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 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 de-formation. 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 fluc-tuations, 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 de-formations by computing angles, perimeter, area, volume, beta-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 doc-umentation are available under the GNU general public license at http://wordom.sf.net.(c) 2023 Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/ licenses/by-nc-nd/4.0/).

Automated summary

This article presents the second update of Wordom, a program for manipulation and analysis of conformational ensembles from molecular simulations. The update expands existing modules and adds 21 new modules, which can be grouped into three sets analyzing atomic fluctuations and communication, ion-channel dynamics, and structural deformation. The updates enhance Wordom's suitability, completeness, user-friendliness, and efficiency for biomolecular simulation analysis.