bioweb: molecular modelling group / grupo de modelado molecular

http://www.cbm.csic.es/bioweb

 

Molecular Modelling Group / Grupo de Modelado Molecular.
Centro de Biología Molecular "Severo Ochoa" (CBMSO, CSIC-UAM).


SOFTWARE:

- 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.  [http://dx.doi.org/10.1093/bioinformatics/btv453].

MEPSA DOWNLOAD (freely available, under GPLv3 license):

MEPSA v1.2 (Feb. 2018):
Perl script to convert a path into molecular dynamics restraints (Amber):  [path_to_rst.zip]

DATA SAMPLES (MEPSA user manual):

     ENERGY MAP -TEST- coordinates:  [test_energy_map.zip]
     Geneva-Turin MAP coordinates:  [Geneva_Turin.zip]

New in version 1.2:
- Fixed well sampling for complex surfaces.
- Well sampling now only requires origin and target definition.
- Well sampling now only displays the wells sampled to reach the highest barrier connecting two states.
- New global connectivity analysis mode "MINIMAL": samples connectivity between states until every state is connected to another one.
- Bug-fix(minor): Modifying map with rectangle mode would print X and Y increments on terminal.
- Bug-fix(minor): saving well sampling to .txt files created files with wrong extension (.tx t instead of .txt).



Previous releases: [HERE]


BIOWEB: MOLECULAR MODELLING GROUP
Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM).
http://www.cbm.csic.es/bioweb
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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