The Chodera Lab is dedicated to advancing human health by building high-quality open source predictive modeling tools to aid the discovery of new therapies and new chemical tools for the study of biology and contributing to the understanding of basic mechanisms of disease. All our industry collaborations directly fund the development of high-quality open source software that all researchers—academic and industrial—can use for free under minimally restrictive Open Source Initiative approved licenses that allow others to use, modification, and redistribution. We follow the Reproducible Research Standard for guidance on open licenses.
Current funding
NIH U19 U19AI171399 (MPI: Chodera [Contact PI]; Alpha Lee, PostEra; Peter Sjö, DNDi)
AI-driven Structure-enabled Antiviral Platform (ASAP)
The goal of this antiviral drug discovery (AViDD) Center is to use an AI-accelerated structure-enabled discovery platform to build a pipeline of novel oral antivirals against coronaviruses, flaviviruses, and picornaviruses using an open science, IP-free discovery paradigm to act as a nexus for global antiviral discovery.
Budget: $67,662,387 total costs / 3 years
Project Dates: 5/16/2022 - 4/30/2025
NIH R01 GM124270 (PI: David Mobley, UCI)
Advancing predictive physical modeling through focused development of model systems to drive new modeling innovations
The goal of this project is to enable blind community challenges that drive progress toward quantitative accuracy in the field of computational physical modeling of drug-receptor interactions.
Budget: $230,352 direct costs to the lab / 4 years
Project Dates: 9/10/2018 - 8/31/2022
Relay Therapeutics Collaboration (SK2018-0162)
Relay Therapeutics
Development of efficient open source cloud-enabled free energy based lead optimization algorithms and integrative Bayesian model of experimental biophysical and molecular simulation data
The goal of this project is to develop open source scalable cloud workflows for lead optimization using relative and absolute alchemical free energy calculations, as well as Bayesian integrative modeling techniques for experimental biophysical data and molecular simulations.
Dates: 4/5/2018 - 4/5/2019
Budget: $74,074 annual direct costs
Vir Biotechnology Collaboration (SK2019-0582)
Vir Biotechnology
Development of alchemical free energy methods for predicting the impact of point mutations on antigen and antibody affinities
The goal of this project is to develop alchemical free energy methods for predicting the impact of point mutations on protein:protein and antibody:antigen affinities for SARS-CoV-2.
Dates: 7/25/2019 - 7/24/2021
Budget: $55,556 annual direct costs
Einstein BIH Visiting Fellowship, Charité Universitätmedizin, Berlin
Stiftung Charité - Einstein Foundation
Computational polypharmacology: A new paradigm for selectively promiscuous kinase inhibitors
The goal of this project is to develop open source tools for integrating structure-informed machine learning and alchemical free energy calculations for the design of selectively promiscuous kinase inhibitors.
Project period: 2/1/2019 — 1/31/2022
Collaborator: Andrea Volkamer (Charité, Berlin)
Budget: EUR150.000/year for three years to collaborator Andrea Volkamer’s laboratory (Charité, Berlin)
Sloan Kettering Institute
NIH P30CA008748 : MSKCC Cancer Center grant (PI: Thompson)
National Institutes of Health
Cycle for Survival
Open Force Field Consortium
Open Force Field Consortium
The Open Force Field Consortium is composed of academic investigators from the Open Force Field Initiative and sponsoring Industry Partners collaborating to advance open force field science, toolkits, and standards for biomolecular drug discovery.
Interline Therapeutics
The goal of this project is to explore quantitative techniques for the prediction of small molecule modulators of protein-protein interactions.
Project period: 1/15/2021-4/15/2023
Budget: $187,992 annual direct costs
Completed funding
NIH R01 GM121505 (PI: Chodera)
National Institutes of Health
The role of reorganization energy in achieving selective kinase inhibition
The goal of this project is to characterize the role of conformational reorganization energetics in achieving targeted kinase inhibitor selectivity.
Budget: $981,250 direct costs to the lab / 5 years
Project Dates: 9/15/2017 - 8/31/2022
Parker Institute for Cancer Immunotherapy Pilot Grant
Parker Institute for Cancer Immunotherapy
Physics-based computational prediction of cancer-associated mutant MHC class II epitopes
Project Period Dates: 4/2/2018 - 4/1/2019
Project period: $75,000 direct costs / $11,250 indirect costs
MSKCC Functional Genomics Initiative
Integrated approaches annotate functions of cancer-associated H3K36 methyltransferases
The goal of this project is to use a combined experimental-computational approach to annotate the functional impact of clinical cancer mutations in H3K36 methyltransferases
co-I: Minkui Luo (MSKCC)
Project period: 12/1/2018 -- 11/30/2020
Budget: $250 annual direct costs / $125,000 annual direct costs to the Chodera lab
Entasis Therapeutics Collaboration
Entasis Therapeutics
Development of efficient equilibrium and nonequilibrium algorithms for predicting small molecule porin permeation with potential of mean force methods
The goal of this project is to develop algorithms and open source tools for efficient equilibrium and nonequilibrium potential of mean force calculations for bacterial porins.
