Memprot.GPCR-ModSim: modelling and simulation of membrane proteins in a nutshell.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 39504465.
- Also identified by DOI 10.1093/bioinformatics/btae662 and PMC identifier 11578594.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Memprot.GPCR-ModSim leverages our previous web-based protocol, which was limited to class-A G protein-coupled receptors, to become the first one-stop web server for the modelling and simulation of any membrane protein system. Motivated by the exponential growth of experimental structures and the breakthrough of deep-learning-based structural modelling, the server accepts as input either a membrane-protein sequence, in which case it reports the associated AlphaFold model, or a 3D (experimental, modelled) structure, including quaternary complexes with associated proteins and/or ligands of any kind. In both cases, the molecular dynamics (MD) protocol produces a membrane-embedded, solvated, and equilibrated system, ready to be used as a starting point for further MD simulations, including ligand-binding free energy calculations. Memprot.GPCR-ModSim web server is publicly available at https://memprot.gpcr-modsim.org/. The standalone modules for 3D modelling (PyModSim) or membrane embedding and MD equilibration (PyMemDyn) are available under CC BY-NC 4.0 license terms at the GitHub repository https://github.com/GPCR-ModSim/.
Medical subject headings
- Molecular Dynamics Simulation
- Software
- Membrane Proteins
- Receptors, G-Protein-Coupled