Framework to build chemistry logfile data repository and access it through web
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Updated
Aug 31, 2017 - Python
Framework to build chemistry logfile data repository and access it through web
OpenBabel 2.4.1 for docker alpine
Conformer searching package.
A Colab notebook explaining the pipeline for smile format, openbabel, autodock vina, pymol and more
Test task for the position of data analyst in the BIOCAD Corporation
Molecular viewer [Work in progress]
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.
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.
small molecule processing scripts
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.
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.
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
Artifical "saturation" of Bemis-Murcko scaffolds retrieved with DataWarrior.
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