Citing Mustguseal protocol and platform

Mustguseal is a bioinformatic protocol to build large alignments of functionally diverse protein families, and a web-platform implementing the original and third-party algorithms to provide a user-friendly web-based interface to the Mustguseal protocol through the World Wide Web. If you used Mustguseal and found it useful in your research or education please cite our work.

If you find Mustguseal or its results useful please cite:

Suplatov D.A., Kopylov K.E., Popova N.N., Voevodin V.V., Švedas V.K. (2018) Mustguseal: a Server for Multiple Structure-Guided Sequence Alignment of Protein Families. Bioinformatics, 34(9), 1583-1585. DOI: 10.1093/bioinformatics/btx831.

Please also cite the work of third-party contributors, whose programs and algorithms are currently implemented in the Mustguseal platform, as well as the integrated sister web-services:

  • 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.
  • Fu, L., Niu, B., Zhu, Z., Wu, S., & Li, W. (2012). CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics, 28(23), 3150-3152.
  • Vouzis, P. D., & Sahinidis, N. V. (2011). GPU-BLAST: using graphics processors to accelerate protein sequence alignment. Bioinformatics, 27(2), 182-188; Altschul,S.F., Gish,W., Miller,W., Myers,E.W., and Lipman,D.J. (1990). Basic local alignment search tool. J.Mol.Biol., 215(3), 403-410.
  • Menke, M., Berger, B., & Cowen, L. (2008). Matt: local flexibility aids protein multiple structure alignment. PLoS Comput Biol, 4(1), e10.
  • Fischer,J.D., Mayer,C.E., and Söding,J. (2008). Prediction of protein functional residues from sequence by probability density estimation. Bioinformatics, 24(5), 613-620; Söding, J., Biegert, A., & Lupas, A. N. (2005). The HHpred interactive server for protein homology detection and structure prediction. Nucleic acids res., 33(suppl 2), W244-W248.
  • Krissinel, E., & Henrick, K. (2004). Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr., 60(12), 2256-2268.

If you used the interactive content at the Analysis section of Results page and found it useful please cite:

  • Gille, C., Fähling, M., Weyand, B., Wieland, T., & Gille, A. (2014). Alignment-Annotator web server: rendering and annotating sequence alignments. Nucleic acids res., 42: W3-6.
  • 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.
  • PyMol: A molecular visualization system., Copyright (C) Schrodinger, LLC

If you used Zebra, pocketZebra, visualCMAT, or Yosshi web-services to study the Mustguseal alignments (either via auto-submission links at the Results page or manually) and found it useful please cite:

  • Suplatov, D., Shalaeva, D., Kirilin, E., Arzhanik, V., & Švedas, V. (2014). Bioinformatic analysis of protein families for identification of variable amino acid residues responsible for functional diversity. J. Biomol. Struct. Dyn., 32(1), 75-87.
  • Suplatov, D., Kirilin, E., Arbatsky, M., Takhaveev, V., & Švedas, V. (2014). pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families. Nucleic acids res., 42(W1), W344-W349.
  • Suplatov, D., Kirilin, E., Takhaveev, V., & Švedas, V. (2014). Zebra: a web server for bioinformatic analysis of diverse protein families. J. Biomol. Struct. Dyn., 32(11), 1752-1758.
  • 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.
  • Suplatov D.A., Timonina D.S., Sharapova Y.A., Švedas V.K. (2019) Yosshi: a web-server for disulfide engineering by bioinformatic analysis of diverse protein families. Nucleic Acids Res., 47(W1), W308–W314.