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Docker GMX Notebook Automatic Ligand Parameterization tutorial

BioBB Building Blocks

Stable

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 ...

Type: Docker

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.825.1

Created: 22nd Apr 2024 at 11:54

Docker Protein Conformational Transitions calculations tutorial

BioBB Building Blocks

Stable

Protein Conformational Transitions calculations tutorial using BioExcel Building Blocks (biobb) and GOdMD

This tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, 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 ...

Type: Docker

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.824.1

Created: 22nd Apr 2024 at 11:50

Docker Macromolecular Coarse-Grained Flexibility tutorial

BioBB Building Blocks

Stable

Macromolecular Coarse-Grained Flexibility (FlexServ) tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, 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 ...

Type: Docker

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.823.1

Created: 22nd Apr 2024 at 11:45

Docker Protein conformational ensembles generation

BioBB Building Blocks

Stable

Protein Conformational ensembles generation

Workflow included in the ELIXIR 3D-Bioinfo Implementation Study:

Building on PDBe-KB to chart and characterize the conformation landscape of native proteins

This tutorial aims to illustrate the process of generating protein conformational ensembles from** 3D structures **and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb).

...

Type: Docker

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.822.1

Created: 22nd Apr 2024 at 11:40

Docker Structural DNA helical parameters tutorial

BioBB Building Blocks

Stable

Structural DNA helical parameters from MD trajectory tutorial using BioExcel Building Blocks (biobb)

Based on the NAFlex server and in particular in its Nucleic Acids Analysis section.

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 ...

Type: Docker

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.821.1

Created: 22nd Apr 2024 at 11:34

Docker Classical Molecular Interaction Potentials

BioBB Building Blocks

Stable

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), ...

Type: Docker

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.820.1

Created: 22nd Apr 2024 at 11:28

Docker Amber Protein MD Setup tutorial

BioBB Building Blocks

Stable

AMBER Protein MD Setup tutorials 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) wrapping the Ambertools MD package.