A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit
Inference of cell-cell communication from single-cell RNAseq data
A script able to extract ligands from pdb structure(s) and remove them from the original structure. The ligands are identified according to the *valid* ligands found in the binding MOAD database. The ligand can be extracted as a pdb or as a xyz (coordinate) file. Other options such as converting the queried pdb to pqr are available .
Library for calculating exact ligand cone angles
Identifies relevant ligands in the PDB
Unofficial MCP server for PoseBusters – validate molecular poses via HTTP or Spaces using the Model Context Protocol (MCP).
Multi-step pipeline that provides tools for filtering ChEMBL protein target using both physical and chemical features. This project was created in terms of my masters thesis which can be read here: https://www.overleaf.com/read/kwmnwnrwkntb
Search engine for mofstructure
Easy to use analysis of six-membered ring in ligands present in prtoein complexes.
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