A toolkit for molecular generation, QSAR prediction (GNN-based), and physicochemical property–based filtering

This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics.

Evaluation of ligand based methods applied to RNA and DNA targets

Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al. (2025), https://doi.org/10.1093/nar/gkaf361

Python tool to convert 2D structures drawn in ChemDraw or similar programs saved as *.mol files into 3D Gaussian input files with realistic bond lengths and geometries//Converte strutture molecolari 2D disegnate in ChemDraw o programmi simili e salvate come file *.mol in file di input 3D per Gaussian, con lunghezze di legame e geometrie realistiche

Artifical "saturation" of Bemis-Murcko scaffolds retrieved with DataWarrior.

A complete step-by-step pipeline to dock multiple ligands using AutoDock Vina. Includes ligand preparation, file format conversion, batch docking, and result extraction.

Curso corto -- Quimioinformática en Python (IIB-UNSAM)

Sampling molecules grown using stochastic Monte Carlo (CBMC) inside zeolites

Dok2any is a small Python package designed to convert dok files generated by LeDock molecular docking software, a non-standard chemical structure file format unique for LeDock, to various other chemical structure formats using Openbabel.

This repository contains the Assurance of Learning (AoL) Project by Jonathan et al. for the Computational Biology course (SCIE6062001). The project received a high distinction with a score of 100 (Grade: A).

Python library to transform a GCMS output file into a DFT input file.

Docker implementation of autodocking, openbabel, rdkit and lots of molecular dynamics utilities.

This repository will help you to screen large library of molecules at early stage. This repo comprises 3 notebooks that split large sdf files into smaller sets that are easy to handle, similarity_check_rdkit that uses tanimoto coefficeient to screen the libraries against your target structure.

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

small molecule processing scripts

A quick prediction of selectivities for the electrophilic substitution of homo- & heteroaromatic systems (Kromann et al., 2018ChemSci660 (http://dx.doi.org/10.1039/C7SC04156J) now ported to Python3.

Open Drug Discovery Toolkit

molecule file format converter using openbabel, slurm