RosettaCommons / foundry
Central repository for biomolecular foundation models with shared trainers and pipeline components
RosettaCommons / foundry
OpenChemistry / avogadrolibs
Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
anthropics / uplifting-biomolecular-modeling
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lammps / lammps
Public development project of the LAMMPS MD software package
milvus-io / bootcamp
Dealing with all unstructured data, such as reverse image search, audio search, molecular search, video analysis, question and answer systems, NLP, etc.
bytedance / Protenix
Toward High-Accuracy Open-Source Biomolecular Structure Prediction.
aqlaboratory / openfold-3
A fully open source biomolecular structure prediction model based on AlphaFold3
JuDFTteam / best-of-atomistic-machine-learning
🏆 A ranked list of awesome atomistic machine learning projects ⚛️🧬💎.
deepmodeling / deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
openmm / openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
schrodinger / pymol-open-source
Open-source foundation of the user-sponsored PyMOL molecular visualization system.
MDAnalysis / mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
BradyAJohnston / MolecularNodes
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
molstar / molstar
A comprehensive macromolecular library
biotite-dev / biotite
A comprehensive library for computational molecular biology
gromacs / gromacs
Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.
mir-group / nequip
NequIP is a code for building E(3)-equivariant interatomic potentials
AspirinCode / papers-for-molecular-design-using-DL
List of Molecular and Material design using Generative AI and Deep Learning
atomistic-machine-learning / schnetpack
SchNetPack - Deep Neural Networks for Atomistic Systems
MolecularAI / REINVENT4
AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.
brucefan1983 / GPUMD
Graphics Processing Units Molecular Dynamics
kyegomez / Open-AF3
Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch
BioPandas / biopandas
Working with molecular structures in pandas DataFrames
mdtraj / mdtraj
An open library for the analysis of molecular dynamics trajectories
nwchemgit / nwchem
NWChem: Open Source High-Performance Computational Chemistry
aligfellow / xyzrender
Publication-quality molecular graphics.
3dem / relion
Image-processing software for cryo-electron microscopy
chemosim-lab / ProLIF
Interaction Fingerprints for protein-ligand complexes and more
CGATOxford / UMI-tools
Tools for handling Unique Molecular Identifiers in NGS data sets
plumed / plumed2
Development version of plumed 2
coleygroup / shepherd2
ShEPhERD-2 code: Interaction Profiles as a Universal Language for Generative Molecular Design
K-Dense-AI / drug-discovery-agent-skills
Agent Skills for small-molecule and protein therapeutics: cheminformatics, molecular ML, docking and dynamics, protein design platforms, and target-discovery knowledge graphs.
patrickbryant1 / EvoBind-multimer
De novo Design of Macrocyclic Molecular Glues
rafwiewiora / molarium
Local-first molecular modeling, WebGPU simulation, and conformer exploration in the browser
microsoft / Graphormer
Graphormer is a general-purpose deep learning backbone for molecular modeling.
3dmol / 3Dmol.js
WebGL accelerated JavaScript molecular graphics library