bioexcel

biobb_amber

Biobb_amber is a BioBB category for AMBER MD package.

biobb_md

Biobb_md is the Biobb module collection to perform molecular dynamics simulations.

biobb_chemistry

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

biobb_analysis

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

biobb_gromacs

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_template

Biobb_template is a complete code template to promote and facilitate the creation of new Biobbs by the community.

biobb_workflows

Global repository for all the BioExcel Building Blocks Workflows

biobb_cp2k

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_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_pytorch

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

biobb_vs

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

biobb_wf_dna_helparms

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).

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_common

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

biobb_documentation

Documentation for the creation of a new BioExcel building block from scratch.

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_pdb_tools

biobb_wf_autoencoder

utils_biobb