The BioExcel Building Blocks (biobb) software library is a collection of Python wrappers on top of popular biomolecular simulation tools. This library offers a layer of interoperability between the wrapped tools, which make them compatible and prepared to be directly interconnected to build complex biomolecular workflows. The building blocks can be used in many different workflow systems, including Galaxy, CWL, Jupyter Notebook and PyCOMPSs – notably their ...

Presented at the BioExcel Summer School 2021 this lecture introduces the BioExcel Building Blocks (BioBB).

See also part 2.

Presented at the BioExcel Summer School 2021 this lecture shows how to use BioExcel Building Blocks (BioBB).

See also part 1.

In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields ...

CMIP tutorial using BioExcel Building Blocks (biobb)

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). Examples shown are Molecular Interaction Potentials (MIPs) grids, protein-protein/ligand interaction potentials, and protein titration. The particular structures used are the Lysozyme protein (PDB code 1AKI), ...

CMIP tutorial using BioExcel Building Blocks (biobb)

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). Examples shown are Molecular Interaction Potentials (MIPs) grids, protein-protein/ligand interaction potentials, and protein titration. The particular structures used are the Lysozyme protein (PDB code 1AKI), ...

Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Sulfasalazine protein (3-letter code SAS), used to treat rheumatoid arthritis, ulcerative colitis, and Crohn's disease.

OpenBabel and ACPype packages are used to **add hydrogens, energetically ...

Protein-Membrane MD analysis tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of analyzing a membrane molecular dynamics (MD) simulation using the BioExcel Building Blocks library (biobb). The particular example used is the heteropentameric ligand-gated chloride channel gated by gamma-aminobutyric acid (GABA), a major inhibitory neurotransmitter in the brain, which was embedded in a DPPC membrane in the ...

Protein-Membrane MD analysis tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of analyzing a membrane molecular dynamics (MD) simulation using the BioExcel Building Blocks library (biobb). The particular example used is the heteropentameric ligand-gated chloride channel gated by gamma-aminobutyric acid (GABA), a major inhibitory neurotransmitter in the brain, which was embedded in a DPPC membrane in the ...

Protein-Membrane MD analysis tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of analyzing a membrane molecular dynamics (MD) simulation using the BioExcel Building Blocks library (biobb). The particular example used is the heteropentameric ligand-gated chloride channel gated by gamma-aminobutyric acid (GABA), a major inhibitory neurotransmitter in the brain, which was embedded in a DPPC membrane in the ...

Protein-Membrane MD analysis tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of analyzing a membrane molecular dynamics (MD) simulation using the BioExcel Building Blocks library (biobb). The particular example used is the heteropentameric ligand-gated chloride channel gated by gamma-aminobutyric acid (GABA), a major inhibitory neurotransmitter in the brain, which was embedded in a DPPC membrane in the ...

Protein-Membrane MD analysis tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of analyzing a membrane molecular dynamics (MD) simulation using the BioExcel Building Blocks library (biobb). The particular example used is the heteropentameric ligand-gated chloride channel gated by gamma-aminobutyric acid (GABA), a major inhibitory neurotransmitter in the brain, which was embedded in a DPPC membrane in the ...

AutoEncoders for Anomaly Detection tutorial using BioExcel Building Blocks (biobb)

This tutorial involves the use of a multilayer AutoEncoder (AE) for feature extraction and pattern recognition by analyzing Molecular Dynamic Simulations, step by step, using the BioExcel Building Blocks library (biobb).

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB ...

AutoEncoders for Anomaly Detection tutorial using BioExcel Building Blocks (biobb)

This tutorial involves the use of a multilayer AutoEncoder (AE) for feature extraction and pattern recognition by analyzing Molecular Dynamic Simulations, step by step, using the BioExcel Building Blocks library (biobb).

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB ...

AutoEncoders for Anomaly Detection tutorial using BioExcel Building Blocks (biobb)

This tutorial involves the use of a multilayer AutoEncoder (AE) for feature extraction and pattern recognition by analyzing Molecular Dynamic Simulations, step by step, using the BioExcel Building Blocks library (biobb).

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB ...

AutoEncoders for Anomaly Detection tutorial using BioExcel Building Blocks (biobb)

This tutorial involves the use of a multilayer AutoEncoder (AE) for feature extraction and pattern recognition by analyzing Molecular Dynamic Simulations, step by step, using the BioExcel Building Blocks library (biobb).

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB ...

AutoEncoders for Anomaly Detection tutorial using BioExcel Building Blocks (biobb)

This tutorial involves the use of a multilayer AutoEncoder (AE) for feature extraction and pattern recognition by analyzing Molecular Dynamic Simulations, step by step, using the BioExcel Building Blocks library (biobb).

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB ...

Mutations Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.

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). The particular example used is the Lysozyme protein (PDB code 1AKI).

Copyright & Licensing

This software has been developed in ...

Protein-protein Docking tutorial using HADDOCK with the BioExcel Building Blocks (biobb)

Based on the official HADDOCK3 Antibody-antigen modelling tutorial.

This tutorial aims to illustrate the process of protein-protein docking, step by step, using HADDOCK3 with the BioExcel Building Blocks library (biobb). The particular systems used in this tutorial are the Interleukin-1β (IL-1β) antigen (PDB ...

Protein-protein Docking tutorial using HADDOCK with the BioExcel Building Blocks (biobb)

Based on the official HADDOCK3 Antibody-antigen modelling tutorial.

This tutorial aims to illustrate the process of protein-protein docking, step by step, using HADDOCK3 with the BioExcel Building Blocks library (biobb). The particular systems used in this tutorial are the Interleukin-1β (IL-1β) antigen (PDB ...

Protein-protein Docking tutorial using HADDOCK with the BioExcel Building Blocks (biobb)

Based on the official HADDOCK3 Antibody-antigen modelling tutorial.

This tutorial aims to illustrate the process of protein-protein docking, step by step, using HADDOCK3 with the BioExcel Building Blocks library (biobb). The particular systems used in this tutorial are the Interleukin-1β (IL-1β) antigen (PDB ...

Protein MD Analysis tutorial using BioExcel Building Blocks (biobb)

This workflow computes a set of Quality Control (QC) analyses on top of an uploaded MD trajectory. QC analyses include positional divergence (RMSd), change of shape (Radius of Gyration), identification of flexible regions (atomic/residue fluctuations), and identification of different molecular conformations (trajectory clustering).

Copyright & Licensing

This software has been developed in the [MMB ...

Protein MD Analysis tutorial using BioExcel Building Blocks (biobb)

This workflow computes a set of Quality Control (QC) analyses on top of an uploaded MD trajectory. QC analyses include positional divergence (RMSd), change of shape (Radius of Gyration), identification of flexible regions (atomic/residue fluctuations), and identification of different molecular conformations (trajectory clustering).

Copyright & Licensing

This software has been developed in the [MMB ...

Mutations Protein MD Setup tutorial using BioExcel Building Blocks (biobb)

Based on the official GROMACS tutorial.

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). The particular example used is the Lysozyme protein (PDB code 1AKI).

Copyright & Licensing

This software has been developed in ...

Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation, and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work ...

Selection of BioExcel Building Blocks (BioBB) Workflows, across three workflow languages (jupyter notebooks, CWL, and Galaxy), demonstrating the use of BioBB tool descriptors for each of these systems.