Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.
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Updated
Sep 4, 2024 - Python
Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.
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
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.
This repository contains Jonathan et al.'s AoL (Assurance of Learning) Project for SCIE6062001 - Computational Biology Course. This project has been declared to have passed with a high distinction (score: 100, grade: A).
Docker implementation of autodocking, openbabel, rdkit and lots of molecular dynamics utilities.
Artifical "saturation" of Bemis-Murcko scaffolds retrieved with DataWarrior.
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.
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.
small molecule processing scripts
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.
Step to reproduce the OpenBabel PDBQT tree error resulting in re-docking failure.
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.
Molecular viewer [Work in progress]
Test task for the position of data analyst in the BIOCAD Corporation
A Colab notebook explaining the pipeline for smile format, openbabel, autodock vina, pymol and more
Conformer searching package.
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