openbabel

There are 1 repository under openbabel topic.

• plip

  pharmai / plip

  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

  scientific-computingbioinformaticsprotein-structureplipsingularitypython-bindingsopenbabelpdbdocker
  Language:Python 413

• oddt / oddt

  Open Drug Discovery Toolkit

  scoringdockingscreeningpythonrdkitopenbabelcheminformatics
  Language:Python 400

• AngelRuizMoreno / Jupyter_Dock

  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.

  autodockautodock-vinacheminformaticscomputational-biologydrug-designdrug-discoverydrug-repurposingjupyter-notebookledockmdanalysismolecular-dockingopenbabelproteinprotein-structurepy3dmolrdkit
  Language:Jupyter Notebook 245

• inpacdb / POAP

  Parallelized Open Babel & Autodock suite Pipeline

  virtualscreeningdockingautodockbashvinaopenbabel
  23

• hmcezar / clusttraj

  Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.

  clusteringrmsdopenbabelpython-scriptmolecular-dynamicsmonte-carlo-trajectorytrajectorydistance-matrix
  Language:Python 18

• duboviy / pymolecule

  :atom: Molecular viewer [Work in progress]

  moleculemolecular-graphicsmoleculesatoms-in-moleculesatommolecular-structurespygletpybelopenbabel
  Language:Python 9

• UnixJunkie / chemoinfo_recipes

  Command line recipes for the working chemoinformatician

  chemoinformaticshowtoopenbabelrdkitligandrmsdchemaxon
  7

• PeaWagon / Kaplan

  Conformer searching package.

  kaplanpsi4openbabelconformerevolutionary-algorithms
  Language:TeX 6

• jeffrichardchemistry / spyn

  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.

  nmr-spectroscopyssnmrchemistryquantum-chemistryquantum-chemistry-packagespythonlinuxquantum-espressoopenbabelopen-sourcefree-software
  Language:Python 5

• vegetablejuiceftw / coronavirus-begone

  A Colab notebook explaining the pipeline for smile format, openbabel, autodock vina, pymol and more

  smile-stringautodock-vinapymolopenbabelcolab-notebookpython3coronavirus
  Language:Jupyter Notebook 4

• nitish6174 / openchemvault

  Framework to build chemistry logfile data repository and access it through web

  flask-frameworkcomputational-chemistrycclibopenbabel
  Language:Python 3

• nbehrnd / datawarrior_saturate_Murcko_scaffolds

  Artifical "saturation" of Bemis-Murcko scaffolds retrieved with DataWarrior.

  pythonsimilaritymurckoopenbabeldatawarriorsubstructurescaffold
  Language:Python 2

• angelj-a / openbabel-docker-alpine

  OpenBabel 2.4.1 for docker alpine

  dockeropenbabelalpine-pythonpython-37
  Language:Dockerfile 1

• bmrb-io / smolscripts

  small molecule processing scripts

  openbabelrdkitpymolnmr-starmetabolomics
  Language:Python 1

• bio-grids / autodocking-utils

  Docker implementation of autodocking, openbabel, rdkit and lots of molecular dynamics utilities.

  autodockingmolecular-dynamicsopenbabelpython3rdkit
  Language:Dockerfile 0

• BryTheGuy / GCMSpyDFT

  Python library to transform a GCMS output file into a DFT input file.

  dftgcmsopenbabelopsinpython3
  Language:Python 0

• nbehrnd / RegioSQM

  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.

  computational-chemistryopenbabelpythonpython27python38rdkitsynthesis
  Language:Python 0

• ruslankhabirov / Biocad-data-analyst-test-task

  Test task for the position of data analyst in the BIOCAD Corporation

  python3sklearnridge-regressionsvm-modellasso-regressiondecision-tree-regressionrdkitopenbabel
  Language:Python 0

• allbegray / mol-converter

  molecule file format converter using openbabel, slurm

  openbabelslurm
  Language:Python

• gkxiao / openbabel_2433

  Step to reproduce the OpenBabel PDBQT tree error resulting in re-docking failure.

  openbabelautodoc-vinavinapdbqt

• shubhamkrpandey19 / molecular_similarity_check

  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.

  openbabelrdkit-chemsdf-2dtanimotosimilaritylarge-sdf-files
  Language:Jupyter Notebook