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eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces

2019; Oxford University Press; Volume: 35; Issue: 18 Linguagem: Inglês

10.1093/bioinformatics/btz104

1367-4811

Laura Orellana, Johan Gustavsson, Cathrine Bergh, Özge Yoluk, Erik Lindahl,

Advanced Fluorescence Microscopy Techniques

Abstract Summary Understanding how proteins transition between different conformers, and how conformers relate to each other in terms of structure and function, is not trivial. Here, we present an online tool for transition pathway generation between two protein conformations using Elastic Network Driven Brownian Dynamics Importance Sampling, a coarse-grained simulation algorithm, which spontaneously predicts transition intermediates trapped experimentally. In addition to path-generation, the server provides an interactive 2D-motion landscape graphical representation of the transitions or any additional conformers to explore their structural relationships. Availability and implementation eBDIMS is available online: http://ebdims.biophysics.se/ or as standalone software: https://github.com/laura-orellana/eBDIMS, https://github.com/cabergh/eBDIMS. Supplementary information Supplementary data are available at Bioinformatics online.