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    47 repositories

    • pdb-data-cruncher

      Public
      PDB data cruncher collects data form PDB and transforms them for ValTrendsDB.
      Python
      •0•1•2•1•Updated Feb 3, 2025Feb 3, 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•1•0•0•Updated Feb 3, 2025Feb 3, 2025

    • moleonline-web

      Public
      MOLEonline is a fast service for calculating tunnels and pores in biomacromolecular structures
      proteinsmoletunnelspores
      TypeScript
      •
      MIT License
      •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • ChargeFW2

      Public
      The core part of Atomic Charge Calculator II.
      partial-atomic-charges
      C++
      •
      MIT License
      •14•27•3•3•Updated Jan 27, 2025Jan 27, 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•10•0•0•Updated Jan 27, 2025Jan 27, 2025

    • gromacs-metadata-extractor

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

    • PDBCharges

      Public
      Workflow to calculate partial atomic charges for structures in PDB database
      proteinspartial-atomic-charges
      Python
      •
      MIT License
      •1•2•0•0•Updated Jan 14, 2025Jan 14, 2025

    • moleonline-api

      Public
      API service for the MOLEonline application
      apiproteinstunnelspores
      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

    • channelsdb

      Public
      ChannelsDB 2 - a comprehensive and regularly updated resource of channels, pores and tunnels
      apiproteinschannels
      JavaScript
      •
      MIT License
      •2•1•0•0•Updated Nov 26, 2024Nov 26, 2024

    • 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

    • AtomicChargeCalculator2

      Public
      Atomic Charge Calculator II (ACC II) is an application for fast calculation of partial atomic charges.
      web-serverpartial-atomic-charges
      TeX
      •
      MIT License
      •6•12•0•0•Updated Sep 26, 2024Sep 26, 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

    • rings-conformation-validation

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 3, 2024Jul 3, 2024

    • FFFold

      Public
      FFFold: A tool for the quick optimisation of protein structures from AlphaFold DB
      protonationalphafold2gfn-ffforce-field-optimisationprotein-structure-optimisation
      JavaScript
      •
      MIT License
      •1•5•0•0•Updated Jun 25, 2024Jun 25, 2024

    • MOLE

      Public
      A universal toolkit for rapid location and characterization of channels and pores in biomacromolecules
      C#
      •
      MIT License
      •0•0•0•0•Updated Jun 8, 2024Jun 8, 2024

    • 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 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

    • sqclib

      Public
      SQCLib is a python library for interacting with the Structure Quality Check server.
      Python
      •0•0•0•0•Updated May 23, 2024May 23, 2024

    • ppropt

      Public
      PPROpt is a Python application for the fast protein structure optimization.
      Python
      •
      MIT License
      •1•1•0•0•Updated May 22, 2024May 22, 2024

    • ConfAnalyser

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 29, 2024Apr 29, 2024

    • rama_z_data

      Public
      Rotamer data from rlabduke for use in SQC
      0•0•0•0•Updated Mar 28, 2024Mar 28, 2024

    • protein-similarity-parent-project

      Public
      Shell
      •0•0•0•0•Updated Mar 23, 2024Mar 23, 2024

    • diplomka-jo-db-integration

      Public
      Java
      •0•0•0•0•Updated Mar 13, 2024Mar 13, 2024

    • mics-proteins

      Public
      Java
      •0•0•0•1•Updated Mar 13, 2024Mar 13, 2024

    • geostd

      Public
      Other
      •24•0•0•0•Updated Mar 12, 2024Mar 12, 2024

    • ProteinSearch

      Public
      Fron tend for the application that searches structurally similar protein chains.
      Python
      •1•0•0•1•Updated Feb 4, 2024Feb 4, 2024

    • rotarama_data

      Public
      Contour data for Ramachandran and rotamer validation in cctbx and MolProbity
      1•0•0•0•Updated Nov 30, 2023Nov 30, 2023

    • golem

      Public
      GOLEM: distribution of Gene regulatOry eLEMents within the plant promoters
      Dart
      •
      MIT License
      •0•0•0•0•Updated Nov 30, 2023Nov 30, 2023