Stars
FAIR Chemistry's library of machine learning methods for chemistry
a python package to analyze short molecular dynamics simulations for the effect of point mutations on stability
Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.
Sidechain conditioning and modeling for full-atom protein sequence design
Example polymers for testing.
PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.
CosolvKit is a versatile tool for cosolvent MD preparation and analysis
Official repository for the Boltz-1 biomolecular interaction model
Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes
Implementation of NeurIPS24 paper "Generalized Protein Pocket Generation with Prior-Informed Flow Matching"
PocketGen (Nature Machine Intelligence 24): Generating Full-Atom Ligand-Binding Protein Pockets
Create a cost sensitive degenerate codon sequence
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196
Derivative-Free Guidance in Diffusion Models with Soft Value-Based Decoding. For controlled generation in DNA, RNA, proteins, molecules (+ images)
CodonTransformer: The ultimate tool for codon optimization, optimizing DNA sequences for heterologous protein expression across 164 species.
A repo for anything users/developers find interesting and want to share
Google Colaboratory Notebooks for Computational Biochemistry
Simulation input files for the paper "Binding Selectivity Analysis from Alchemical Receptor Hopping and Swapping Free Energy Calculations"
repo for DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model
Simple protein-ligand complex simulation with OpenMM
Data generation and submission scripts for the QCArchive ecosystem.
Derivation of non-bonded force field paramaters from Atom-in-Molecules density partitioning