bioweb: molecular modelling group / grupo de modelado molecular

[ http://www.cbm.csic.es/bioweb ]  [ http://bioweb.cbm.uam.es ]

 


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]  [https://doi.org/10.1093/bioinformatics/btz649]


MEPSAnd DOWNLOAD (freely available, under GPLv3 license):

MEPSAnd v1.6 (Mar. 2022):
    MEPSAnd v1.6 source code:  [MEPSAnd_v1.6.zip]

    MEPSAnd v1.6 user manual (42.5 MB):  [MEPSAnd_manual_v1.6.zip]

    DATA SAMPLES (MEPSAnd user manual):  [examples.zip]

    New in version 1.6:
    - New "Assume grid" connectivity prediction mode that significantly accelerates the neighboring calculations for homogeneously distributed datasets (the most common use case).
    - Fixed subtle bug with global node ids annotation that could produce an error when selecting non-minimum origin or target points and could block network plots from working with networks containing disconnected regions.
    - Added a check for the existence of disconnected regions that reports a warning message.
    - Added a check for coordinate redundancy to prevent the use of artefactual surfaces.
    - Thanks to Dr. Marcelo D. Polęto's feedback, an automatic data type reduction function to reduce memory usage was implemented.
    - Thanks to Dr. Marcelo D. Polęto's feedback, the connectivity calculations were rewritten to reduce memory usage.
    - Changed the way fragmentwise path is saved to avoid extensive memory use when extremely complex paths are calculated.
    - Major overhaul of the "Energy profiles" and "Coordinate projections" point labeling logic. Now only minimum or barrier points are labeled, indicating the cluster number to which they belong.
    - Made it possible to plot "Coordinate projections" without choosing any point.
    - MEPSAnd no longer requires igraph, ForceAtlas2 or cairo to run. If any of these packages is not detected, "Network projections" will be disabled but everything else will work as usual.
    - Replaced "dype=np.int" instances with "dtype=np.int_".
    - Added terminal report messages indicating the number of neighbors found as a quick sanity check for connectivity calculations.
    - Added terminal report messages indicating minima propagation progress.
    - Removed instances of fig.gca(projection='3d') as it is deprecated matplotlib.
    - Instances of "map_" in the source code have been replaced with "surface_" to unify terminology.
    - Fixed well sampling calculations not identifying origin or target clusters correctly.
    - Minor code cleaning.
    - A "Good practices" section has been added to the manual, with a particular focus on metadynamics, based on Dr. Marcelo D. Polęto's reports.

FORMER VERSIONS (no longer supported):

MEPSAnd v1.41 (Jul. 2020):
    MEPSAnd v1.41 source code:  [MEPSAnd_v1.41.zip]

    MEPSAnd v1.41 user manual (higher resolution -43 MB- ):  [MEPSAnd_manual_v1.41_l.zip]
    MEPSAnd v1.41 user manual (lower resolution -3 MB- ):  [MEPSAnd_manual_v1.41_s.zip]

    DATA SAMPLES (MEPSAnd user manual):  [examples.zip]

    New in version 1.41:
    - Added the correct citation reference to MEPSAnd.py, replacing the previous "XXXX..." placeholder.
    - Updated the citation reference in the manual, as the paper is no longer "in press".

MEPSAnd v1.4 (Nov. 2019):
    MEPSAnd v1.4 source code:  [MEPSAnd_v1.4.zip]

    MEPSAnd v1.4 user manual:  [MEPSAnd_manual_v1.4.zip]

    New in version 1.4:
    - Number formatting in "save_simplified_path_to_txt" method has been modified to improve the readability of the resulting files.
MEPSAnd v1.35 (Nov. 2019):
    MEPSAnd v1.35 source code:  [MEPSAnd_v1.35.zip]

    New in version 1.35:
    - BUGFIX: a bug introduced during network projection rewriting in 1.3 broke the ability to properly assign default plotting parameters in "barriers as vertices" graphs.
MEPSAnd v1.3 (Nov. 2019):
    MEPSAnd v1.3 source code:  [MEPSAnd_v1.3.zip]

    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 (Oct. 2019):
    MEPSAnd v1.2 source code:  [MEPSAnd_v1.2.zip]

    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 the terminal when it is launched to improve version readability.
MEPSAnd v1.1 (Sep. 2019):
    MEPSAnd v1.1 source code:  [MEPSAnd_v1.1.zip]

    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.
MEPSAnd v1.0 (Aug. 2019):



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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