Treffer: MLLPA: A Machine Learning-assisted Python module to study phase-specific events in lipid membranes

Title:
MLLPA: A Machine Learning-assisted Python module to study phase-specific events in lipid membranes
Authors:
Walter, Vivien, Ruscher, Céline, Benzerara, Olivier, Thalmann, Fabrice
Contributors:
King‘s College London, Institut Charles Sadron (ICS), Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie - CNRS Chimie (INC-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie - CNRS Chimie (INC-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)
Source:
Journal of Computational Chemistry, 2021, ⟨10.1002/jcc.26508⟩
Publisher Information:
CCSD; Wiley, 2021.
Publication Year:
2021
Collection:
collection:INSERM
collection:CNRS
collection:UNIV-STRASBG
collection:INSA-STRASBOURG
collection:INC-CNRS
collection:SITE-ALSACE
collection:INSA-GROUPE
collection:TEST2-HALCNRS
collection:ICS-MCUBE
collection:UNIVOAK
Subject Terms:
Lipid membrane analysis, Molecular dynamics, Phase transition, Tessellation, Machine Learning, [PHYS.COND.CM-SCM]Physics [physics], Condensed Matter [cond-mat], Soft Condensed Matter [cond-mat.soft]
Original Identifier:
PUBMED: 33675541
HAL: hal-03597389
Document Type:
Zeitschrift article<br />Journal articles
Language:
English
ISSN:
0192-8651
1096-987X
Relation:
info:eu-repo/semantics/altIdentifier/doi/10.1002/jcc.26508; info:eu-repo/semantics/altIdentifier/pmid/33675541
DOI:
10.1002/jcc.26508
Access URL:
https://hal.science/hal-03597389
https://hal.science/hal-03597389v1/document
https://hal.science/hal-03597389v1/file/Walter_MLLPA.pdf
Rights:
info:eu-repo/semantics/OpenAccess
Accession Number:
edshal.hal.03597389v1
Database:
HAL

Weitere Informationen

MLLPA is a new Python 3 module developed to analyse phase domains in a lipid membrane based on lipid molecular states. Reading standard simulation coordinate and trajectory files, the software first analyse the phase composition of the lipid membrane by using Machine Learning tools to label each individual molecules with respect to their state, and then decompose the simulation box using Voronoi tessellations to analyse the local environment of all the molecules of interest. MLLPA is versatile as it can read from multiple format (e.g. GROMACS, LAMMPS) and from either all-atom (e.g. CHARMM36) or coarse-grain models (e.g. Martini). It can also analyse multiple geometries of membranes (e.g. bilayers, vesicles). Finally, the software allows for training with more than two phases, allowing for multiple phase coexistence analysis.