ligand

There are 2 repositories under ligand 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
paiardin / DockingPie
A Consensus Docking Plugin for PyMOL
molecular-modeling pymol pymol-extension pymol-plugin ligand molecular molecular-docking molecular-dynamics
Language:Python 61
lmdu / dockey
an integrated tool for molecular docking and virtual screening
docking ligand molecular molecule receptor
Language:Python 46
annapurna
filipsPL / annapurna
AnnapuRNA: a scoring function for predicting RNA-small molecule interactions.
rna scoring ligand molecular-docking small-molecules
Language:Python 19
MooersLab / jupyterlabpymolpysnips
Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.
jupyter jupyter-notebook jupyterlab notebook python snippets grayscale ribbon-diagram protein-structure rna-structure dna-structure molecular-representation literate-programming moleclar-graphics pdb mmcif ligand biomolecular molecular
Language:HTML 19
UnixJunkie / smi2sdf3d
3D diverse conformers generation using rdkit
rdkit python-script conformer ligand chemoinformatics 3d smiles sdf smi
Language:Python 19
UnixJunkie / ACPC
Chemoinformatics tool for ligand-based virtual screening
lbvs chemoinformatics ligand ocaml partial-charges
Language:OCaml 18
StructureAnalyzer
Cardypro / StructureAnalyzer
A program analyzing 3D protein structures from PDB to generate 2D binding motifs
3d-to-2d binding-motifs chemistry ligand pdb protein protein-ligand-interactions pymol supramolecular
Language:Python 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
UnixJunkie / align-it
backup of silicos-it's align-it-1.0.4
pharmacophore lbvs ligand
Language:C++ 9
UnixJunkie / consent
ligand-based virtual screening with consensus queries
chemical chemoinformatics consensus ecfp4 fingerprint lbvs ligand maccs molprint2d ocaml
Language:OCaml 8
weng-lab / libzdock
ZDOCK predictions and PDB structures in C++ and Python
zdock pdb libpdb m-zdock cpp zlab wenglab libzdock transformation ligand receptor structure
Language:C++ 8
MolSSI / mmic_docking
Strategy MMIC for molecular docking
docking drug interoperability ligand mmic mmschema molssi protein receptor standards
Language:Python 7
UnixJunkie / chemoinfo_recipes
Command line recipes for the working chemoinformatician
chemoinformatics howto openbabel rdkit ligand rmsd chemaxon
7
UnixJunkie / elekit2
EleKit2 computes the electrostatic complementarity between a docked ligand and its protein receptor
electrostatic-potential similarity-score sbvs protein ligand
Language:Python 5
UnixJunkie / MMO
Molecular Mechanics in OCaml
ani-2x docking ligand molecular-mechanics monte-carlo ocaml-library ocaml-program protein universal-force-field
Language:OCaml 4
jkarolczak / ligand-classification
Project examing sparse deep learning architectures for ligand classification.
deep-learning machine-learning classification sparsity minkowski-engine ligand
Language:Jupyter Notebook 3
UnixJunkie / elekit
EleKit measures the similarity of electrostatic potentials between a small molecule and a protein.
electrostatic-potential similarity-score sbvs protein ligand
Language:Python 3
AlexisMolinaMR / PeleAI
Create scoring functions from simulation data.
graph graph-statistics ligand scoring-functions
Language:Python 2
maxmeixner / ClassTor
A python tool for Classification of ligand conformations based on Torsion angles
dihedral-angles classification ligand conformational-analysis molecular-dynamics
Language:Python 2
abdulsalam-bande / swifty
This is a work to improve molecular docking speed. Normally docking a ligand on a target protein is done with some very complex functions and it is often slow. This work uses Neural Networks to model ligands on target proteins to measure whether they are active or not.
machine-learning bioinformatics protein ligand docking natural-language-processing deep-learning neural-network python pytorch
Language:Python 1
Amirreza-Mousavi / Aspartate_Racemase_Ligands_Simlarity_Score
An R script that uses MACCS166 chemical fingerprint and calculates Jaccard Index/Tanimoto Coefficient for a list of Aspartate Racemase Ligands
aspartate-racemase chemoinformatics dti dti-prediction jaccard-index ligand maccs-fingerprint r tanimoto-coefficient
Language:R 1
Amirreza-Mousavi / Aspartate_Racemase_Ligands_Bioactivity_Prediction
This scripts tries to predict the bioactivity of 131 compounds related to Aspartate Racemase enzyme with the aid of decision trees and SVM
aspartate-racemase bioactivity chembl chemoinformatics decision-trees dti dti-prediction ligand maccs-fingerprint smiles support-vector-machines svm svm-model
Language:R 0
chao1224 / NeuralMD
NeuralMD for protein-ligand binding MD simulation
binding binding-affinity ligand md molecular-dynamics molecular-dynamics-simulation protein protein-ligand-binding
Sarah-Hesham-2022 / Drug-Design-AutoDock-Tools-MBP-D-Ribose
Molecular docking is one of the molecular modeling methods that predicts the preferred orientation of one molecule (ligand) to another (receptor) when bound to each other to form a stable complex (lowest energy state).
active-sites autodock bioinformatics biology blind-docking ligand molecular-docking protein receptor structural-analysis structural-biology receptor-ligand-interaction escherichia-coli mbp d-ribose computer-graphics-algorithms
YogiOnBioinformatics / Bioinformatics-for-Protein-Ligand-Interactions
Published work of mine in Pitt Biological Sciences Advising Blog about using Bioinformatics to predict Ligand-Protein interactions.
publication bioinformatics pitt computationalbiology computational-proteomics docking ligand drugs drug-discovery