Overview of PyeMap
PyeMap is a python package aimed at automatic identification of electron and hole transfer pathways in proteins. The analysis is based on a coarse-grained version of Beratan and Onuchic’s Pathway model, and only accounts for through-space hopping between aromatic residues side chains [Beratan1992]. Side chains of aromatic residues and non-protein electron transfer active moieties are modeled as vertices in a weighted graph, where the edge weights are modified distance dependent penalty functions.
For single proteins, PyeMap identifies the shortest pathways between a specified donor to the surface, or to a specified acceptor. For groups of proteins, PyeMap identifies shared pathways/motifs using graph mining techniques.
PyeMap serves as the backend for the web application eMap, and can also be used as a fully functional Python package.
Current Features
- Single protein
Identification of most probable electron/hole transfer pathways from a specified donor to the protein surface or a specified electron/hole acceptor
Accepts valid .pdb or .cif structures provided by the user or fetched from RCSB database
Automatic detection of non-protein aromatic moieties such as porphyrins, nucleobases, and other aromatic cofactors
Automatic detection of 60+ inorganic clusters such as iron-sulfur clusters and others
Automatic detection of redox-active metal ions
User specified custom fragments
Visualization of chemical structures and graphs
Automatic identification of surface exposed residues using residue depth or solvent accessibility criteria
Control over various parameters which determine connectivity of graph theory model
Tested on structures as large as 5350 residues (51599 atoms)
- Graph Mining
Mining families of protein graphs for all patterns up to a given support threshold
Mining families of protein graphs for specific patterns
Classification of protein subgraphs based on similarity
In Development
Improving the physical model of electron transfer by incorporating information on geometry-dependent electronic couplings and site sensitive energetics
Generalization to DNA, protein-DNA complexes etc.