OleinikovasV's Stars
plinder-org/plinder
Protein Ligand INteraction Dataset and Evaluation Resource
baker-laboratory/RoseTTAFold-All-Atom
PDBeurope/arpeggio
Calculation of interatomic interactions in molecular structures
choderalab/espaloma
Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196
OmicsML/awesome-molecule-protein-pretrain-papers
patrickbryant1/AFProfile
Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile
aidos-lab/dect-evaluation
Differentiable Euler Characteristic Transform
OleinikovasV/CrypticSWISH
Scripts that are helpful to setup SWISH simulations (documentation under development, use with caution)
t7morgen/misato-dataset
openmm/spice-dataset
A collection of QM data for training potential functions
openforcefield/smirnoff99Frosst
A general small molecule force field descended from AMBER99 and parm@Frosst, available in the SMIRNOFF format
openforcefield/smarty
Chemical perception tree automated exploration tool.
leelasd/OPLS-AAM_for_Gromacs
Gromacs Implementation of OPLS-AAM Force field
DEShawResearch/SIMPLEchangepoint
mdtraj/tftraj
Molecular dynamics trajectory analysis in Tensorflow
jparkhill/TensorMol
Tensorflow + Molecules = TensorMol
sagieppel/Molecular-Dynamic-with-tensorflow
Molecular Dynamic (M.D) with tensorflow: Tensor Graph flow demonstration of the molecular dynamic model
choderalab/software-development
A primer on software development best practices for computational chemistry
choderalab/openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
michellab/Sire
Sire Molecular Simulations Framework
drugdata/D3R
Drug Design Data Resource is a suite of software to enable filtering, docking, and scoring of new sequences from wwpdb.
salilab/cryptosite
Library for prediction of cryptic binding sites
deepchem/deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
nglviewer/nglview
Jupyter widget to interactively view molecular structures and trajectories
ParmEd/ParmEd
Parameter/topology editor and molecular simulator
markovmodel/molPX
IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook
JFDama/plumed2
Development version of plumed 2
maccallumlab/meld-openmm-plugin
Meld plugin for OpenMM
maccallumlab/meld
Modeling with limited data
openmm/pdbfixer
PDBFixer fixes problems in PDB files