2023 Workshop on Free Energy Methods in Drug Design

Introduction

This workshop has been rolled over from the schedule 2020 event, and will focus on the current state of free energy techniques. Registration for the 2020 conference will be held. Refunds are available and more places may become available.

Our goal in this workshop is to bring together experts from pharma and supporting industries, as well as academia, in an intense and focused workshop to identify challenges and help chart the path forward. We are particularly interested in hearing about use cases, pitfalls and their solutions. We also firmly believe we can learn a great deal from failure, so we hope participants will go beyond just highlighting success stories to provide more detailed insight into successes and failures.

Dates and Location

The conference is scheduled for 10-12 May 2023, at the Novartis Institutes for BioMedical Research, Cambridge, MA: 250 Massachusetts Ave, Cambridge MA 02139. Signage for the conference will be visible from there.

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Accommodation

Discount rates may be available for some hotels in the area. Novartis suggests that attendants individually book online or call and used the booking codes below:

Hyatt Regency Cambridge

Booking code – 19296

Cambridge, MA Hotels Near MIT | Hyatt Regency Boston/Cambridge

When making reservations from the Special Rates dropdown choose Corporate or Group Code then a new box will open to add the code above

Marriott Hotels

Any Marriott will use this code – NVT

When making reservations from the Special Rates dropdown choose Corp/Promo Code then add the code above

Novartis is close to the Central stop on the red line, as well as the number 1 bus route, and there may be more affordable accommodation options using these transport links.

Registration

Registration will cost $100 for admission to the 2.5 day conference, which will cover both snacks and lunch, as well as refreshments in the evening sessions.

• Registration is full! If you are no longer planning to attend, please let us know and we can refund your fee via paypal.

Poster session

Abstract submission for posters is open until 15th March 2023. Please submit an abstract using this form.

Workshop Themes

As this is the 10(+3)th birthday of the first 2010 free energy workshop, we will be holding a session celebrating the last 10 years - how far have we come, and where do we still need to go?

Other sessions will be held to discuss the current software that is currently available to the field - both commercial packages, and open-source academic efforts.

Discussions about the novel methods and algorithms that are in development and where these can be best applied will be held.

Results of free energy methods will be presented - both the successes and the limitations - with the idea of addressing what the community would like to see at the following meeting.

Finally, half a day of talks will be dedicated to the intersection of free energy methods with machine learning.

Sponsors, Social Media and Streaming

Sponsors

We would like to thank the following sponsors:

We are currently looking for sponsorship for the event. If your organisation would be interested, please contact any of the organisers.

Particular thanks to the Boston Area Group for Informatics and Modeling (BAGIM)for helping with the financial organisation of this meeting.

Social Media

Twitter hashtags: #alchemy2023
Slack: https://alchemistry.slack.com

Join the slack using this link

Recording

The organizing committee has arranged for some talks to be recorded, and will upload them after the conference. However, please refrain from doing so yourself since the recording of any talk is at the discretion of the speaker, their employer and collaborators.

Schedule

Tuesday 9th May (6PM - 8PM) --- informal evening social hosted by Psivant Therapeutics | 70 Fargo St, Boston, MA 02210

Wednesday 10th May

Time	Speaker	Title
8.45 - 9.00		arrival
9.00 - 9.05	Jose Duca	Welcome to NIBR
9.05 - 9.10	Kira + Hannah	Opening remarks
	Session Chair
9.10 - 9.35	Michael Shirts	Free energies: What we’ve learned about how to estimate them
9.35 - 10.00	Sereina Riniker	10+ Years with (RE-)EDS: Efficient Free-Energy Calculations with a Multistate Method
10.00 - 10.25	Huafeng Xu	Adaptive optimization of binding free energy networks and integration of experimental data
10.25 - 10.40	BREAK	BREAK
	Session Chair
10.40 - 11.05	Bill Jorgensen	Free Energy Calculations from Butane to COVID-19
11.05 - 11.30	Jonathan Essex	Enhancing protein and ligand sampling in molecular simulations by fully adaptive simulated tempering
11.30 - 12.15	Derek Lowe (keynote)	FEP and Drug Discovery: Where We've Been and Where We'd Like to Go
12.15 - 1.30	LUNCH	LUNCH
1.30 - 1.35	Zoe Cournia	Welcome back
	Session Chair
1.35 - 2.00	Jonah Vilseck	Rapid and Accurate Free Energies of Binding from λ-Dynamics with Bias Updated Gibbs Sampling
2.00 - 2.25	David Mobley	Separated Topologies: A flexible approach for relative binding free energy calculations
2.25 - 2.50	Christopher Bayly	Making Binding Free Energies Practical in a Massively Parallel Universe
2.50 - 3.05	BREAK	BREAK
	Session Chair	Ernest Awoonor-Williams
3.05 - 3.30	Ana Silveira	On the use of high-throughput binding free energy simulations in design cycles for drug discovery
3.30 - 3.55	Katharina Meier	Free Energy Calculations in Pharmaceutical and Crop Science R&D at Bayer
3.55 - 5.40	Poster Session	Poster Session

