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., Lopez-Viñas, E. & Gómez-Puertas, P. (2020). MEPSAnd: Minimum Energy Path Surface Analysis over n-dimensional surfaces. Bioinformatics 36, 956–958. [Free-access article link] [http://dx.doi.org/10.1093/bioinformatics/btz649]
MEPSAnd DOWNLOAD (freely available, under GPLv3 license):
MEPSAnd v1.4 (Nov. 2019):
MEPSAnd v1.4 source code: [MEPSAnd_v1.4.zip]
FORMER VERSIONS (no longer supported):
MEPSAnd v1.4 user manual: [MEPSAnd_manual_v1.4.zip]
DATA SAMPLES (MEPSAnd user manual): [examples.zip]
New in version 1.4:
-Number formatting in "save_simplified_path_to_txt" method has been modfied to improve readability of the resulting files.
MEPSAnd v1.35 (Nov. 2019):
MEPSAnd v1.35 source code: [MEPSAnd_v1.35.zip]
MEPSAnd v1.3 (Nov. 2019):
New in version 1.35:
-BUGFIX: a bug introduced during network projection rewritting in 1.3 broke the ability to properly assing default plotting parameters in "barriers as vertices" graphs.
MEPSAnd v1.3 source code: [MEPSAnd_v1.3.zip]
MEPSAnd v1.2 (Oct. 2019):
New in version 1.3:
-Major fix: network projection edge selection was not working as intended and has been completely rewritten.
-Minor bugfixes to the GUI.
-Minor code cleaning.
MEPSAnd v1.2 source code: [MEPSAnd_v1.2.zip]
MEPSAnd v1.1 (Sep. 2019):
New in version 1.2:
- BUGFIX: As reported by Oriol Esquivias, the method to save minimum and barrier clusters was broken when clusters of more than one point were present. Fixed using an index array ("index_array") with the adequate shape in the "np.column_stack" calls of the "save_minbar_clusters_to_txt" method.
- Changed how the MEPSAnd version is printed on terminal when it is launched to improve version readability.
MEPSAnd v1.1 source code: [MEPSAnd_v1.1.zip]
MEPSAnd v1.0 (Aug. 2019):
New in version 1.1:
- BUGFIX: As reported by Oriol Esquivias, instances of pandas compat.StringIO could lead to incompatibility issues with pandas 0.25.1.
Thus, all instances of pd.compat.StringIO have been replaced with io.StringIO.
BIOWEB: MOLECULAR MODELLING GROUP |
Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM).
C/ Nicolás Cabrera, 1. Campus UAM, Cantoblanco. |
28049 Madrid. Spain
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