BioExcel Building Blocks tutorials: ABC MD Setup

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).

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).

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).

SQUARNA is a tool for RNA secondary structure prediction. It can take a single RNA sequence or an alignment of sequences as input. SQUARNA handles pseudoknots and can predict alternative structures. SQUARNA allows structural restraints and chemical probing data as additional input and is available at https://github.com/febos/SQUARNA and https://larnal.imol.institute/.

Converts Protein Data Bank structures into 3D-printable models. Each polymer chain is meshed separately and written as a named object in a single 3MF file, so a multi-material printer can assign one filament per chain. Protein chains can be rendered as a solvent-excluded surface, a cartoon, or a backbone tube; nucleic acids as a tube-and-rung form with the strands of a duplex welded at every base pair. Press-fit magnet pockets are optionally placed at chain interfaces, so a complex comes apart where its subunits actually meet. All meshes are checked for watertightness before export.

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).