THE CONSURF DATABASE
SERVER FOR THE IDENTIFICATION OF FUNCTIONAL REGIONS IN PROTEINS
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: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins.
Protein Science 29:258–267. 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
· 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
· UniProt Consortium. (2019). UniProt: a worldwide hub of protein knowledge. Nucleic Acids Research, 47:D506-D515; PMID: 30395287. PDF
· 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
· 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
· Schrödinger L.L.C. (2015). The PyMOL Molecular Graphics System, Version 2.3.3.
· 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
· 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
· 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
· 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
· 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
· 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
· 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
· Martz E. (2005).
· FirstGlance in Jmol. firstglance.jmol.org
· 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
· 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
· 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
· 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.