BioExcel Building Blocks workflows

Protein MD Setup
2020.4

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).

Jupyter Notebook

Execute in binder * View tutorial Open Github repository Open documentation

(*) Binder for biobb is a small installation and to promote fair use of our resources, one user is allowed to run only one notebook server at a time. Launching a new notebook server should stop the previous one. Users cannot see the notebooks run by other users, but please avoid entering secret data to the notebooks.
Automatic Ligand parameterization
2020.4

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 Ibuprofen small compound (3-letter code IBP, Drugbank code DB01050), a non-steroidal anti-inflammatory drug (NSAID) derived from propionic acid and it is considered the first of the propionics.

Jupyter Notebook

Execute in binder * View tutorial Open Github repository Open documentation

(*) Binder for biobb is a small installation and to promote fair use of our resources, one user is allowed to run only one notebook server at a time. Launching a new notebook server should stop the previous one. Users cannot see the notebooks run by other users, but please avoid entering secret data to the notebooks.
Protein-Complex MD Setup
2020.4

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 2-propylphenol small molecule (3-letter Code JZ4).

Jupyter Notebook

Execute in binder * View tutorial Open Github repository Open documentation

(*) Binder for biobb is a small installation and to promote fair use of our resources, one user is allowed to run only one notebook server at a time. Launching a new notebook server should stop the previous one. Users cannot see the notebooks run by other users, but please avoid entering secret data to the notebooks.
Mutation Free Energy Calculations
2020.4

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). The particular example used is the Staphylococcal nuclease protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial.

Jupyter Notebook

Execute in binder * View tutorial Open Github repository Open documentation

(*) Binder for biobb is a small installation and to promote fair use of our resources, one user is allowed to run only one notebook server at a time. Launching a new notebook server should stop the previous one. Users cannot see the notebooks run by other users, but please avoid entering secret data to the notebooks.
Protein-ligand Docking (Binding Site)
2021.2

This tutorial aims to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is 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 STI, DrugBank Ligand Code DB00619), a small molecule kinase inhibitor used to treat certain types of cancer.

Execute in binder * View tutorial Open Github repository Open documentation

(*) Binder for biobb is a small installation and to promote fair use of our resources, one user is allowed to run only one notebook server at a time. Launching a new notebook server should stop the previous one. Users cannot see the notebooks run by other users, but please avoid entering secret data to the notebooks.
Protein-ligand Docking (PDBe REST-API)
2021.2

This tutorial aims to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Mitogen-activated protein kinase 14 (p38-α) protein (PDB code 3LFA), a well-known Protein Kinase enzyme, in complex with the FDA-approved Dasatinib, (PDB Ligand code 1N1, DrugBank Ligand Code DB01254), a small molecule kinase inhibitor used for the treatment of lymphoblastic or chronic myeloid leukemia with resistance or intolerance to prior therapy.

Execute in binder * View tutorial Open Github repository Open documentation

(*) Binder for biobb is a small installation and to promote fair use of our resources, one user is allowed to run only one notebook server at a time. Launching a new notebook server should stop the previous one. Users cannot see the notebooks run by other users, but please avoid entering secret data to the notebooks.
Protein-ligand Docking (fpocket)
2021.2

This tutorial aims to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is 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 STI, DrugBank Ligand Code DB00619), a small molecule kinase inhibitor used to treat certain types of cancer.

Execute in binder * View tutorial Open Github repository Open documentation

(*) Binder for biobb is a small installation and to promote fair use of our resources, one user is allowed to run only one notebook server at a time. Launching a new notebook server should stop the previous one. Users cannot see the notebooks run by other users, but please avoid entering secret data to the notebooks.