Citing visualCMAT

If you find visualCMAT or its results useful please cite our work:

Suplatov D., Sharapova Y., Timonina D., Kopylov K., Švedas V. (2018) The visualCMAT: a web-server to select and interpret correlated mutations/co-evolving residues in protein families. J Bioinform Comput Biol., 16(2), 1840005. DOI: 10.1142/S021972001840005X.

Please also cite the work of third-party contributors, whose programs and algorithms are currently implemented in the visualCMAT web-server:

The CMAT algorithm is implemented to predict the correlated mutations/co-evolving residues: Jeong, C. S., & Kim, D. (2012). Reliable and robust detection of coevolving protein residues. Protein Eng Des Sel., 25 (11), 705-713.

The MAFFT program is implemented to compare the sequence of the representative PDB with the multiple sequence alignment: Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol., 30(4), 772-780

The FPOCKET program is implemented to predict binding sites in the representative protein structure: Schmidtke, P., Le Guilloux, V., Maupetit, J., Tuffery, P. (2010). Fpocket: online tools for protein ensemble pocket detection and tracking. Nucleic acids res., 38(suppl_2), W582-W589.

The PyMol program is implemented to compile the binary PSE session with the annotated representative structure: PyMol: A molecular visualization system. http://pymol.org/, Copyright (C) Schrodinger, LLC

The JSmol program is implemented to provide the HTML5-based tool for the on-line analysis of visualCMAT results: Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T., & Sussman, J. L. (2013). JSmol and the Next‐Generation Web‐Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr J Chem., 53(3‐4), 207-216.