Thursday 11th May

Time	Speaker	Title
9.00 - 9.10	Sereina + Camilo	Welcome + Opening remarks
	Session Chair
9.10 - 9.35	Chia-en Chang	Ligand Binding Kinetics: Pathways, Transient States and Unbinding Free Energy Profile
9.35 - 10.00	Alex Dickson	Learning and sampling complex ligand binding pathways with weighted ensemble techniques
10.00 - 10.25	Josh Fass	A local resampling trick for focused molecular dynamics
10.25 - 10.40	BREAK	BREAK
	Session Chair	'
10.40 - 11.05	Robert Abel	Accelerating drug discovery with ultra-large scale collaborative deployment of predictive modeling
11.05 - 11.30	Marco De Vivo	Pushing the boundaries: FEP for protein-protein and protein-nucleic acids interaction
11.30 - 11.55	Xin (Cindy) Yan	Promises and Limitations: Free Energy Methods in Drug Discovery Projects
11.55 - 1.15	LUNCH	LUNCH
	Session Chair	Antonia Mey
1.15 - 1.20	Zoe Cournia	Welcome back
1.20 - 1.45	Julien Michel	Engineering FEP science in the open
1.45 - 2.10	Jay Ponder	Accuracy of the AMOEBA Force Field in Binding Free Energy Simulations
2.10 - 2.35	Lance M. Westerhoff	Fast, absolute binding free energy calculations using MovableType: the impact of different global sampling regimes on predictive performance
2.35 - 2.50	BREAK	BREAK
	Session Chair
2.50 - 3.15	Emilio Galliachio	AToM-OpenMM: An Open-Source Software Package for Relative Binding Free Energy Estimation in Drug Discovery
3.15 - 3.40	Francesca Deflorian	Expanding the Realm of FEP and GPCR Drug Design
3.40 - 4.05	John Chodera	Teaching free energy calculations to learn
4.05 - 4.25	BREAK	BREAK
	Session Chair
4.25 - 4.50	Gianni De Fabritiis	Relative binding affinity calculations towards accuracy and scalability
4.50 - 5.15	Lingle Wang	Beyond Small Molecule Binding: Free Energy Calculations for Antibody Affinity, pH Sensing, Small Molecule Solubility and More
5.15 - 5.40	David Hahn	Impacting drug discovery with open source free energy calculation tools.

Thursday 11th May (6.30PM) --- informal evening social sponsored by Schrodinger - 730 Tavern

Friday 12th May

Time	Speaker	Title
9.00 - 9.10	Kira + Jonah	Welcome + Opening remarks
	Session Chair	Jonah Vilseck
9.10 - 9.35	Darrin York	Enhancing Precision and Accuracy in Alchemical Free Energy Simulations
9.35 - 10.00	David Pearlman	Free Energy Perturbation calculations incorporating a quantum representation of the ligand binding site
10.00 - 10.25	Mark Mackey	Improving efficiency of free energy calculations with adaptive lambda schedules
10.25 - 10.40	BREAK	BREAK
	Session Chair	Camilo Velez-Vega
10.40 - 11.05	Hugo Gutierrez de Teran	QFEP: combining ligand SAR and in silico mutagenesis for ligand design
11.05 - 11.30	Andrey Frolov	Dealing with high flexibility of crosslinked peptides in FEP calculation
11.30 - 11.55	-	-
11.55 - 1.15	LUNCH	LUNCH
	Session Chair
1.15 - 1.20	Zoe Cournia	Welcome back
1.20 - 1.45	Michael Schnieders	An Alchemical Pipeline for Polymorph Discovery and Optimization
1.45 - 2.10	David Minh	Binding pose prediction using absolute binding free energy calculations
2.10 - 2.35	Lucy Colwell	Machine learning to predict protein function from sequence with therapeutic applications
2.35 - 2.50	Kira + Hannah	Closing remarks

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.