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 all 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_flexdyn	Biobb_flexdyn is the Biobb module collection 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_godmd	Biobb_godmd is the Biobb module collection to compute protein conformational transitions with the GOdMD method.
biobb_gromacs	Biobb_gromacs is the Biobb module collection to perform molecular dynamics simulations using the GROMACS MD suite.
biobb_haddock	biobb_haddock is the Biobb module collection to compute classical molecular interaction potentials.
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_pdb_tools	Biobb PDB Tools is a swiss army knife for manipulating and editing PDB files
biobb_pmx	Biobb_pmx is the Biobb module collection to perform PMX executions
biobb_pytorch	biobb_pytorch is the Biobb module collection to train and create ML & DL models using the popular PyTorch Python library
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 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 is the Biobb module collection to perform analysis of molecular dynamics simulations

Go to biobb_analysis repository

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

Go to biobb_cmip repository

biobb_common

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

Go to biobb_common repository

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 is a package composed of different analyses for nucleic acid trajectories

Go to biobb_dna repository

biobb_flexdyn

Biobb_flexdyn is the Biobb module collection for studies on the conformational landscape of native proteins.

Go to biobb_flexdyn repository

biobb_flexserv

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

Go to biobb_flexserv repository

biobb_godmd

Biobb_godmd is the Biobb module collection to compute protein conformational transitions with the GOdMD method.

Go to biobb_godmd repository

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_haddock

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

Go to biobb_haddock repository

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 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 is the Biobb module collection to perform machine learning predictions.

Go to biobb_ml repository

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_pdb_tools

Biobb PDB Tools is a swiss army knife for manipulating and editing PDB files

Go to biobb_pdb_tools repository

biobb_pmx

Biobb_pmx is the Biobb module collection to perform PMX executions

Go to biobb_pmx repository

biobb_pytorch

biobb_pytorch is the Biobb module collection to train and create ML & DL models using the popular PyTorch Python library

Go to biobb_pytorch repository

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 is the Biobb module collection to perform virtual screening studies.

Go to biobb_vs repository

BioExcel Building Blocks modules