protein-ligand-interactions

There are 9 repositories under protein-ligand-interactions 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 224
hkmztrk / DeepDTA
convolutional-neural-networks protein-ligand-interactions
Language:Python 212
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++ 67
sbl-sdsc / mmtf-pyspark
Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.
apache-spark big-data binder jupyter jupyter-notebook machine-learning protein-data-bank protein-ligand-interactions protein-protein-interaction protein-sequences protein-structure pyspark scientific-computing
Language:Python 67
sbl-sdsc / mmtf-workshop-2018
Structural Bioinformatics Training Workshop & Hackathon 2018
pyspark binder protein-data-bank jupyter-notebook jupyter machine-learning big-data protein-protein-interaction protein-ligand-interactions 3d-visualization apache-spark workshop-materials hackathon
Language:Jupyter Notebook 58
zaixizhang / FLAG
Implementation of ICLR23 paper "Molecule Generation for Target Protein Binding with Structural Motifs"
drug-discovery generative-ai geometric-deep-learning protein-ligand-interactions
Language:Python 54
zaixizhang / PocketGen
Implementation of PocketGen: Generating Full-Atom Ligand-Binding Protein Pockets
generative geometric-deep-learning protein-language-model protein-ligand-interactions protein-structure
Language:Python 52
lucidrains / neural-plexer-pytorch
Implementation of Nvidia's NeuralPlexer, for end-to-end differentiable design of functional small-molecules and ligand-binding proteins, in Pytorch
artificial-intelligence deep-learning denoising-diffusion drug-design protein-ligand-interactions
Language:Python 48
XieResearchGroup / Physics-aware-Multiplex-GNN
Code for our Nature Scientific Reports paper "A universal framework for accurate and efficient geometric deep learning of molecular systems"
computational-biology computational-chemistry docking geometric-deep-learning graph-neural-networks machine-learning protein-ligand-interactions rna-structure-prediction
Language:Python 48
lhm30 / PIDGINv3
Protein target prediction using random forests and reliability-density neighbourhood analysis
target-prediction cheminformatics chemoinformatics protein-ligand-interactions applicability-domain reliability-density rdkit
Language:Python 41
chengwang88 / deltavina
DeltaVina scoring function
scoring-functions random-forest protein-ligand-interactions
Language:Python 40
dwhswenson / contact_map
Contact map analysis for biomolecules; based on MDTraj
bioinformatics biochemistry protein-protein-interaction molecular-dynamics protein-ligand-interactions computational-biology
Language:Python 38
PaccMann / paccmann_kinase_binding_residues
Comparison of active site and full kinase sequences for drug-target affinity prediction and molecular generation. Full paper: https://pubs.acs.org/doi/10.1021/acs.jcim.1c00889
kinases protein-ligand-interactions active-sites machine-learning proteochemometrics knn
Language:Python 35
AndMastro / protein-ligand-GNN
This repository contains the code for the work on protein-ligand interaction with GNNs and XAI
gnns protein-ligand-interactions xai
Language:Python 30
hkmztrk / SMILESVecProteinRepresentation
protein protein-ligand-interactions word-embeddings
Language:Python 28
sbl-sdsc / mmtf-genomics
Methods for mapping genomic data onto 3D protein structure.
binder cyverse dbsnp genomics mmtf-pyspark mutations protein-data-bank protein-drug-interactions protein-ligand-interactions protein-protein-interaction protein-structure pyspark
Language:Jupyter Notebook 27
sbl-sdsc / mmtf-spark
Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.
protein-structure protein-data-bank protein-sequences protein-ligand-interactions protein-protein-interaction machine-learning big-data apache-spark scientific-computing
Language:Java 22
huankoh / PSICHIC
PSICHIC (pronounced Psychic) - PhySIcoCHemICal graph neural network for learning protein-ligand interaction fingerprints from sequence data
binding-affinity drugdiscovery functional-effects protein-ligand-interactions
Language:Jupyter Notebook 20
YanjunLi-CS / dyscore
Open source code for DyScore
de-novo-drug-design drug-discovery protein-ligand-interactions scoring-functions virtual-screening
Language:Python 20
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
StructureAnalyzer
Cardypro / StructureAnalyzer
A program analyzing 3D protein structures from PDB to generate 2D binding motifs
chemistry pdb 3d-to-2d supramolecular protein-ligand-interactions pymol ligand protein binding-motifs
Language:Python 14
ldomic / lintools
Python script that creates 2D protein-ligand interaction images
protein-ligand-interactions molecular-dynamics analysis
Language:Python 14
mtplr / pyMol-cookbook
Some notes (cookbook) for pyMol. Protein Crystallography course.
cookbook protein-ligand-interactions protein-stability protein-structure pymol
14
jendelel / PrankWebApp
Web application for protein-ligand binding sites analysis and visualization
protein-ligand-interactions web-application protein-homology visualization protein conservation web webapp ligand protein-structure protein-sequence pdb conservation-scores analyses
Language:JavaScript 13
Shen-Lab / CPAC
[Bioinformatics 2022] Cross-Modality and Self-Supervised Protein Embedding for Compound-Protein Affinity and Contact Prediction
multimodal-deep-learning protein-ligand-interactions self-supervised-learning
Language:Python 13
rasbt / HbindViz
Tools for generating hydrogen-bond interaction visualizations from Hbind
computational-biology bioinformatics protein-ligand-interactions hydrogen-bonds protein-structure
Language:Python 10
ADicksonLab / mastic
Multi-Atom Structure/Selection Toolkit with Interaction Capabilities
computational-biology computational-chemistry protein-structure protein-ligand-interactions
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
YangLing0818 / BindDM
[AAAI 2024] Binding-Adaptive Diffusion Models for Structure-Based Drug Design
3d-molecules-models diffusion-models protein-ligand-interactions sbdd
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
DockM8
DrugBud-Suite / DockM8
All in one Structure-Based Vitual Screening workflow based on the concept of consensus docking.
cheminformatics cheminformatics-and-compchem compchem computational-chemistry docking drug-design drug-discovery molecular-docking molecular-modeling protein-ligand-interactions sbvs virtual-screening
Language:Jupyter Notebook 7
VeaLi / MLT-LE
MLT-LE: predicting drug–target binding affinity with multi-task residual neural networks : https://arxiv.org/abs/2209.06274
drug-target-affinity protein-ligand-interactions drug-target-interactions dta
Language:Python 7
jbellamycarter / pepfoot
PepFoot: a user friendly GUI for protein footprinting analysis
python gui-application mass-spectrometry data-visualization data-analysis protein-protein-interaction protein-ligand-interactions footprinting lc-ms mz5
Language:Python 6
primaryodors / primarydock
PrimaryOdors.org molecular docker.
gpcr molecular-docking molecular-viewer molecular-visualization olfaction protein-function-prediction protein-ligand-interactions side-chain-orientation path-based-docking side-chain-flexion
Language:C++ 6
insilichem / tangram_plipgui
Depict protein-ligand interactions, as calculated with PLIP, in UCSF Chimera
ucsf-chimera protein-ligand-interactions
Language:Python 4
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