J. Baker
Alexander Williams, PhD
Organizer’s Photo

Keynote Speakers

Dennis Hu	Rommie E. Amaro
Institution: Chief Executive Officer, Drug Hunter	Institution: Professor and Endowed Chair of Chemistry and Biochemistry and the Director of the National Biomedical Computation Resource at University of California, San Diego
Title: “Not Your Grandparents’ Drugs: Modern Highlights in Small Molecule Drug Discovery”	Title: “Multiscale Computational Microscopy (For Drug and Immunogen Design)”
Video: YouTube	Video: YouTube

Schedule

May 6th, 2025 (Day 1)

Time (EST)	Speaker	Title
8:00		Venue opens; Set up posters for evening poster session; continental breakfast
8:40	George Giambasu	Welcome + Opening Remarks
Session Chair: George Giambasu
9:00	David Mobley	Binding free energy calculations with separated topologies – successes and challenges
9:25	Junjie Zou	XFF: Development and benchmarking of small molecule force field and its applications in binding free energy predictions
9:50	Emilio Gallicchio	The Alchemical Transfer Method: Theory, Methods, and Applications
10:15		Break
Session Chair: Alexander Williams
10:35	Barbara Farkas	Revisiting fragment screening campaigns through the eye of absolute binding FEP
11:00	Daniel Cole	A transferable double exponential force field for condensed phase simulations
11:25	Vytautas Gapsys	ABFE pitfalls in virtual screening
11:50		Lunch
Session Chair: Heidi Koldsø
1:10	Dennis Hu	Keynote Speaker #1: Not Your Grandparents’ Drugs: Modern Highlights in Small Molecule Drug Discovery
2:00	Matthew Segall	Physical Model Induction with QuanSA: Affinity Prediction that is Synergistic with Simulation-Based Methods
2:25	Ara Abramyan	Accurate Physics-Based Prediction of Binding Affinities of RNA- and DNA-Targeting Ligands
2:50		Break
Session Chair: AK Nandkeolyar
3:10	Jonathan Essex	Grand Canonical Nonequilibrium Candidate Monte Carlo for In Silico Prediction of Fragment Binding Sites, Modes, and Affinities
3:35	Hannah Baumann	The Alchemist’s toolbox: Expanding the domain of applicability of the OpenFE ecosystem
4:00		1-min Poster Flash Talks
4:30		Poster Session 1 - Sponsored by JCIM
6:00		Travel to evening social
6:30		Social Hosted by Schrödinger

May 7th, 2025 (Day 2)

Time (EST)	Speaker	Title
8:00		Venue opens; Set up posters for evening poster session; continental breakfast
8:30		Opening Announcements; poster prizes
Session Chair: Cesar Mendoza-Martinez
8:35	John Chodera	Teaching free energy calculations to learn
9:00	Michael Shirts	Playing Mr. Potato Head with Free Energy Methods: Alchemical Metadynamics, Replica Exchange of Expanded Ensembles (REXEE), and Multi-Topology Replica Exchange of Expanded Enseble (MT-REXEE)
9:25	Finlay Clark	Robust Automated Truncation Point Selection for Molecular Simulations
9:50	Michael Liesen	Implementing Ligand Overlay in λ-Dynamics with Bias-Updated Gibbs Sampling (LaDyBUGS) as an Alternative Topology Model for Free Energy Calculations
10:15		Break
Session Chair: Cristian Gabellini
10:35	Anupam Ojha	End-to-end automated simulation pipeline with machine-learned force fields for accelerated drug-target kinetic and thermodynamic predictions
11:00	William (Zhiyi) Wu	Target deconvolution with ABFE calculations
11:25	Gianni De Fabritiis	Accurate Relative Binding Free Energy Calculations Using AceForce 1.0
11:50		Lunch
Session Chair: Jonah Vilseck
1:10	Rommie Amaro	Keynote Speaker #2: Multiscale Computational Microscopy
2:00	Shams Mehdi	AI-augmented Molecular Dynamics for Drug Dissociation Kinetics and Interpretable Insights into Drug-Target Interactions
2:25	Natasja Brooijmans	Drugging the undruggable using covalency and computationally-driven design
2:50		Break + Group Photo
Session Chair: Dima Lupyan
3:10	Abba Leffler	Exploiting solvent exposed salt-bridge interactions for the discovery of potent inhibitors of SOS1 using free-energy perturbation simulations
3:35	Olivia Pierce	Computational Modeling of Heterobifunctional Degraders of Catalytically Inactive Interleukin Receptor Associated Kinase 3 (IRAK3)
4:00	Steven Albanese	Free Energy Calculations for ADMET Liabilities: A Cyp2D6 case study
4:25	Shi Zhang	Advanced alchemical free energy methods for drug discovery in AMBER/AMBER Drug Discovery Boost
5:00		Poster Session 2 - Sponsored by JCTC

May 8th, 2025 (Day 3)

Time (EST)	Speaker	Title
8:00		Venue opens; continental breakfast
8:30		Opening Announcements; poster prizes
Session Chair: Monica Barron
8:35	Lingle Wang	Free Energy Calculations to Advance Drug Discovery: Small Molecules, Peptides, and Biologics
9:00	Stefan Boresch	Direct free energy simulations with neural network potentials
9:25	Sirish Kaushik Lakkaraju	MDFit+: Integrating machine-learning & molecular simulations to predict ligand potency
9:50	Xinqiang Ding	Improve Free Energy Estimate for Free
10:15		Break
Session Chair: Michael Liesen
10:35	Huafeng Xu	Free energy calculations in the discovery and optimization of targeted protein degraders
11:00	Niels Kristian Madsen	Residence-time scoring for high-throughput computer-aided drug design
11:25	Abir Ganguly	Accurate binding affinity predictions for protein-peptide systems using physics-based methods.
11:50		Closing Remarks

Poster Session Winners

Edward Francisco Mendez-Otalvaro	Sara Tkaczyk
“Tuning the Affinity of Potential Activators for a K2P Channel”	“Alchemical Free Energy Calculations with Neural Network Potentials”

Acellera-sponsored Poster Prize Awarded to Edward by Dr. Elisa Donati	Atommap-sponsored Poster Prize Awarded to Sara by Drs. Huafeng Xu and Dmitry Lupyan