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