Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
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.
Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.
Molecular viewer [Work in progress]
Conformer searching package.
A software for ssnmr shield tensors calculations based on GIPAW method, Visualization of theoretical and experimental spectra, Conformer Generator with Genetic Algorithm and Boltzmann Probability of conformers.
A Colab notebook explaining the pipeline for smile format, openbabel, autodock vina, pymol and more
Framework to build chemistry logfile data repository and access it through web
Artifical "saturation" of Bemis-Murcko scaffolds retrieved with DataWarrior.
OpenBabel 2.4.1 for docker alpine
small molecule processing scripts
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.
Docker implementation of autodocking, openbabel, rdkit and lots of molecular dynamics utilities.
Step to reproduce the OpenBabel PDBQT tree error resulting in re-docking failure.
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.
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