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

Laura Orellana; Johan Gustavsson; Cathrine Bergh; Ozge Yoluk; Erik Lindahl

doi:10.1093/bioinformatics/btz104

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

Bioinformatics. 2019 Sep 15;35(18):3505-3507. doi: 10.1093/bioinformatics/btz104.

Authors

Laura Orellana¹, Johan Gustavsson², Cathrine Bergh³, Ozge Yoluk³, Erik Lindahl^{1

3}

Affiliations

¹ Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
² Department of Computational Science and Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
³ Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Solna, Sweden.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computers
Molecular Dynamics Simulation
Protein Conformation
Proteins
Software*

Substances

Proteins