Virtual Conference 21-22nd September 2022

To occupy the interim between the last virtual conference, and the in-person Free Energy Meeting to be held in May 2023, we are hosting a virtual free energy meeting to give an opportunity to early career researchers* to present their work and network. The conference will consist of two half-day sessions, morning for West Coast/evening for Europe.

Registration is free and open! Spaces are many but finite, please only register with one email address and only if you plan to attend. Register Here

early career is very loosely defined as <10 years within the field, excluding any career breaks. If you believe that you qualify, then you do.

Schedule

Wednesday 21st September 2022

PDT	ET	GMT	CET	Speaker	Title
7.45am	10.45am	3.45pm	4.45pm	Introduction
8.00am	11.00am	4.00pm	5.00pm	Jenke Scheen, University of Edinburgh	Data-driven Generation of Perturbation Networks for Relative Binding Free Energy Calculations
8.20am	11.20am	4.20pm	5.20pm	Mary Pitman, The University of California, Irvine	Optimal is not enough, beyond free energy perturbation designs
8.40am	11.40am	4.40pm	5.40pm	Michael Gillhofer, Janssen	Enhancing the results of relative binding free energy calculations by making use of clustering of ligand series and optimization of perturbation networks
9.00am	12.00pm	5.00pm	6.00pm	Poster session A and break
9.50am	12.50pm	5.50pm	6.50pm	Narjes Ansari, IIT	The role of water in the static and dynamic properties of ligand-protein binding
10.10am	1.10pm	6.10pm	7.10pm	Jaehoon Yang, The Ohio State University	A new approach to the multiple potential problem in statistical mechanics
10.30am	1.30pm	6.30pm	7.30pm	Xinqiang Ding, MIT	DeepBAR: A Fast and Exact Method for Binding Free Energy Computation
10.50am	1.50pm	6.50pm	7.50pm	break
11.10am	2.10pm	7.10pm	8.10pm	Richard Gowers, Open Molecular Software Foundation	OpenFE: Towards Reproducible Open-Source Alchemical Free Energy Calculations
11.30am	2.30pm	7.30pm	8.30pm	Ivy Zhang, Memorial Sloan Kettering Cancer Center	Exploration of sampling challenges in estimating the relative binding free energies of protein mutations in protein-protein interactions

Poster session A	Title
Sondos Musleh, University of Manchester	Absolute Binding Free Energy Calculations of Monosaccharide and Oligosaccharide Ligands of Concanavalin A
J. Jasmin Güven, University of Edinburgh	Putting potential inhibitors for beta-lactamases under the alchemical microscope
Anna Cavalleri, University of Southampton	Reparameterising Ligand Force Field Paremeters for application in Relative Binding Free Energies
Matheus Ferraz, Heidelberg Institute for Theoretical Studies	Artificial neural network to predict the free energy of binding for protein-protein complexes from Rosetta calculated parameters
Adele Hardie, University of Edinburgh	Deconstructing Allostery: Computational Assessment of the Binding Determinants of Allosteric PTP1B Modulators
Mateusz Bieniek, Newcastle University	FEgrow: An Open-source molecular builder and free energy preparation workflow

Thursday 22nd September 2022

PDT	ET	GMT	CET	Speaker	Title
7.55am	10.55am	3.55pm	4.55pm	Introduction
8.00am	11.00am	4.00pm	5.00pm	Linfeng Zhang, DP Technology	AI Engineering of FEP, by FEP and for FEP
8.20am	11.20am	4.20pm	5.20pm	Emilia P. Barros, ETH Zurich	Accounting for solvation correlation effects in the computational prediction of water energetics
8.40am	11.40am	4.40pm	5.40pm	break
9.00am	12.00pm	5.00pm	6.00pm	Ollie Melling, University of Southampton	Enhanced grand canonical sampling of occluded water sites using nonequilibrium candidate Monte Carlo
9.20am	12.20pm	5.20pm	6.20pm	Will Poole, University of Southampton	Expansion of Grand Canonical Monte Carlo to Sample the Binding of Small Molecules
9.40am	12.40pm	5.40pm	6.40pm	Poster session B and break
10.30am	1.30pm	6.30pm	7.30pm	Ana Rojas, Schrodinger Inc.	Predictions of aqueous crystalline solubility using a free energy perturbation approach
10.50am	1.50pm	6.50pm	7.50pm	Anastasia Saar, Yale University	Absolute Free Energy Calculations for Ranking Binding Affinities of SARS-CoV-2 Main Protease Inhibitors
11.10am	2.10pm	7.10pm	8.10pm	Alexander Williams, GlaxoSmithKline	Development of Accurate and Efficient Computational Methodologies for Predicting Protein-Protein Binding Free Energies

