This is parent repository for MolToPDB. MolToPDB is a RDKit plug-in developed by the authors to improve the Protein Data Bank (PDB) files generation for Molecular Dynamics (MD) simulations. In order to obtain the PDB files for the molecular dynamics simulations, it was necessary to generate the PDB files of the peptides in Mol object format. The RDKit package is a valuable tool for the generation of PDB files from Mol object. However, it should be noted that the package is only able to generate files with a general description of the Mol object chemical structure. To perform molecular dynamics simulations of molecules that contain amino acids in their structure, such as proteins and peptides, it is necessary to have a particular description of the atoms and residues. In this regard, MolToPDB was implemented to generate the required description of the atoms and residues of amino acids in a PDB file created with RDKit. In this sense, MolToPDB was used to generate the three dimensional structures of the peptides chosen for the validation of clustering method. The source code is published at: https://gitlab.jyu.fi/brdesouz/moltopdb

2025