Repositories list

• webchemistry

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

  C#

  •

  MIT License

  •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

• dareg-ui

  Public
  JavaScript

  •0•0•0•0•Updated Aug 12, 2025Aug 12, 2025

• gromacs-bioid

  Public
  TypeScript

  •

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

  •0•2•0•0•Updated Aug 10, 2025Aug 10, 2025

• ChargeFW2

  Public
  The core part of Atomic Charge Calculator II.

  partial-atomic-charges

  C++

  •

  MIT License

  •12•29•3•0•Updated Aug 5, 2025Aug 5, 2025

• gromacs-metadump

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

  metadataannotationsmolecular-dynamics

  TypeScript

  •

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

  •2•2•2•1•Updated Aug 5, 2025Aug 5, 2025

• moleonline-web

  Public
  MOLEonline is a fast service for calculating tunnels and pores in biomacromolecular structures

  proteinsmoletunnels+ 1pores

  TypeScript

  •

  MIT License

  •1•2•0•0•Updated Aug 5, 2025Aug 5, 2025

• AtomicChargeCalculator

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

  web-serverpartial-atomic-charges

  Python

  •

  MIT License

  •6•15•0•0•Updated Aug 4, 2025Aug 4, 2025

• tunnels-schema

  Public
  mmCIF schema describing the tunnel entries from MOLEonline

  proteinstunnels

  Python

  •

  MIT License

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

• dareg-api

  Public
  Python

  •0•0•0•0•Updated Jul 31, 2025Jul 31, 2025

• rings-conformation-validation

  Public
  Python

  •

  MIT License

  •0•1•0•1•Updated Jul 28, 2025Jul 28, 2025

• webchem-wiki

  Public
  Config files for setting up WebChemistry 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

• channelsdb

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

  apiproteinschannels

  JavaScript

  •

  MIT License

  •2•1•0•0•Updated Jul 16, 2025Jul 16, 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 code review and issue tracking.

  C++

  •

  GNU Lesser General Public License v2.1

  •359•1•0•0•Updated Jun 17, 2025Jun 17, 2025

• PDBCharges_website

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

  proteinspartial-atomic-charges

  TypeScript

  •

  MIT License

  •1•4•0•0•Updated Jun 11, 2025Jun 11, 2025

• ppropt

  Public
  PPROpt is a Python application for the fast protein structure optimization.

  Python

  •

  MIT License

  •2•1•0•0•Updated May 27, 2025May 27, 2025

• chemtools

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated May 18, 2025May 18, 2025

• FFFold

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

  protonationalphafold2gfn-ff+ 2force-field-optimisationprotein-structure-optimisation

  JavaScript

  •

  MIT License

  •0•5•0•0•Updated May 14, 2025May 14, 2025

• PDBCharges

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

  proteinspartial-atomic-charges

  Python

  •

  MIT License

  •2•2•0•1•Updated Apr 16, 2025Apr 16, 2025

• pdb-data-cruncher

  Public
  PDB data cruncher collects data form PDB and transforms them for ValTrendsDB.

  Python

  •0•1•2•0•Updated Feb 28, 2025Feb 28, 2025

• AlphaCharges

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

  protonationpartial-atomic-chargesalphafold2

  Python

  •

  MIT License

  •2•12•0•0•Updated Jan 27, 2025Jan 27, 2025

• moleonline-api

  Public
  API service for the MOLEonline application

  apiproteinstunnels+ 1pores

  HTML

  •

  MIT License

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• c1473-public

  Public
  Výukové materiály pro předmět PřF:C1473

  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Jan 9, 2025Jan 9, 2025

• RBP-Tar

  Public
  RBP-Tar is a web server for the retrieval of experimentally derived binding sites for hundreds of RNA Binding Proteins on the human genome.

  rnabinding-sites

  HTML

  •

  MIT License

  •1•1•0•1•Updated Nov 13, 2024Nov 13, 2024

• metadata-extractors

  Public
  Metadata exctractors for various types of data

  metadata-extraction

  Python

  •0•0•0•0•Updated Jul 24, 2024Jul 24, 2024

• ceitec-schemas

  Public
  Metadata schemas for various life-science data sources

  metadataschema

  TypeScript

  •0•0•0•0•Updated Jul 24, 2024Jul 24, 2024

• MOLE

  Public
  A universal toolkit for rapid location and characterization of channels and pores in biomacromolecules

  C#

  •

  MIT License

  •0•1•1•0•Updated Jun 8, 2024Jun 8, 2024

• sqc

  Public
  SQC (Structure Quality Check) is a reimplementation of the PDB validation server.

  Python

  •

  MIT License

  •0•0•0•0•Updated May 29, 2024May 29, 2024