John Chodera
Co-Founder, CEO, And President at Weill Cornell Medicine
New York, New York, United States
Summary
🤩
Rockstar🎓
Top SchoolJohn Chodera is a computational biophysicist, entrepreneur, and leader with 16+ years developing predictive molecular models and scalable drug-discovery platforms, currently serving as Co-Founder, CEO, and President of Achira and a member of Memorial Sloan Kettering Cancer Center. He leads a multidisciplinary lab that couples rigorous statistical mechanics, high-performance GPU and distributed computing (including Folding@Home and national supercomputers), and automated biophysical measurement to design selective small-molecule ligands and understand mechanisms of drug resistance. A hands-on open-source contributor, he has improved core molecular simulation toolkits such as OpenMM, MDTraj, ParmEd, and PDBFixer—work that underpins many academic and industrial workflows. He also brings expertise in CI/CD automation, Bayesian experimental design, and high-throughput binding affinity assays that bridge theory and experiment. Based in New York with faculty ties at Weill Cornell, he combines deep academic rigor (PhD in Biophysics from UCSF) with startup pragmatism to translate simulation-driven insights into actionable therapeutics discovery.
16 years of coding experience
5 years of employment as a software developer
California Institute of TechnologyDoctor of Philosophy (Ph.D.), Biophysics, Doctor of Philosophy (Ph.D.), Biophysics at University of California, San Francisco
English
Github Skills (19)
serializable10
c-language10
serializer10
python10
molecular-simulation10
testing10
travis-ci10
mdm10
cicd10
numpy10
serialization10
deserialization10
molecular-dynamics-simulation10
mdt10
nonlinear-dynamics10
Programming languages (20)
Github contributions (5)
openmm/pdbfixer
Mar 2014 - Apr 2016
PDBFixer fixes problems in PDB files
Role in this project:
Automation Engineer / Build & Release Engineer
Automation Engineer / Build & Release EngineerContributions:69 commits, 13 PRs, 249 comments in 2 years
Contributions summary:John's contributions primarily focused on setting up and refining the continuous integration and continuous deployment (CI/CD) pipeline for the `pdbfixer` repository. This involved creating and modifying the `.travis.yml` file to automate testing, including the addition of unit tests using Python, and also integrating with external services, like Binstar. They also added debugging code and made attempts to incorporate timeouts into the testing process to improve stability and reliability within the CI/CD process.
pdb-files
openmm/openmm
Dec 2009 - Nov 2022
OpenMM is a toolkit for molecular simulation using high performance GPU code.
Role in this project:Back-end Developer & Test Automation Engineer
Back-end Developer & Test Automation EngineerContributions:33 reviews, 289 commits, 91 PRs in 13 years 1 month
Contributions summary:John primarily contributed to the OpenMM molecular simulation toolkit by addressing critical issues and improving code robustness. Their work included fixing unit conversion bugs in the Monte Carlo barostat and related tests, resolving memory leaks in the OpenCL platform, and addressing uninitialized value problems. Furthermore, the user improved serialization for CustomNonbondedForce and performed related tests.
gpumolecular-simulationsimulationmolecular-dynamics
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