Citing Mustguseal protocol and platform

Mustguseal is a bioinformatic protocol designed to build alignments of protein families and superfamilies, 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:

D.A. Suplatov, K.E. Kopylov, N.N. Popova, Vl.V. Voevodin, V.K. Švedas. Mustguseal: Server for Multiple Structure-Guided Sequence Alignments of Protein Families, submitted

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

  • Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution, 30(4), 772-780.
  • 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., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research, 25(17), 3389-3402.
  • 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.
  • Söding, J., Biegert, A., & Lupas, A. N. (2005). The HHpred interactive server for protein homology detection and structure prediction. Nucleic acids research, 33(suppl 2), W244-W248.
  • Menke, M., Berger, B., & Cowen, L. (2008). Matt: local flexibility aids protein multiple structure alignment. PLoS Comput Biol, 4(1), e10.
  • Krissinel, E., & Henrick, K. (2004). Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallographica Section D: Biological Crystallography, 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 research, 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. Israel Journal of Chemistry, 53(3‐4), 207-216.
  • PyMol: A molecular visualization system., Copyright (C) Schrodinger, LLC

If you used Zebra, pocketZebra, visualCMAT 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., 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 research, 42(W1), W344-W349.
  • Suplatov, D., Kirilin, E., Takhaveev, V., & Švedas, V. (2014). Zebra: a web server for bioinformatic analysis of diverse protein families. Journal of Biomolecular Structure and Dynamics, 32(11), 1752-1758.
  • 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. Journal of Biomolecular Structure and Dynamics, 32(1), 75-87.
  • Suplatov D.A., Sharapova Ya.A., Kopylov K.E., Švedas V. (2017) The visualCMAT tool to select and interpret correlated mutations/co-evolving residues in protein structures. submitted
  • Jeong C.S. and Kim D. (2012). Reliable and robust detection of coevolving protein residues. Protein Eng. Des. Sel., 25 (11), 705-713

Finally, if you used parMATT to build core structural alignment locally and found it useful please cite:

  • Shegai M., et al. (2017) parMATT: Parallel multiple alignment with translations and twists for distributed-memory systems, in preparation