*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 use, modification, and redistribution. *

## Current funding

**NIH ****R01 GM121505**** (PI: Chodera)**

*National Institutes of Health*

**Quantitative dissection of the origin of kinase inhibitor selectivity**

The goal of this project is to characterize the role of conformational reorganization energetics in achieving targeted kinase inhibitor selectivity.

Budget: $1.25M direct costs to the lab / 5 years

Project Dates: 9/15/2017 - 8/31/2022

**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: $504,494 direct costs to the lab / 4 years

Project Dates: 9/10/2018 - 8/31/2022

**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

**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.**

Developing automated workflows for absolute alchemical free energy calculations with YANK

Developing automated workflows for absolute alchemical free energy calculations with YANK

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

**Relay Therapeutics Collaboration**

*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

**Entasis Therapeutics Collaboration**

*Entasis Therapeutics*

**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.**

*Development of efficient equilibrium and nonequilibrium algorithms for predicting small molecule porin permeation with potential of mean force methods*

Dates: 4/5/2018 - 4/5/2019

Budget: $74,074 annual direct costs

**Parker Institute for Cancer Immunotherapy Pilot Grant**

*Parker Institute for Cancer Immunotherapy*

**Project Period Dates: 4/2/2018 - 4/1/2019**

Physics-based computational prediction of cancer-associated mutant MHC class II epitopes

Physics-based computational prediction of cancer-associated mutant MHC class II epitopes

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: $320,000 annual direct costs / $160,000 annual direct costs to the lab

**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**

**XtalPi Open Force Field Consortium Distinguished Postdoctoral Fellowship**

*XtalPi*

**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.*

## Completed funding

**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

## Advisory board memberships

Current:

**OpenEye Scientific**** (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.*

Previous:

**Schrödinger**** (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.*