BioExcel

biobb

Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools.

biobb_structure_checking

biobb_amber

Biobb_amber is a BioBB category for AMBER MD package.

biobb_chemistry

Biobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations.

biobb_gromacs

biobb_wf_md_setup

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).

biobb_analysis

Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations.

biobb_workflows

Global repository for all the BioExcel Building Blocks Workflows

biobb_io

Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.

biobb_pmx

Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.

biobb_structure_utils

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.

biobb_flexdyn

biobb_flexdyn is a BioBB category for studies on the conformational landscape of native proteins.

biobb_flexserv

Biobb_flexserv is a BioBB category for biomolecular flexibility studies on protein 3D structures.

biobb_model

Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms.

biobb_vs

Biobb_vs is the Biobb module collection to perform virtual screening studies.

biobb_wf_pmx_tutorial

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).

biobb_wf_structure_checking

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).

biobb_dna

Biobb_dna is the Biobb module collection to perform analyses and transformations on nucleic acid trajectories and helical parameter data.

biobb_adapters

Biobb_adapters is the Biobb module collection to use the building blocks with several workflow managers.

biobb_cmip

biobb_community_wfs

Repository for all the community BioExcel Building Blocks Workflows

biobb_godmd

biobb_godmd is a BioBB category for the GOdMD tool

biobb_haddock

biobb_haddock is the Biobb module collection to compute information-driven flexible protein-protein docking.

biobb_wf_amber

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.

biobb_wf_cmip

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).

biobb_wf_flexdyn

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).

biobb_wf_flexserv

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).

biobb_wf_ligand_parameterization

This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb).

galaxy-tools-compchem

:mega: Galaxy Tools for Computational Chemistry

utils_biobb