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    119 repositories

    • biobb_mem

      Public
      Python
      •
      Apache License 2.0
      •0•0•1•0•Updated Feb 7, 2025Feb 7, 2025

    • biobb_common

      Public
      Biobb_common is the base package required to use the biobb packages.
      Python
      •
      Apache License 2.0
      •1•0•3•0•Updated Feb 7, 2025Feb 7, 2025

    • biobb_workflows

      Public
      Global repository for all the BioExcel Building Blocks Workflows
      Common Workflow Language
      •2•4•0•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_analysis

      Public
      Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations.
      Python
      •
      Apache License 2.0
      •2•4•0•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_vs

      Public
      Biobb_vs is the Biobb module collection to perform virtual screening studies.
      Python
      •
      Apache License 2.0
      •2•1•0•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_structure_utils

      Public
      Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file, such as pulling out a particular model or chain, removing water molecules or ligands, or renumbering or sorting atoms or residues.
      Python
      •
      Apache License 2.0
      •3•2•1•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_pytorch

      Public
      Biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular PyTorch Python library.
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_pdb_tools

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_model

      Public
      Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms.
      Python
      •
      Apache License 2.0
      •1•1•2•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_gromacs

      Public
      Python
      •
      Apache License 2.0
      •1•5•12•2•Updated Jan 28, 2025Jan 28, 2025

    • biobb_godmd

      Public
      biobb_godmd is a BioBB category for the GOdMD tool
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_flexserv

      Public
      Biobb_flexserv is a BioBB category for biomolecular flexibility studies on protein 3D structures.
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_flexdyn

      Public
      biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins.
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_dna

      Public
      Biobb_dna is the Biobb module collection to perform analyses and transformations on nucleic acid trajectories and helical parameter data.
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_cp2k

      Public
      Python
      •
      Apache License 2.0
      •1•1•0•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_cmip

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_chemistry

      Public
      Biobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations.
      Python
      •
      Apache License 2.0
      •2•5•0•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_io

      Public
      Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_amber

      Public
      Biobb_amber is a BioBB category for AMBER MD package.
      Python
      •
      Apache License 2.0
      •3•11•2•0•Updated Jan 28, 2025Jan 28, 2025

    • biobb_wf_virtual-screening

      Public
      This tutorials aim to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb).
      HTML
      •
      Apache License 2.0
      •4•5•0•0•Updated Jan 27, 2025Jan 27, 2025

    • biobb_wf_structure_checking

      Public
      This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation using the BioExcel Building Blocks library (biobb).
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • biobb_wf_protein-complex_md_setup

      Public
      This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb).
      HTML
      •
      Apache License 2.0
      •6•5•0•0•Updated Jan 27, 2025Jan 27, 2025

    • biobb_wf_pmx_tutorial

      Public
      This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb).
      HTML
      •
      Apache License 2.0
      •1•2•0•0•Updated Jan 27, 2025Jan 27, 2025

    • biobb_wf_md_setup

      Public
      This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb).
      HTML
      •
      Apache License 2.0
      •4•4•0•0•Updated Jan 27, 2025Jan 27, 2025

    • biobb_wf_godmd

      Public
      This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks library (biobb).
      HTML
      •
      Apache License 2.0
      •1•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • biobb_wf_flexserv

      Public
      This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).
      HTML
      •
      Apache License 2.0
      •1•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • biobb_wf_flexdyn

      Public
      This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).
      HTML
      •
      Apache License 2.0
      •0•1•0•0•Updated Jan 27, 2025Jan 27, 2025

    • biobb_wf_dna_helparms

      Public
      This tutorial aims to illustrate the process of extracting structural and dynamical properties from a DNA MD trajectory helical parameters, step by step, using the BioExcel Building Blocks library (biobb).
      HTML
      •
      Apache License 2.0
      •1•1•0•0•Updated Jan 27, 2025Jan 27, 2025

    • biobb_wf_cmip

      Public
      This tutorial aims to illustrate the process of computing classical molecular interaction potentials from protein structures, step by step, using the BioExcel Building Blocks library (biobb).
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • biobb_wf_amber

      Public
      This tutorials aim to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) wrapping the Ambertools MD package.
      HTML
      •
      Apache License 2.0
      •3•1•0•0•Updated Jan 27, 2025Jan 27, 2025