The software enables automated robust identification of possible electron or hole transfer channels in proteins based on their crystal structures. The model is based on the coarse-grained version of the Pathways model and is aimed at capturing electron/hole hopping between the side chains of aromatic amino acids. A specified protein crystal structure is used to build a pairwise distance map between aromatic residue side chains (nodes). The application searches for the shortest path connecting a user-defined source node to one of the surface-exposed residues or a user-defined target node. For more details, please refer to the manual or the quick start guide.
R.N. Tazhigulov, J.R. Gayvert, M. Wei, and K.B. Bravaya, eMap: A Web Application for Identifying and Visualizing Electron or Hole Hopping Pathways in Proteins. J. Phys. Chem. B, 2019, 123, 6946
Specify options for file processing. Choose algorithm that is used to compute the pairwise distance matrix for building the graph: center of mass (default) or closest atoms. Determine, how the surface-exposed residues are identified: based on residue depth (default) or relative solvent accesibility. Pick the aromatic residues included in the analysis: Trp (W) (default), Tyr (Y) (default), Phe (F), His (H). Specify that are considered in the analysis. By default, all protein chains are included. All automatically determined non-protein ET moieties are listed in "Additional Residues" tab and are included by default (see below). For the details regarding "Advanced" section, please refer to the manual. The preliminary graph with all connected nodes will be displayed below once "Process File" button is clicked.
Optional: Additional Residues
All aromatic moieties with π-conjugated systems are automatically identified and included in the analysis. One can select/deselect them, and specify additional residues using "Custom Atom Range" option. The syntax for the "Custom Atom Range" option is as follows. Atom indices for atoms belonging to the same custom residues are given in parentheses. Continues ranges of atomic indices are defined using "-", atomic indices and residues are separated with ",". For example, "(160-162,164),(180-185)" will define two custom residues: the first "160-162,164" residue will be labeled as "CUST-1"; the second "180-185" residue will be labeled as "CUST-2".
Specify source and, optionally, target
Once the file is processed, a valid source node for electron/hole hopping pathways should be specified. By default, when only source node is specified, electron/hole hopping pathways from the given source to the surface-exposed residues will be identified. Optionally, when the target is specified, 5 shortest pathways from the given source to the given target will be computed.
2D graph visualization
Predicted pathways are visualized on a 2D graph. The residues are color-coded accordingly.
3D visualization options
The user can select pathways for visualizaing in 3D using either checkboxes or provided list. All pathways and their IDs are provided in the table at the bottom of the page.
Last updated 05/20/2019