Iñigo Marcos-Alcalde1, Javier Setoain2, Jesús I Mendieta-Moreno3, Jesús Mendieta4, Paulino Gómez-Puertas1. 1. Molecular Modelling Group, CBMSO (CSIC-UAM), ES-28049 Madrid, Spain. 2. Departamento de Arquitectura de Computadores y Automática, UCM, ES-28040 Madrid, Spain. 3. Molecular Modelling Group, CBMSO (CSIC-UAM), ES-28049 Madrid, Spain, Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), UAM and. 4. Molecular Modelling Group, CBMSO (CSIC-UAM), ES-28049 Madrid, Spain, Biomol-Informatics SL, Campus UAM, ES-28049 Madrid, Spain.
Abstract
UNLABELLED: From conformational studies to atomistic descriptions of enzymatic reactions, potential and free energy landscapes can be used to describe biomolecular systems in detail. However, extracting the relevant data of complex 3D energy surfaces can sometimes be laborious. In this article, we present MEPSA (Minimum Energy Path Surface Analysis), a cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective. Some of its most relevant features are: identification of all the barriers and minima of the landscape at once, description of maxima edge profiles, detection of the lowest energy path connecting two minima and generation of transition state theory diagrams along these paths. In addition to a built-in plotting system, MEPSA can save most of the generated data into easily parseable text files, allowing more versatile uses of MEPSA's output such as the generation of molecular dynamics restraints from a calculated path. AVAILABILITY AND IMPLEMENTATION: MEPSA is freely available (under GPLv3 license) at: http://bioweb.cbm.uam.es/software/MEPSA/ CONTACT: pagomez@cbm.csic.es. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
UNLABELLED: From conformational studies to atomistic descriptions of enzymatic reactions, potential and free energy landscapes can be used to describe biomolecular systems in detail. However, extracting the relevant data of complex 3D energy surfaces can sometimes be laborious. In this article, we present MEPSA (Minimum Energy Path Surface Analysis), a cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective. Some of its most relevant features are: identification of all the barriers and minima of the landscape at once, description of maxima edge profiles, detection of the lowest energy path connecting two minima and generation of transition state theory diagrams along these paths. In addition to a built-in plotting system, MEPSA can save most of the generated data into easily parseable text files, allowing more versatile uses of MEPSA's output such as the generation of molecular dynamics restraints from a calculated path. AVAILABILITY AND IMPLEMENTATION: MEPSA is freely available (under GPLv3 license) at: http://bioweb.cbm.uam.es/software/MEPSA/ CONTACT: pagomez@cbm.csic.es. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Rory M Crean; Michal Biler; Marc W van der Kamp; Alvan C Hengge; Shina C L Kamerlin Journal: J Am Chem Soc Date: 2021-03-04 Impact factor: 15.419
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