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eMap: A Web Application for Identifying and Visualizing Electron or Hole Hopping Pathways in Proteins

preprint
revised on 21.06.2019 and posted on 21.06.2019 by Ruslan N. Tazhigulov, James R. Gayvert, Melissa Wei, Ksenia B. Bravaya

eMap is a web-based platform for identifying and visualizing electron or hole transfer pathways in proteins based on their crystal structures. The underlying model can be viewed as a coarse-grained version of the Pathways model, where each tunneling step between hopping sites represented by electron transfer active (ETA) moieties is described with one effective decay parameter that describes protein-mediated tunneling. ETA moieties include aromatic amino acid residue side chains and aromatic fragments of cofactors that are automatically detected, and, in addition, electron/hole residing sites that can be specified by the users. The software searches for the shortest paths connecting the user-specified electron/hole source to either all surface-exposed ETA residues or to the user-specified target. The identified pathways are ranked based on their length. The pathways are visualized in 2D as a graph, in which each node represents an ETA site, and in 3D using available protein visualization tools. Here, we present the capability and user interface of eMap 1.0, which is available at https://emap.bu.edu.

Funding

MolSSI graduate fellowship, NSF grant ACI-1547580

Boston University Hariri Institute for Computational Science and Engineering (2016-10-003)

History

Email Address of Submitting Author

bravaya@bu.edu

Institution

Boston University

Country

United States

ORCID For Submitting Author

0000-0002-5033-8240

Declaration of Conflict of Interest

The authors have no conflict of interest to declare.

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