João Rodrigues
Summary
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RockstarJoão Rodrigues is a Senior Principal Scientist and team lead at Schrödinger with 15+ years in computational biology, specializing in protein structure prediction, docking, and simulation. He directs method development for structure refinement from cryo-EM and X-ray data, translating academic advances into robust tools for real-world modeling. A long-time Biopython maintainer and contributor to OpenMM, he brings deep open-source engineering experience—improving parsers, mmCIF/PDB handling, and simulation accuracy on widely used projects. His background spans postdoctoral work at Stanford and Utrecht and practical collaborations that added VR structural visualization and educational materials, reflecting a talent for communication and tooling. Based in Palo Alto, he blends rigorous research training (Utrecht doctorate) with hands-on software craftsmanship in Python and molecular simulation. Colleagues rely on him to bridge reproducible code, rigorous error handling, and high-accuracy refinement methods that scale to production.
11 years of coding experience
Github Skills (19)
simulation10
python10
molecular-simulation10
testing10
simulations10
data-parsing10
molecular-dynamics-simulation10
nonlinear-dynamics10
bioinformatics10
error-handling10
data-structure9
debug9
biom9
debugging9
fileio9
Programming languages (13)
Github contributions (5)
biopython/biopython
Apr 2015 - Jul 2022
Official git repository for Biopython (originally converted from CVS)
Role in this project:
Back-end Developer & QA Engineer
Back-end Developer & QA EngineerContributions:148 reviews, 84 commits, 143 PRs in 7 years 4 months
Contributions summary:João primarily contributed to the development and maintenance of the Biopython library's PDB module. They focused on improving the robustness and error handling of the PDB and mmCIF parsers by implementing new exceptions and warnings for malformed input files, particularly related to residue definitions and atom numbering. Additionally, they introduced tests to ensure correct parsing and conversion between different structural formats and to prevent incomplete files being written due to errors. The user also addressed bugs in existing code, improving the overall reliability of the library's data processing.
git-repositoryphylogeneticspythondnagenomics
openmm/openmm
Sep 2017 - Oct 2019
OpenMM is a toolkit for molecular simulation using high performance GPU code.
Role in this project:Back-end Developer
Back-end DeveloperContributions:29 commits, 10 PRs, 80 comments in 2 years 1 month
Contributions summary:João primarily focused on improving the mmCIF file input/output functionality, fixing chain labeling issues, and making the code compatible with PDB format specifications. They added tests for multi-chain mmCIF files. Additionally, the user corrected an issue in the Lennard-Jones force calculations and implemented a method for ion placement in the solvent box. These changes suggest a focus on improving the accuracy and usability of molecular simulation data.
cudamolecular-dynamicsopenmmgpusimulation
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