Docker implementation of autodocking, openbabel, rdkit and lots of molecular dynamics utilities.
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Updated
Apr 14, 2024 - Dockerfile
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.
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.
Test task for the position of data analyst in the BIOCAD Corporation
This repository contains Jonathan et al.'s AoL (Assurance of Learning) Project for SCIE6062001 - Computational Biology Course.
OpenBabel 2.4.1 for docker alpine
small molecule processing scripts
Artifical "saturation" of Bemis-Murcko scaffolds retrieved with DataWarrior.
Framework to build chemistry logfile data repository and access it through web
A Colab notebook explaining the pipeline for smile format, openbabel, autodock vina, pymol and more
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.
Conformer searching package.
Molecular viewer [Work in progress]
Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.
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.
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