Dates: 4/5/2018 - 4/5/2019
Budget: $74,074 annual direct costs
XtalPi Open Force Field Consortium Distinguished Postdoctoral Fellowship
XtalPi
NSF CHE-1738979 : NSF Data-Driven Discovery Science in Chemistry (D3SC)
National Science Foundation
D3SC: EAGER: Collaborative research: A probabilistic framework for automated force field parameterization from experimental datasets
The goal of this proposal is to explore Bayesian approaches to determining forcefield parameters from experimental data and propagating uncertainty in predictions.
Budget: $179,907 total costs to the lab
Project Dates: 8/1/2017-7/31/2019
Project Direct Costs: $104,113
Project Indirect Costs: $75,794
Merck KGaA Collaboration
Merck KGaA
Developing automated workflows for absolute alchemical free energy calculations with YANK
The goal of this project is to develop automated workflows for absolute alchemical free energy calculations with YANK, an open source code developed in the lab.
Dates: 7/26/2016 - 1/25/2019
Total costs $387,176 / 2 years
Silicon Therapeutics Collaboration
Silicon Therapeutics
Development of efficient open source free energy-based lead optimization algorithms
The goal of this project is to compare the performance of single-replica and nonequilibrium alchemical free energy methods for relative free energy calculations.
Dates: 5/17/2017 - 11/17/2018
Total costs: $84,076
Starr Foundation Grant I8-A8-058 (PI: Minkui Luo)
Designing sinefungin scaffolds as specific protein methyltransferase inhibitors
The goal of this project is to design selective inhibitors for protein lysine methyltransferases
Budget: $125K direct costs to our lab / year for 2 years
Dates: 01/01/2015 - 6/30/2017
co-Is: Scott Armstrong, Angela Koehler (Broad), Lei Shi (WCMC)
Astra-Zeneca iMED Collaboration (PI: Chodera)
Evaluating the potential for Markov state models of conformational dynamics to advance quantitative prediction of thermodynamics and kinetics of selective kinase inhibitors
The goal of this project is to evaluate the potential for Markov state models of conformational dynamics to quantitatively predict the thermodynamics and kinetics of selective kinase inhibitors to CK2 and SYK.
Dates: 7/30/2015 - 1/30/2017
Total costs $176,258 / 15 months
Louis V Gerstner Young Investigators Award
Budget: $75K direct costs / year for three years
Dates: 2/1/2013-1/31/2016
Scientific Advisory activities (John Chodera)
Current:
OpenEye Scientific Scientific Advisory Board (21 Aug 2018 - )
Role: Consulting on the deployment of our open source software tools through a cloud-based platform that will allow academics to use our software without license fees without needing their own GPU hardware.
Interline Therapeutics Scientific Advisory Board (8 Feb 2021 - )
Role: Consulting on the deployment of open source software tools within a drug discovery company that supports the external development of open source software and uses it internally to discovery new drugs.
Note: John Chodera and MSKCC both have equity interests in Interline. Interline also sponsors research within the Chodera lab to develop open source software and publish openly on research on small molecules that modulate protein-protein interactions.
Redesign Science Scientific Advisory Board (23 Feb 2021 - )
Role: Consulting on the use of Markov state models for drug discovery.
Note: John Chodera has equity interests in Redesign Science. Redesign Science also sponsors a postdoctoral fellow within the Chodera lab developing open source software and publishing openly on research into small molecule drug discovery methodologies.
Ventus Therapeutics Scientific Advisory Board (16 Nov 2021 - )
Role: Consulting on the use of free energy calculations in accelerating hit-to-lead progression
Previous:
Schrödinger Scientific Advisory Board (6 Nov 2013 - 17 Aug 2018)
Role: Consulting on the development of easy-to-use software that implements community best practices for alchemical free energy calculations for optimizing ligand potency, so that academic and industrial laboratories can use modern predictive tools to develop new potential therapeutics or chemical probes.
Foresite Labs Scientific Advisor (8 Jan 2020 - 7 Jan 2021)
Role: Consulting on the deployment of open source software tools within a drug discovery company concept that supports the external development of open source software and uses it internally to discovery new drugs.
Speaking fees or one-day consulting fees:
As a scientific advisor or invited speaker, John Chodera has received consulting or speaking fees from Abbvie, Astex, Boehringer-Ingelheim, Blueprint Medicines, Celgene, Foresite Capital, Foresite Labs, Interline Therapeutics, MPM Capital, OpenEye Scientific, Schrödinger, and Ventus Therapeutics.
