BioExcel Building Blocks tutorials: Protein MD Setup (Gromacs Version)

This BioExcel Building Blocks library (BioBB) workflow provides a pipeline to setup DNA structures for the Ascona B-DNA Consortium (ABC) members. It follows the work started with the NAFlex tool to offer a single, reproducible pipeline for structure preparation, ensuring reproducibility and coherence between all the members of the consortium.

This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks (biobb) REST API. The particular example used is the Lysozyme protein (PDB code 1AKI).

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).

Open-source PyMOL plugin for membrane-aware review of predicted, designed and experimental protein structures. Membrane Visual QC provides planar membrane-relative geometry, residue core/interface classification, hydropathy and ligand-context review, solvent-accessibility context, PDBTM/OPM orientation-source checks, and reproducible batch reporting. It is designed as a review assistant rather than a biological structure validator.

This tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation, step by step, using the BioExcel Building Blocks (biobb).

High-performance molecular simulation toolkit