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Orellana L, Gustavsson J, Bergh C, Yoluk O, Lindahl E
Bioinformatics 35 (18) 3505-3507 [2019-09-15; online 2019-03-07]
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. eBDIMS is available online: http://ebdims.biophysics.se/ or as standalone software: https://github.com/laura-orellana/eBDIMS, https://github.com/cabergh/eBDIMS. Supplementary data are available at Bioinformatics online.
PubMed 30838394
DOI 10.1093/bioinformatics/btz104
Crossref 10.1093/bioinformatics/btz104
pmc: PMC6748756
pii: 5341428