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eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces
Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, S-10691 Stockholm, Sweden..ORCID iD: 0000-0003-1927-555X
KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.ORCID iD: 0000-0001-7540-5887
KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. Univ Maryland, Sch Pharm, Dept Pharmaceut Sci, Baltimore, MD 21201 USA..ORCID iD: 0000-0001-8354-0253
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2019 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 35, no 18, p. 3505-3507Article in journal (Refereed) Published
Abstract [en]

A 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.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS , 2019. Vol. 35, no 18, p. 3505-3507
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:kth:diva-261959DOI: 10.1093/bioinformatics/btz104ISI: 000487327500044PubMedID: 30838394Scopus ID: 2-s2.0-85065714382OAI: oai:DiVA.org:kth-261959DiVA, id: diva2:1361030
Note

QC 20191015

Available from: 2019-10-15 Created: 2019-10-15 Last updated: 2019-10-15Bibliographically approved

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Gustavsson, JohanBergh, CathrineYoluk, OzgeLindahl, Erik

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Orellana, LauraGustavsson, JohanBergh, CathrineYoluk, OzgeLindahl, Erik
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