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**: |br|
MSMS_: |br| Sanner, M. F.; Olson, A. J.; Spehner, J. C. *Biopolymers*, **1996**, 38, 305-320. |br|
RD Reference: |br|
Chakravarty, S.; Varadarajan, R. *Structure*, **1999**, 7, 723-732. |br|
Threshold: |br|
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**: |br|
DSSP_: |br|
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. |br|
Wolfgang, K.; Christian, S. *Biopolymers*, **1983**, 22, 2577-2637. |br|
Threshold: |br|
Tien, M. Z.; Meyer, A. G.; Sydykova, D. K.; Spielman, S. J.; Wilke, C. O. *PLoS ONE*, **2013**, 8, 1-8.

**Multiple Sequence Alignment** |br|
MUSCLE_: |br|
Edgar RC. *Nucleic Acids Res.* **2004** 32(5) 1792-1797.

**Graph Mining** |br|
gSpan_: |br|
X. Yan and J. Han. *Proc. Int'l Conf. Data Mining*, **2002**.

Biopython_: |br|
Application note:|br|
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.  |br|
PDB Parser: |br|
Hamelryck, T.; Manderick, B. *Bioinformatics*, **2003**, 19, 2308-2310.

NetworkX_: |br|
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_

.. _MSMS: http://mgltools.scripps.edu/packages/MSMS/

.. _DSSP: https://swift.cmbi.umcn.nl/gv/dssp/index.html

.. _Biopython: https://biopython.org/wiki/Documentation

.. _NetworkX: https://networkx.github.io/

.. _RDKit: https://www.rdkit.org/

.. _SciPy: https://www.scipy.org/

.. _NumPy: https://www.numpy.org/

.. _PyGraphviz: https://pygraphviz.github.io/

.. _Graphviz: https://graphviz.gitlab.io/

.. _MUSCLE: https://www.drive5.com/muscle/

.. _gSpan: https://sites.cs.ucsb.edu/~xyan/papers/gSpan-short.pdf

.. _gspan-mining: https://pypi.org/project/gspan-mining/

.. _pysmiles: https://github.com/pckroon/pysmiles

.. |br| raw:: html

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