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Python Amber Protein Ligand Complex MD Setup tutorial
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.

Copyright & Licensing

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

Type: Python

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.284.3

Jupyter Notebook Amber Protein Ligand Complex MD Setup tutorial
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.

Copyright & Licensing

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

Type: Jupyter

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.131.5

Python Amber Protein MD Setup tutorial
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.

Copyright & Licensing

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

Type: Python

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.283.3

Python Protein-ligand Docking tutorial (Fpocket)
Stable

Protein-ligand Docking tutorials using BioExcel Building Blocks (biobb)

This tutorials aim to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). The particular examples used are based on the Mitogen-activated protein kinase 14 (p38-α) protein (PDB code 3HEC), a well-known Protein Kinase enzyme, in complex with the FDA-approved Imatinib (PDB Ligand code ...

Type: Python

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.282.3

Jupyter Notebook Protein-ligand Docking tutorial (Fpocket)
Stable

Protein-ligand Docking tutorials using BioExcel Building Blocks (biobb)

This tutorials aim to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). The particular examples used are based on the Mitogen-activated protein kinase 14 (p38-α) protein (PDB code 3HEC), a well-known Protein Kinase enzyme, in complex with the FDA-approved Imatinib (PDB Ligand code ...

Type: Jupyter

Creators: Douglas Lowe, Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.129.5

Jupyter Notebook Protein-ligand Docking tutorial (PDBe REST API)
Stable

Protein-ligand Docking tutorials using BioExcel Building Blocks (biobb)

This tutorials aim to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). The particular examples used are based on the Mitogen-activated protein kinase 14 (p38-α) protein (PDB code 3HEC), a well-known Protein Kinase enzyme, in complex with the FDA-approved Imatinib (PDB Ligand code ...

Type: Jupyter

Creators: Adam Hospital, Douglas Lowe, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.128.5

Jupyter Notebook Protein-ligand Docking tutorial (Cluster90)
Stable

Protein-ligand Docking tutorials using BioExcel Building Blocks (biobb)

This tutorials aim to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). The particular examples used are based on the Mitogen-activated protein kinase 14 (p38-α) protein (PDB code 3HEC), a well-known Protein Kinase enzyme, in complex with the FDA-approved Imatinib (PDB Ligand code ...

Type: Jupyter

Creators: Douglas Lowe, Genís Bayarri, Adam Hospital

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.127.6

Python Protein Ligand Complex MD Setup tutorial
Stable

Protein Ligand Complex 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 in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the ...

Type: Python

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.281.3

Jupyter Notebook Protein Ligand Complex MD Setup tutorial
Stable

Protein Ligand Complex 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 in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the ...

Type: Jupyter

Creators: Genís Bayarri, Adam Hospital

Submitters: Douglas Lowe, Genís Bayarri

DOI: 10.48546/workflowhub.workflow.56.7

Python GMX Automatic Ligand Parameterization tutorial
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: Python

Creators: Adam Hospital, Genís Bayarri

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.280.4

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