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Updated: Jan 22, 2026

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy
Published on: March 5, 2017
eMap: A Web Application for Identifying and Visualizing Electron or Hole Hopping Pathways in Proteins
Ruslan N Tazhigulov1, James R Gayvert1, Melissa Wei1
1Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States.
Abstract:
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 the user-specified target. The identified pathways are ranked according to their effective 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 .
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