ligand

P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.

A Consensus Docking Plugin for PyMOL

an integrated tool for molecular docking and virtual screening

NeuralMD for Protein-ligand Binding Simulation, Nature Communicaitons 2025 https://www.nature.com/articles/s41467-025-67808-z

User friendly molecular dynamics simulation combining Modeller, OpenMM and Google Colab: A complete guide

Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.

3D diverse conformers generation using rdkit

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

Chemoinformatics tool for ligand-based virtual screening

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

Web application for protein-ligand binding sites analysis and visualization

ZDOCK predictions and PDB structures in C++ and Python

AutoCorrelation of Pharmacophore Features

[ICLR 2025] CheapNet: Cross-attention on Hierarchical representations for Efficient protein-ligand binding Affinity Prediction

Curated PyMOL configs and scripts for publication-quality rendering.

Project examing sparse deep learning architectures for ligand classification.

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

ligand-based virtual screening with consensus queries

Molecular Mechanics in OCaml

Strategy MMIC for molecular docking