How to cite

Primary citation

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, 32, 6946-6951. https://doi.org/10.1021/acs.jpcb.9b04816

Third Party Software

In addition to the primary citation, please cite the relevant third party software we depend on:

Residue Depth:
MSMS:
Sanner, M. F.; Olson, A. J.; Spehner, J. C. Biopolymers, 1996, 38, 305-320.
RD Reference:
Chakravarty, S.; Varadarajan, R. Structure, 1999, 7, 723-732.
Threshold:
Song, J.; Tan, H.; Mahmood, K.; Law, R. H. P.; Buckle, A. M.; Webb, G. I.; Akutsu, T.; Whisstock, J. C. PLoS ONE, 2009, 4, 1-14.

Solvent Accessibility:
DSSP:
Touw, W. G.; Baakman, C.; Black, J.; te Beek, T. A.; Krieger, E.; Joosten, R. P.; Vriend, G. Nucleic Acids Res., 2015, 43, D364-D368.
Wolfgang, K.; Christian, S. Biopolymers, 1983, 22, 2577-2637.
Threshold:
Tien, M. Z.; Meyer, A. G.; Sydykova, D. K.; Spielman, S. J.; Wilke, C. O. PLoS ONE, 2013, 8, 1-8.

Multiple Sequence Alignment
MUSCLE:
Edgar RC. Nucleic Acids Res. 2004 32(5) 1792-1797.

Graph Mining
gSpan:
X. Yan and J. Han. Proc. Int’l Conf. Data Mining, 2002.

Biopython:
Application note:
Cock, P. J. A.; Antao, T.; Chang, J. T.; Chapman, B. A.; Cox, C. J.; Dalke, A.; Friedberg, I.; Hamelryck, T.; Kauff, F.; Wilczynski, B.; de Hoon, M. J. L. Bioinformatics, 2009, 25, 1422-1423.
PDB Parser:
Hamelryck, T.; Manderick, B. Bioinformatics, 2003, 19, 2308-2310.

NetworkX:
Hagberg, A. A.; Schult, D. A.; Swart, P. J. Exploring Network Structure, Dynamics, and Function using NetworkX. Pasadena, CA USA, 2008.

Other Supporting Software

RDKit , NumPy , SciPy , PyGraphviz , Graphviz, pysmiles, gspan-mining