BioExcel Building Blocks modules

Modules

The BioExcel Building Blocks are divided in categories (biobb modules) depending on their functionalities and tools wrapped. Every module is available from an independent GitHub repository and has an associated BioConda package, Docker/Singularity container and readthedocs documentation pages.

The collection of building blocks and modules is growing. Examples of available modules are:

Module Description Go to block
biobb_amber biobb_amber is a BioBB category for AMBER MD package, allowing setup and simulation of atomistic MD simulations using AMBER MD package and its associated AMBER tools
biobb_analysis Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations
biobb_chemistry Biobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations.
biobb_cmip Biobb_cmip is the Biobb module collection to compute classical molecular interaction potentials.
biobb_common Biobb_common is the base package required to use the biobb packages.
biobb_cp2k Biobb_cp2k is a BioBB category for CP2K QM package, allowing setup and simulation of QM simulations using CP2K QM package.
biobb_dna Biobb_dna is a package composed of different analyses for nucleic acid trajectories.
biobb_gromacs Biobb_gromacs is the Biobb module collection to perform molecular dynamics simulations using the GROMACS MD suite.
biobb_io Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.
biobb_md Biobb_md is the Biobb module collection to perform molecular dynamics simulations. IMPORTANT: This package has been discontinued, superseeded by biobb_gromacs.
biobb_ml Biobb_ml is the Biobb module collection to perform machine learning predictions.
biobb_model Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms
biobb_pmx Biobb_pmx is the Biobb module collection to perform PMX executions.
biobb_structure_utils Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file.
biobb_vs Biobb_vs is the Biobb module collection to perform virtual screening studies.
biobb_amber

biobb_amber

biobb_amber is a BioBB category for AMBER MD package, allowing setup and simulation of atomistic MD simulations using AMBER MD package and its associated AMBER tools

Go to biobb_amber repository
biobb_analysis

biobb_analysis

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

Go to biobb_analysis repository
biobb_chemistry

biobb_chemistry

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

Go to biobb_chemistry repository
biobb_cmip

biobb_cmip

Biobb_cmip is the Biobb module collection to compute classical molecular interaction potentials.

Go to biobb_cmip repository
biobb_common

biobb_common

Biobb_common is the base package required to use the biobb packages.

Go to biobb_common repository
biobb_cp2k

biobb_cp2k

Biobb_cp2k is a BioBB category for CP2K QM package, allowing setup and simulation of QM simulations using CP2K QM package.

Go to biobb_cp2k repository
biobb_dna

biobb_dna

Biobb_dna is a package composed of different analyses for nucleic acid trajectories.

Go to biobb_dna repository
biobb_gromacs

biobb_gromacs

Biobb_gromacs is the Biobb module collection to perform molecular dynamics simulations using the GROMACS MD suite.

Go to biobb_gromacs repository
biobb_io

biobb_io

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

Go to biobb_io repository
biobb_md

biobb_md

Biobb_md is the Biobb module collection to perform molecular dynamics simulations. IMPORTANT: This package has been discontinued, superseeded by biobb_gromacs.

Go to biobb_md repository
biobb_ml

biobb_ml

Biobb_ml is the Biobb module collection to perform machine learning predictions.

Go to biobb_ml repository
biobb_model

biobb_model

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

Go to biobb_model repository
biobb_pmx

biobb_pmx

Biobb_pmx is the Biobb module collection to perform PMX executions.

Go to biobb_pmx repository
biobb_structure_utils

biobb_structure_utils

Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file.

Go to biobb_structure_utils repository
biobb_vs

biobb_vs

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

Go to biobb_vs repository