y1zhou

carbonmatrix_public

DiffPack

Implementation of DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing

ABangle

A tool for calculating and analysing the VH-VL orientation in antibodies.

getcontacts

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

GeoDock

Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.

pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

protpardelle

Diffusion-based all-atom protein generative model.

alphaflow

AlphaFold Meets Flow Matching for Generating Protein Ensembles

flamegraph

Easy flamegraphs for Rust projects and everything else, without Perl or pipes <3

schedule_free

Schedule-Free Optimization in PyTorch

AlphaLink

AlphaLink: Integrating crosslinking MS data into OpenFold

rapidgzip

Gzip Decompression and Random Access for Modern Multi-Core Machines

gemmi

macromolecular crystallography library and utilities

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

Betterfox

Firefox user.js for speed, privacy, and security. Your favorite browser, but better.

EdgyArc-fr

Firefox Userchrome and sidebery style

VerticalFox

Firefox theme with Edge like auto-hide vertical tab bar and minimalism design. Powerd by Sidebery.

Floorp

The most of source code of version 10 or later of Floorp Browser, the most Advanced and Fastest Firefox derivative 🦊

arpeggio

Calculation of interatomic interactions in molecular structures

papers-for-molecular-design-using-DL

List of molecular design using Generative AI and Deep Learning

rosetta

The Rosetta Bio-macromolecule modeling package.

huey

a little task queue for python

uv

An extremely fast Python package installer and resolver, written in Rust.

foldingdiff

Diffusion models of protein structure; trigonometry and attention are all you need!

dMaSIF

AlignmentViewer2.0

AntPack

Tools for annotation, processing and ML for antibody sequences

Stirling-PDF

#1 Locally hosted web application that allows you to perform various operations on PDF files

RoseTTAFold2NA

RoseTTAFold2 protein/nucleic acid complex prediction

teachopencadd

TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data