Repositories list

• proptimus_live

  Public
  Constrained α-carbons optimisation of protein structures

  proteinoptimisation

  proteinoptimisation

  TypeScript

  •

  MIT License

  •0•0•0•0•Updated Mar 13, 2026Mar 13, 2026

• proptimus_raphan

  Public
  Application for the rapid optimisation with constrained alpha carbons

  Python

  •

  MIT License

  •4•2•0•0•Updated Mar 12, 2026Mar 12, 2026

• ChargeFW2

  Public
  The core part of Atomic Charge Calculator III.

  partial-atomic-charges

  partial-atomic-charges

  C++

  •

  MIT License

  •12•29•3•1•Updated Mar 11, 2026Mar 11, 2026

• AtomicChargeCalculator

  Public
  Atomic Charge Calculator III (ACC III) is an application for fast calculation of partial atomic charges.

  web-serverpartial-atomic-charges

  web-serverpartial-atomic-charges

  Python

  •

  MIT License

  •6•16•0•0•Updated Mar 11, 2026Mar 11, 2026

• proptimus_prime

  Public
  Python

  •

  MIT License

  •1•2•0•0•Updated Feb 25, 2026Feb 25, 2026

• dareg-api

  Public
  Python

  •0•0•0•0•Updated Feb 24, 2026Feb 24, 2026

• mddash-notebooks

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Feb 11, 2026Feb 11, 2026

• rings-conformation-validation

  Public
  Python

  •

  MIT License

  •1•2•0•0•Updated Jan 11, 2026Jan 11, 2026

• c1473-public

  Public

  sb-ncbr/c1473-public’s past year of commit activity
  Výukové materiály pro předmět PřF:C1473

  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Jan 8, 2026Jan 8, 2026

• AlphaCharges

  Public
  𝛂Charges: A tool for the quick calculation of partial atomic charges for protein structures from AlphaFold DB

  protonationpartial-atomic-chargesalphafold2

  protonationpartial-atomic-chargesalphafold2

  Python

  •

  MIT License

  •2•12•0•0•Updated Dec 16, 2025Dec 16, 2025

• gromacs-metadump

  Public
  A tool to describe GROMACS molecular dynamics simulations with powerful metadata.

  metadataannotationsmolecular-dynamics

  metadataannotationsmolecular-dynamics

  TypeScript

  •

  BSD 3-Clause "New" or "Revised" License

  •3•4•2•0•Updated Dec 8, 2025Dec 8, 2025

• sb-ncbr-tools

  Public
  Overview of SB NCBR tools and services

  servicestoolsstructural-bioinformatics

  servicestoolsstructural-bioinformatics

  TypeScript

  •0•0•0•0•Updated Dec 6, 2025Dec 6, 2025

• webchemistry

  Public
  Webchemistry is a set of tools for analysis of 3D structural data from the Protein Data Bank implemented in C#.

  JavaScript

  •

  MIT License

  •1•1•0•0•Updated Dec 3, 2025Dec 3, 2025

• charges-schema

  Public
  mmCIF schema describing the charges entries from Atomic Charge Calculator

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 3, 2025Dec 3, 2025

• channelsdb

  Public
  ChannelsDB 2 - a comprehensive and regularly updated resource of channels, pores and tunnels

  apiproteinschannels

  apiproteinschannels

  TypeScript

  •

  MIT License

  •2•1•0•0•Updated Nov 25, 2025Nov 25, 2025

• dareg-ui

  Public
  JavaScript

  •0•0•0•0•Updated Nov 20, 2025Nov 20, 2025

• moleonline-web

  Public

  sb-ncbr/moleonline-web’s past year of commit activity
  MOLEonline is a fast service for calculating tunnels and pores in biomacromolecular structures

  proteinsmoletunnels+ 1

  proteinsmoletunnelspores

  TypeScript

  •

  MIT License

  •1•2•0•0•Updated Nov 20, 2025Nov 20, 2025

• FFFold

  Public
  FFFold: A tool for the quick optimisation of protein structures from AlphaFold DB

  protonationalphafold2gfn-ff+ 2

  protonationalphafold2gfn-ffforce-field-optimisationprotein-structure-optimisation

  JavaScript

  •

  MIT License

  •1•6•0•0•Updated Nov 12, 2025Nov 12, 2025

• time-lapse_imaging_workflow

  Public
  Image processing workflow

  Python

  •

  BSD 2-Clause "Simplified" License

  •2•0•0•0•Updated Nov 5, 2025Nov 5, 2025

• gromacs-bioid

  Public
  TypeScript

  •

  BSD 3-Clause "New" or "Revised" License

  •0•2•0•0•Updated Oct 9, 2025Oct 9, 2025

• bioid

  Public
  0•0•0•0•Updated Oct 3, 2025Oct 3, 2025

• PDBCharges

  Public
  Workflow to calculate partial atomic charges for structures in PDB database

  proteinspartial-atomic-charges

  proteinspartial-atomic-charges

  Python

  •

  MIT License

  •3•3•1•1•Updated Sep 2, 2025Sep 2, 2025

• PDBCharges_website

  Public
  PDBCharges is a web application providing partial atomic charges of protein structures from the Protein Data Bank.

  proteinspartial-atomic-charges

  proteinspartial-atomic-charges

  TypeScript

  •

  MIT License

  •1•4•0•0•Updated Sep 2, 2025Sep 2, 2025

• MOLE

  Public

  sb-ncbr/MOLE’s past year of commit activity
  A universal toolkit for rapid location and characterization of channels and pores in biomacromolecules

  C#

  •

  MIT License

  •1•2•2•0•Updated Aug 25, 2025Aug 25, 2025

• tunnels-schema

  Public
  mmCIF schema describing the tunnel entries from MOLEonline

  proteinstunnels

  proteinstunnels

  Python

  •

  MIT License

  •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025

• webchem-wiki

  Public
  Config files for setting up WebChemistry wiki

  wiki

  wiki

  PHP

  •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

• mdrepo-visualisations

  Public
  TypeScript

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Jul 18, 2025Jul 18, 2025

• mddash-fs-mapper

  Public
  Python

  •0•0•0•0•Updated Jul 14, 2025Jul 14, 2025

• dareg-lab

  Public
  TypeScript

  •

  Apache License 2.0

  •0•0•0•0•Updated Jun 23, 2025Jun 23, 2025

• gromacs

  Public
  Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for cod…

  C++

  •

  GNU Lesser General Public License v2.1

  •382•1•0•0•Updated Jun 17, 2025Jun 17, 2025