Molecular Modeling Group / Grupo de Modelado Molecular.
Centro de Biología Molecular Severo Ochoa (CBM, CSIC-UAM).
SOFTWARE:
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- 2019-2022. MEPSAnd: Minimum Energy Path Surface Analysis over n-dimensional surfaces.
n-dimensional energy surfaces are becoming computationally accessible, yet interpreting their information is not straightforward. We present MEPSAnd, an open source GUI-based program that natively calculates minimum energy paths across energy surfaces of any number of dimensions. Among other features, MEPSAnd can compute the path through lowest barriers and automatically provide a set of alternative paths. MEPSAnd offers distinct plotting solutions as well as direct python scripting.
Availability and implementation: MEPSAnd is freely available (under GPLv3 license) at this page: [http://bioweb.cbm.uam.es/software/MEPSAnd/]
CITATION: Marcos-Alcalde, I., L-V, E. & Gómez-Puertas, P. (2020). MEPSAnd: Minimum Energy Path Surface Analysis over n-dimensional surfaces. Bioinformatics 36, 956–958. [https://doi.org/10.1093/bioinformatics/btz649]
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- 2015-2019. MEPSA: Minimum Energy Pathway Analysis for energy landscapes.
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. Here 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 this page: [http://bioweb.cbm.uam.es/software/MEPSA/]
CITATION: Marcos-Alcalde, I., Setoain, J., Mendieta-Moreno, J.I., Mendieta, J. & Gómez-Puertas, P. (2015). MEPSA: minimum energy pathway analysis for energy landscapes. Bioinformatics 31, 3853-3855. [https://doi.org/10.1093/bioinformatics/btv453].
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BIOWEB: MOLECULAR MODELING GROUP
Centro de Biología Molecular Severo Ochoa
(CBM, CSIC-UAM)
http://bioweb.cbm.uam.es |
C/ Nicolás Cabrera, 1. Campus UAM, Cantoblanco
28049 Madrid. Spain
Tel: (+34) 91 196 4662 / 4663
Fax: (+34) 91 196 4420
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