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.
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Updated
Apr 12, 2024 - Groovy
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.
A Consensus Docking Plugin for PyMOL
3D diverse conformers generation using rdkit
Web application for protein-ligand binding sites analysis and visualization
Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.
AnnapuRNA: a scoring function for predicting RNA-small molecule interactions.
A program analyzing 3D protein structures from PDB to generate 2D binding motifs
ligand-based virtual screening with consensus queries
Chemoinformatics tool for ligand-based virtual screening
EleKit measures the similarity of electrostatic potentials between a small molecule and a protein.
EleKit2 computes the electrostatic complementarity between a docked ligand and its protein receptor
An R script that uses MACCS166 chemical fingerprint and calculates Jaccard Index/Tanimoto Coefficient for a list of Aspartate Racemase Ligands
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).
Published work of mine in Pitt Biological Sciences Advising Blog about using Bioinformatics to predict Ligand-Protein interactions.
A python tool for Classification of ligand conformations based on Torsion angles
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