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_common Base package required to use the biobb library.
biobb_io Collection to fetch data from biological databases.
biobb_md Collection to perform Molecular Dynamics simulations.
biobb_analysis Collection to perform analysis over MD simulations.
biobb_pmx Collection to perform free energy calculations.
biobb_structure_utils Collection to modify or extract information from a PDB structure file.
biobb_chemistry Collection to perform cheminformatics analyses and format conversions.
biobb_model Collection to check and model 3D structures.
biobb_ml Collection to perform machine learning predictions.
biobb_vs Collection to perform virtual screening studies.
biobb_amber Category for AMBER MD package.
biobb_common

biobb_common: base package required to use the biobb library

The biobb_common module contains functionalities used by the whole collection of building blocks. Examples of these functionalities include the command-line execution of the wrapped tool, managing of log files, creation and removing of temporary folders required for an execution, zipping/unzipping compressed files, unit testing auxiliary functions, etc.

biobb_io

biobb_io: collection to fetch data from biological databases

The biobb_io module contains operations to retrieve relevant information from biological databases, typically using REST API services to retrieve the data. Examples of these operations are downloading of PDB structures, a list of mutations (variants) mapped to a PDB code, and a list of PDB files contained in a particular cluster of a certain sequence similarity with a give structure.

biobb_md

biobb_md: collection to perform Molecular Dynamics simulations

The biobb_md module is one of the central modules of the library. It contains operations related to MD simulations, mainly using the GROMACS MD package. Examples of these operations are setup processes (solvation, energy minimization, system equilibration), simulation runs and free energy calculations. Predefined configuration files are given for the most standard simulation processes (e.g. minimization, NVT, NPT).

biobb_analysis

biobb_analysis: collection to perform analysis over MD simulations

The biobb_analysis module contains methods to analyse MD trajectories, including tools wrapped from the analysis set available in the GROMACS MD package and building blocks build using the Ambertools Cpptraj program. Examples of these operations are trajectory imaging, format conversion, RMSd, Rgyr, atomic fluctuation, etc.

biobb_pmx

biobb_pmx: collection to perform free energy calculations

The biobb_pmx module wraps the tools included in the pmx package to generate hybrid protein structures and topologies to compute free energy calculations with them. These operations are Mutate, to insert mutated residues in structures, GenTop, to generate hybrid GROMACS topologies, and Analyse, to calculate free energies from fast growth thermodynamic integration simulations.

biobb_structure_utils

biobb_structure_utils: collection to modify or extract information from a PDB structure file

The biobb_structure_utils module contains a collection of useful methods to work with PDB files, modifying or extracting information from them. Examples of these operations are extract ligand, chain, atoms, etc. from a PDB file, renumber a structure or cat two PDB files.

biobb_chemistry

biobb_chemistry: collection to perform cheminformatics analyses and format conversions

The biobb_chemistry module contains a set of cheminformatics methods to work with small molecules, of particular interest in pharmaceutical studies. Examples of these operations are adding/removing protons, minimizing energy, or obtaining force-field parameters. Format conversion between a large number of molecular formats is also included, thanks to the wrapped OpenBabel Chemistry Toolbox.

biobb_model

biobb_model: collection to check and model 3D structures

The biobb_model module contains a couple of useful molecular modeling tools: FixSideChain, to automatically add missing side chain atoms to a protein or nucleic acid structure, and Mutate, to introduce a residue mutation in a protein structure.

biobb_ml

biobb_ml: collection to perform machine learning predictions

The biobb_ml module contains a set of machine learning tools to implement several algorithms such as clustering, classification, dimensionality reduction or regression. The software libraries wrapped in this package are Scikit Learn and TensorFlow.

biobb_vs

biobb_vs: collection to perform virtual screening studies

The biobb_vs module contains a set of virtual screening tools such as autodock vina or fpocket as well as some in house tools for calculating boxes or binding sites.

biobb_amber

biobb_amber: category for AMBER MD package

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