Software & Tools

§ below indicates repositories that are no longer being actively maintained

Our repositories:

Our lab's code is available on github!

Check out my code on Github @sukritsingh

We collaboratively maintain(ed) many open-source software packages

The MDTraj package for MD trajectory analysis

PALE: the Protein Alchemical Landscape Explorer (built on OpenFE)

CardsReader: Allostery via the Correlation of All Rotameric and Dynamical States (CARDS)

MTENN: Modular Training and Evaluation of Neural Networks for binding affinity prediction

§Perses: A pre-OpenFE package for relative free energy calculations

We collaborate with the following teams on open source software development

Folding@home distributed computing consortium

The OpenFreeEnergy Consortium

The OpenMM simulation engine

The OpenFold consortium for structural generative modeling

§KinoML: Structure-informed machine learning for kinase modeling

Sometimes the lab will also tinker with tools and repositories relevant to others

PicoViz: A light-weight visualization tool for browsers

Offline Overleaf-like editor for LaTeX writing - with Text-to-speech!

An online applet to simulate binding curves

Sonya Hanson and my guide to massively parallel simulations