protein-ligand-docking

There are 7 repositories under protein-ligand-docking topic.

p2rank
rdk / p2rank
P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
bioinformatics machine-learning protein-structure pdb binding-sites proteins ligand protein-surface structural-bioinformatics protein-ligand-interactions java random-forest mmcif pymol groovy protein-ligand-docking molecular-structures drug-discovery virtual-screening p2rank
Language:Groovy 234
awesome-molecular-docking
Thinklab-SJTU / awesome-molecular-docking
We would like to maintain a list of resources which aim to solve molecular docking and other closely related tasks.
ai-aided-drug-discovery awesome drug-discovery molecular-docking paper-list bioinformatics machine-learning protein-protein-interaction molecular-dynamics binding generative-model drug-design equivariant-representations drug-protein-interactions geometric-deep-learning awesome-list deep-learning optimal-transport protein-ligand-docking drugai
90
rxdock / rxdock
RxDock is a fork of rDock. Note: the latest code is under development. Please do git checkout patched-rdock after clone if you want patched rDock. [IMPORTANT NOTE: pull requests should be posted on GitLab, this is a read-only source code mirror]
docking molecular-docking virtual-screening ligand-screening drug-discovery protein-drug-interactions protein-ligand-docking protein-ligand-interactions protein-ligand-binding-conformation protein-ligand-interfaces cxx cxx11 python python3
Language:C++ 68
insilichem / gaudi
GaudiMM: A modular optimization platform for molecular design
computational-chemistry molecular-design genetic-algorithm protein-ligand-docking
Language:Python 32
suneelbvs / DiffDock
Colab version of "DiffDock: : Diffusion Steps, Twists, and Turns for Molecular Docking"
docking diffdock diffusion-models protein-ligand-docking small-molecules blind-docking
Language:Jupyter Notebook 24
LDeng0205 / confidence-bootstrapping
Implementation of the Confidence Bootstrapping procedure for protein-ligand docking.
diffusion-models equivariant-graph-neural-network machine-learning protein-ligand-docking iclr2024
Language:Python 19
rasbt / siteinterlock
A novel approach to pose selection in protein-ligand docking based on graph theory.
protein-ligand-docking protein-structure python
Language:Python 19
NRGlab / FlexAID
Flexible Artificial Intelligence Docking
docking molecular-docking protein-ligand-docking ligand-screening protein-ligand-binding-conformation protein-ligand-interactions protein-ligand-interfaces
Language:C 15
ShirleyWISiu / LigTMap
LigTMap currently supports prediction for 17 protein target classes that include 6000+ protein targets.
computational-chemistry computer-aided-drug-design drug-discovery drug-repurposing target-prediction protein-ligand-docking
Language:Python 13
psa-lab / siteinterlock
A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed by graph theoretic constraint counting on the covalent and noncovalent bond network. Raschka et al. (2016) Proteins: Structure, Function, and Bioinformatics
protein-ligand-docking bioinformatics biological-data-analysis protein-structure virtual-screening python computational-biology
Language:Python 9
rasbt / protein-recognition-index
Protein Recognition Index (PRI), measuring the similarity between H-bonding features in a given complex (predicted or designed) and the characteristic H-bond trends from crystallographic complexes
protein-ligand-interactions protein-ligand-docking computational-biology bioinformatics scoring-algorithm
Language:Python 8
azevedolab / taba
Repository for the Taba tool
binding-affinity protein-ligand-docking protein-ligand-interactions scoring-function-space machine-learning mass-spring-systems python scikit-learn
Language:Python 7
neudinger / pyDockRMSD
Root-mean-square deviation of atomic positions
cheminformatics cython docking-programs linux macos protein-binding-pocket protein-ligand-docking protein-receptor-structures python3 rdkit-chem
Language:C 6
YangLing0818 / IRDiff
[ICML 2024] Interaction-based Retrieval-augmented Diffusion Models for Protein-specific 3D Molecule Generation
3d-molecules-models diffusion-models molecule-generation protein-ligand-binding-affinity protein-ligand-docking protein-ligand-interactions
6
kevinshliu / Protein-Ligand-Interaction-Analysis
Analysis on the number of non-hydrogen atomic contacts between a ligand and each of specified residues on the protein following molecular docking of multiple ligands to a protein structure.
autodock-vina protein-ligand-docking protein-ligand-interactions
Language:Python 3
lmorency / NRGsuite
The NRGsuite is a PyMOL plugin (GUI) for FlexAID
molecular-docking protein-ligand-interactions protein-ligand-docking protein-ligand-binding-conformation
Language:Python 3
michabirklbauer / PIAWeb
PIAWeb - a graphical web interface for PIA
protein-ligand-docking protein-ligand-interactions drug-design drug-discovery docking frequency scoring docker streamlit
Language:Python 3
NRGlab / NRGsuite
NRGsuite is a PyMOL plugin (GUI) for FlexAID
protein-ligand-interactions protein-ligand-docking molecular-docking pymol-plugin
Language:Python 3
manaakiwhenua / gold-functions
Some shell functions to help scale and manage GOLD molecular docking jobs on an HPC
protein-ligand-docking
Language:Lua 1
michabirklbauer / protein_docking
Automatic identification of important interactions and interaction-frequency-based scoring in protein-ligand complexes
docking drug-design drug-discovery frequency protein-ligand-docking protein-ligand-interactions scoring screening virtual-screening vs
Language:Jupyter Notebook 1
drhuangwc / hSTING-ExcB-protein-ligand-docking
hSTING-ExcB protein-ligand docking
covalent-drug protein-ligand-docking hsting-excb
Language:Python 0
lmorency / FlexAID
Flexible Artificial Intelligence Docking
docking protein-ligand-docking protein-ligand-interactions protein-ligand-binding-conformation ligand-screening
Language:C 0
UnixJunkie / SEED-mirror
mirror of https://gitlab.com/CaflischLab/SEED
docking protein-ligand-docking sbvs
Language:C++