Repositories list

• pdb2pqr

  Public
  PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

  bioinformaticschemistryhelp-wanted+ 2hacktoberfestbiophysics

  Python

  •

  Other

  •38•132•49•4•Updated Dec 22, 2024Dec 22, 2024

• apbs-aws

  Public
  APBS in an AWS environment

  bioinformaticschemistrybiophysics

  Python

  •

  Creative Commons Zero v1.0 Universal

  •2•0•10•1•Updated Dec 11, 2024Dec 11, 2024

• apbs

  Public
  Software for biomolecular electrostatics and solvation calculations

  bioinformaticschemistryhelp-wanted+ 2hacktoberfestbiophysics

  C

  •

  Other

  •26•96•81•1•Updated Sep 7, 2024Sep 7, 2024

• metis-fork

  Public
  A fork of the METIS code from the Karypis group.

  C

  •

  Other

  •0•0•0•0•Updated Dec 11, 2022Dec 11, 2022

• FETK

  Public
  Fork of the Finite Element ToolKit from fetk.org.

  applied-mathematicshacktoberfestfinite-element-methods

  C

  •

  Other

  •4•4•5•1•Updated Oct 15, 2022Oct 15, 2022

• VR

  Public
  Virtual reality for biomolecular electrostatics

  chemistryvirtual-realitybiophysics

  Other

  •2•5•0•0•Updated Oct 6, 2022Oct 6, 2022

• go2pdb

  Public
  Extract PDB entries annotated with specific GO codes

  bioinformaticsstructural-bioinformatics

  Python

  •

  Other

  •3•2•1•0•Updated Jul 22, 2022Jul 22, 2022

• electrostatics.github.io

  Public
  APBS & PDB2PQR - software for biomolecular electrostatics and solvation

  bioinformaticschemistryhacktoberfest+ 1biophysics

  Python

  •5•29•0•0•Updated Jun 11, 2022Jun 11, 2022

• geoflow_c

  Public
  C++

  •1•0•1•1•Updated Apr 1, 2022Apr 1, 2022

• pb_solvers

  Public
  Analytic and Semi-Analytic solvers for Poisson-Boltzmann equations

  GLSL

  •7•0•1•0•Updated Jan 21, 2022Jan 21, 2022

• apbs-etl

  Public
  Refactor of PDB2PQR as an ETL program

  python

  Python

  •

  Other

  •0•2•4•0•Updated Jan 4, 2022Jan 4, 2022

• apbs-web

  Public
  APBS web interface

  bioinformaticschemistrybiophysics

  JavaScript

  •

  Creative Commons Zero v1.0 Universal

  •1•0•3•0•Updated Dec 28, 2021Dec 28, 2021

• pdb2cif

  Public
  Convert between PDB and CIF formats

  bioinformaticschemistrybiophysics+ 1structural-bioinformatics

  Python

  •

  Creative Commons Zero v1.0 Universal

  •1•1•2•0•Updated Nov 14, 2021Nov 14, 2021

• cache

  Public
  Cache for prebuilt packages

  1•0•0•0•Updated Sep 30, 2021Sep 30, 2021

• pygbe

  Public
  Python GPU Boundary Element Solver for APBS

  0•0•0•0•Updated Jun 23, 2021Jun 23, 2021

• apbs-rest

  Public archive
  Web server and RESTful backend services for APBS and PDB2PQR

  bioinformaticschemistrybiophysics

  JavaScript

  •

  Creative Commons Zero v1.0 Universal

  •8•3•0•0•Updated May 7, 2021May 7, 2021

• mmcif_pdbx

  Public
  Yet another version of PDBx/mmCIF Python implementation

  bioinformaticschemistrystructural-biology+ 1biophysics

  Python

  •

  Creative Commons Zero v1.0 Universal

  •2•6•8•0•Updated Apr 24, 2021Apr 24, 2021

• osmolytes

  Public
  This code attempts to predict the influence of osmolytes on protein stability

  chemistrybiochemistryhacktoberfest+ 1biophysics

  Python

  •

  Creative Commons Zero v1.0 Universal

  •4•1•2•0•Updated Mar 30, 2021Mar 30, 2021

• old_pdb

  Public archive
  Reading and writing old-format PDB data

  bioinformaticschemistrybiology

  Python

  •

  Creative Commons Zero v1.0 Universal

  •0•0•3•0•Updated Mar 1, 2021Mar 1, 2021

• TABIPB

  Public
  This TABIPB repo serves as a submodule to APBS, and also works as a standalone distribution.

  C

  •2•0•0•0•Updated Nov 2, 2020Nov 2, 2020

• apbs-pdb2pqr

  Public archive
  APBS - software for biomolecular electrostatics and solvation

  bioinformaticschemistrybiophysics

  62•127•0•0•Updated Jul 27, 2020Jul 27, 2020

• propka-3.1

  Public archive
  PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

  Python

  •

  GNU Lesser General Public License v2.1

  •59•0•0•0•Updated Jun 19, 2020Jun 19, 2020

• UQ

  Public
  UQ toolkit for APBS

  MATLAB

  •0•0•0•0•Updated Jan 10, 2020Jan 10, 2020

• 2017-apbs-paper

  Public archive
  2017 APBS update paper

  TeX

  •0•0•0•0•Updated Aug 21, 2017Aug 21, 2017

• GIBS

  Public
  GIBS: Grand Canonical Monte Carlo (GCMC) simulation program for simulating ion-biomolecule interactions with molecular solvent models

  C++

  •4•4•1•0•Updated Jul 27, 2017Jul 27, 2017

• pdb2pqr_flask

  Public archive
  Trying to bring the PDB2PQR web server into the 21st century

  CSS

  •3•0•0•0•Updated Dec 27, 2016Dec 27, 2016

• APBS_Sphinx

  Public archive
  APBS Rewrite

  C++

  •3•1•29•0•Updated Aug 7, 2016Aug 7, 2016

• PB-AM-deprecated

  Public archive
  Poisson-Boltzmann Analytical Method

  C++

  •0•1•6•0•Updated Jun 15, 2016Jun 15, 2016

• PB-SAM-deprecated

  Public archive
  Poisson-Boltzmann Semi-Analytical Method

  GLSL

  •0•0•0•0•Updated Jun 15, 2016Jun 15, 2016

• graphcut

  Public archive
  Sandbox for experimental graph cut code to replace Monte Carlo in PDB2PKA.

  Java

  •

  MIT License

  •0•1•0•0•Updated Jan 26, 2016Jan 26, 2016