Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles
We present the second update of Wordom, a user-friendly and efficient program for manipulation and analysis of conformational ensembles from molecular simulations. The actual update expands some of the existing modules and adds 21 new modules to the update 1 published in 2011. The new adds can be di...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037023000272 |
| _version_ | 1797384128299008000 |
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| author | Angelo Felline Simone Conti Michele Seeber Marco Cecchini Francesca Fanelli |
| author_facet | Angelo Felline Simone Conti Michele Seeber Marco Cecchini Francesca Fanelli |
| author_sort | Angelo Felline |
| collection | DOAJ |
| description | We present the second update of Wordom, a user-friendly and efficient program for manipulation and analysis of conformational ensembles from molecular simulations. The actual update expands some of the existing modules and adds 21 new modules to the update 1 published in 2011. The new adds can be divided into three sets that: 1) analyze atomic fluctuations and structural communication; 2) explore ion-channel conformational dynamics and ionic translocation; and 3) compute geometrical indices of structural deformation. Set 1 serves to compute correlations of motions, find geometrically stable domains, identify a dynamically invariant core, find changes in domain-domain separation and mutual orientation, perform wavelet analysis of large-scale simulations, process the output of principal component analysis of atomic fluctuations, perform functional mode analysis, infer regions of mechanical rigidity, analyze overall fluctuations, and perform the perturbation response scanning. Set 2 includes modules specific for ion channels, which serve to monitor the pore radius as well as water or ion fluxes, and measure functional collective motions like receptor twisting or tilting angles. Finally, set 3 includes tools to monitor structural deformations by computing angles, perimeter, area, volume, β-sheet curvature, radial distribution function, and center of mass. The ring perception module is also included, helpful to monitor supramolecular self-assemblies. This update places Wordom among the most suitable, complete, user-friendly, and efficient software for the analysis of biomolecular simulations. The source code of Wordom and the relative documentation are available under the GNU general public license at http://wordom.sf.net. |
| first_indexed | 2024-03-08T21:31:01Z |
| format | Article |
| id | doaj.art-4b8bc8328e4d44f39654eb195fb9bd53 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-03-08T21:31:01Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-4b8bc8328e4d44f39654eb195fb9bd532023-12-21T07:30:49ZengElsevierComputational and Structural Biotechnology Journal2001-03702023-01-012113901402Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensemblesAngelo Felline0Simone Conti1Michele Seeber2Marco Cecchini3Francesca Fanelli4Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy; Corresponding authors.Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USADepartment of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy; Corresponding authors.Strasbourg Institute of Chemistry, UMR7177, CNRS, Strasbourg University, F-67083 Strasbourg Cedex, FranceDepartment of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy; Center for Neuroscience and Neurotechnology, via Campi 287, 41125 Modena, Italy; Corresponding author at: Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy.We present the second update of Wordom, a user-friendly and efficient program for manipulation and analysis of conformational ensembles from molecular simulations. The actual update expands some of the existing modules and adds 21 new modules to the update 1 published in 2011. The new adds can be divided into three sets that: 1) analyze atomic fluctuations and structural communication; 2) explore ion-channel conformational dynamics and ionic translocation; and 3) compute geometrical indices of structural deformation. Set 1 serves to compute correlations of motions, find geometrically stable domains, identify a dynamically invariant core, find changes in domain-domain separation and mutual orientation, perform wavelet analysis of large-scale simulations, process the output of principal component analysis of atomic fluctuations, perform functional mode analysis, infer regions of mechanical rigidity, analyze overall fluctuations, and perform the perturbation response scanning. Set 2 includes modules specific for ion channels, which serve to monitor the pore radius as well as water or ion fluxes, and measure functional collective motions like receptor twisting or tilting angles. Finally, set 3 includes tools to monitor structural deformations by computing angles, perimeter, area, volume, β-sheet curvature, radial distribution function, and center of mass. The ring perception module is also included, helpful to monitor supramolecular self-assemblies. This update places Wordom among the most suitable, complete, user-friendly, and efficient software for the analysis of biomolecular simulations. The source code of Wordom and the relative documentation are available under the GNU general public license at http://wordom.sf.net.http://www.sciencedirect.com/science/article/pii/S2001037023000272Molecular simulation analysisMolecular DynamicsStructural communicationIon channel dynamics |
| spellingShingle | Angelo Felline Simone Conti Michele Seeber Marco Cecchini Francesca Fanelli Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles Computational and Structural Biotechnology Journal Molecular simulation analysis Molecular Dynamics Structural communication Ion channel dynamics |
| title | Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles |
| title_full | Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles |
| title_fullStr | Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles |
| title_full_unstemmed | Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles |
| title_short | Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles |
| title_sort | wordom update 2 a user friendly program for the analysis of molecular structures and conformational ensembles |
| topic | Molecular simulation analysis Molecular Dynamics Structural communication Ion channel dynamics |
| url | http://www.sciencedirect.com/science/article/pii/S2001037023000272 |
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