Citing and Credits

Citing and Credits

In citing the ConSurf-DB server please refer to:

  1. Ben Chorin A., Masrati G., Kessel A., Narunsky A., Sprinzak J., Lahav S., Ashkenazy H. and Ben-Tal N. (2020).
    ConSurf-DB: accurate estimate of the evolutionary conservation pattern for 83% of PDB proteins.
    Protein Science (in review). PDF

  2. Goldenberg O., Erez E., Nimrod G. and Ben-Tal N. (2009).
    The ConSurf-DB: Pre-calculated evolutionary conservation profiles of protein structures.
    Nucleic Acids Research (Database issue), 37:D323-D327; PMID: 18971256. PDF

Main References

  1. Burley S.K., et al. (2019).
    RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy.
    Nucleic Acids Research, 47:D464–D474; PMID: 30357411. PDF

  2. UniProt Consortium. (2019).
    UniProt: a worldwide hub of protein knowledge.
    Nucleic Acids Research, 47:D506-D515; PMID: 30395287. PDF

  3. Rose A.S., Bradley A.R., Valasatava Y., Duarte J.M., Prlic A. and Rose P.W. (2018).
    NGL viewer: web-based molecular graphics for large complexes.
    Bioinformatics, 34:3755-3758; PMID: 29850778. PDF

  4. Laskowski R.A., Jabłońska J., Pravda L., Vařeková R.S., Thornton J.M. (2018).
    PDBsum: Structural summaries of PDB entries.
    Protein Science, 27:129-134; PMID: 28875543. PDF

  5. Schrödinger L.L.C. (2015).
    The PyMOL Molecular Graphics System, Version 2.3.3.

  6. Suzek B.E., Wang Y., Huang H., McGarvey P.B., Wu C.H. and UniProt Consortium. (2015).
    UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.
    Bioinformatics, 31:926-932; PMID: 25398609. PDF

  7. Katoh K. and Standley D.M. (2013),
    MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
    Molecular Biology and Evolution, 30:772–780; PMID: 23329690. PDF

  8. Mistry J., Finn R.D., Eddy S.R., Bateman A. and Punta M. (2013).
    Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.
    Nucleic Acids Research, 41:e121; PMID: 23598997. PDF

  9. Fu L., Niu B., Zhu Z., Wu S. and Li W. (2012).
    CD-HIT: accelerated for clustering the next-generation sequencing data.
    Bioinformatics, 28:3150-3152; PMID: 23060610. PDF

  10. Darriba D., Taboada G.L., Doallo R. and Posada D. (2011).
    ProtTest 3: fast selection of best-fit models of protein evolution.
    Bioinformatics, 27:1164-1165; PMID: 21335321. PDF

  11. Hodis E., Prilusky J. and Sussman J.L. (2010).
    Proteopedia: A collaborative, virtual 3D web-resource for protein and biomolecule structure and function.
    Biochemistry and Molecular Biology Education, 38:341-342; PMID: 21567857. PDF

  12. Wang G. and Dunbrack R.L. (2005).
    PISCES: recent improvements to a PDB sequence culling server.
    Nucleic Acids Research, 33:W94-W98; PMID: 15980589. PDF

  13. Martz E. (2005).
    FirstGlance in Jmol. firstglance.jmol.org

  14. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C. and Ferrin T.E. (2004).
    UCSF Chimera--a visualization system for exploratory research and analysis.
    Journal of Computational Chemistry, 25:1605-1612; PMID: 15264254. PDF

  15. Mayrose I., Graur D., Ben-Tal N. and Pupko T. (2004).
    Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior.
    Molecular Biology and Evolution, 21:1781-1791; PMID: 15201400. PDF

  16. Pupko T., Bell R.E., Mayrose I., Glaser F. and Ben-Tal N. (2002).
    Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues.
    Bioinformatics, 18:S71-S77; PMID: 12169533. PDF

  17. Saitou N. and Nei M. (1987).
    The neighbor-joining method: a new method for reconstructing phylogenetic trees.
    Molecular Biology and Evolution, 4:406-425; PMID: 3447015. PDF

Acknowledgements:

The development was funded in parts by the Israel Science Foundation and the Edmond J. Safra Center for Bioinformatics at Tel Aviv University.


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