ligand

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.

Chemoinformatics tool for ligand-based virtual screening

Web application for protein-ligand binding sites analysis and visualization

3D diverse conformers generation using rdkit

ligand-based virtual screening with consensus queries

A program analyzing 3D protein structures from PDB to generate 2D binding motifs

AnnapuRNA: a scoring function for predicting RNA-small molecule interactions.

Strategy MMIC for molecular docking

backup of silicos-it's align-it-1.0.4

Command line recipes for the working chemoinformatician

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

Create scoring functions from simulation data.

Published work of mine in Pitt Biological Sciences Advising Blog about using Bioinformatics to predict Ligand-Protein interactions.