Poster session B	Title
Sukrit Singh, Memorial Sloan Ketting Cancer Center	Predicting and modeling drug-resistant mutations using exascale supercomputing
Ernest Williams, Novartis	Benchmarking Tools for in silico Cysteine pKa Prediction
Gauri Thapa, Indian Institute of Technology Bombay	Understanding allosteric regulation of SAMHD1
Anna Herz, University of Edinburgh	Using BioSimSpace to create an interoperable RBFE pipeline
Ana Caldaruse, University of California, Irvine	Investigating ring transformations in binding free energy calculations
Dominic Rufa, Memorial Sloan Kettering Cancer Center	Reparameterising Ligand Force Field Paremeters for application in Relative Binding Free Energies
Finlay Clark, University of Edinburgh	Comparing Protein-Ligand Restraints in Alchemical Absolute Binding Free Energy Calculations

Sponsors, Social Media and Streaming

Social Media

Twitter hashtags: #alchemy2022
Slack: https://alchemistry.slack.com

Organizers

Kira Armacost, GlaxoSmithKline Pharmaceuticals (kira.x.armacost@gsk.com)
Hannah Bruce Macdonald, Memorial-Sloan Kettering Cancer Center (hannah.brucemacdonald@choderalab.org)
Jonah Vilseck, Indiana University School of Medicine (jvilseck@iu.edu)
Zoe Cournia, Biomedical Research Foundation Academy of Athens (zcournia@bioacademy.gr)
Michael Gilson, UC San Diego (mgilson@ucsd.edu)
Camilo Velez-Vega, Novartis Institutes for BioMedical Research (camilo.velez-vega@novartis.com)
Sereina Riniker, ETH Zürich (sriniker@ethz.ch)
Anthony Arvanites, Eli Lilly and BAGIM (aarvanites@bagim.org)

We also thank current advisors and previous organizers:

Brian McClain, Vertex (brian_mcclain@vrtx.com)
Vijay Pande, Stanford University (pande@stanford.edu)
Michael Shirts, University of Colorado Boulder (michael.shirts@colorado.edu)
Camilo Velez-Vega, Novartis Institutes for BioMedical Research (camilo.velez-vega@novartis.com)
John Chodera, Memorial-Sloan Kettering Cancer Center (john.chodera@choderalab.org)
Greg Bowman, Washington University in St. Louis (bowman@biochem.wustl.edu)
Callum Dickson, Novartis (callum.dickson@novartis.com)
Jose Duca, Novartis (jose.duca@novartis.com)
Viktor Hornak, Novartis (viktor.hornak@novartis.com)
John Manchester, Novartis (john.manchester@novartis.com)
Antonia Mey, University of Edinburgh (antonia.mey@ed.ac.uk)
David Mobley, University of California at Irvine (dmobley@uci.edu)
Michael Schnieders, The University of Iowa (michael-schnieders@uiowa.edu)
Jana Shen, The University of Maryland (Jana.Shen@rx.umaryland.edu)
Woody Sherman, Silicon Therapeutics (woody@silicontx.com)

Conference Code of Conduct

All attendees, speakers, sponsors and volunteers at our conference are required to agree with the following code of conduct. Organisers will enforce this code throughout the event. We expect cooperation from all participants to help ensure a safe environment for everybody.

Need Help? Please contact the organising committee either in person or via email. Members of the organising committee are listed above.

The Quick Version

Our conference is dedicated to providing a harassment-free conference experience for everyone, regardless of gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race, ethnicity, religion (or lack thereof), or technology choices. We do not tolerate harassment of conference participants in any form. Sexual language and imagery is not appropriate for any conference venue, including talks, workshops, parties, Twitter and other online media. Conference participants violating these rules may be sanctioned or expelled from the conference without a refund at the discretion of the conference organisers.

The Less Quick Version

Harassment includes offensive verbal comments related to gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race, ethnicity, religion, technology choices, sexual images in public spaces, deliberate intimidation, stalking, following, harassing photography or recording, sustained disruption of talks or other events, inappropriate physical contact, and unwelcome sexual attention.

Participants asked to stop any harassing behavior are expected to comply immediately.

Sponsors are also subject to the anti-harassment policy. In particular, sponsors should not use sexualised images, activities, or other material. Booth staff (including volunteers) should not use sexualised clothing/uniforms/costumes, or otherwise create a sexualised environment.

If a participant engages in harassing behavior, the conference organisers may take any action they deem appropriate, including warning the offender or expulsion from the conference with no refund.

If you are being harassed, notice that someone else is being harassed, or have any other concerns, please contact a member of the organising committee immediately.

A member of the organising committee will be happy to help participants contact local law enforcement, provide escorts, or otherwise assist those experiencing harassment to feel safe for the duration of the conference. We value your attendance.

We expect participants to follow these rules at conference and workshop venues and conference-related social events.

The code of conduct text was taken from https://github.com/confcodeofconduct/confcodeofconduct.com in a slightly adapted form.

2022 Virtual Workshop on Free Energy Methods in Drug Design

Contents