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eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).ORCID iD: 0000-0003-1927-555X
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Number of Authors: 52019 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 35, no 18, p. 3505-3507Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2019. Vol. 35, no 18, p. 3505-3507
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Biological Sciences
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URN: urn:nbn:se:su:diva-175085DOI: 10.1093/bioinformatics/btz104ISI: 000487327500044PubMedID: 30838394OAI: oai:DiVA.org:su-175085DiVA, id: diva2:1364840
Available from: 2019-10-22 Created: 2019-10-22 Last updated: 2019-12-09Bibliographically approved

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Orellana, LauraLindahl, Erik
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