Scoring residue conservation - PubMed (original) (raw)
Review
. 2002 Aug 1;48(2):227-41.
doi: 10.1002/prot.10146.
Affiliations
- PMID: 12112692
- DOI: 10.1002/prot.10146
Review
Scoring residue conservation
William S J Valdar. Proteins. 2002.
Abstract
The importance of a residue for maintaining the structure and function of a protein can usually be inferred from how conserved it appears in a multiple sequence alignment of that protein and its homologues. A reliable metric for quantifying residue conservation is desirable. Over the last two decades many such scores have been proposed, but none has emerged as a generally accepted standard. This work surveys the range of scores that biologists, biochemists, and, more recently, bioinformatics workers have developed, and reviews the intrinsic problems associated with developing and evaluating such a score. A general formula is proposed that may be used to compare the properties of different particular conservation scores or as a measure of conservation in its own right.
Copyright 2002 Wiley-Liss, Inc.
Similar articles
- A new method for quantifying residue conservation and its applications to the protein folding nucleus.
Liu X, Li J, Guo W, Wang W. Liu X, et al. Biochem Biophys Res Commun. 2006 Dec 29;351(4):1031-6. doi: 10.1016/j.bbrc.2006.10.157. Epub 2006 Nov 7. Biochem Biophys Res Commun. 2006. PMID: 17097065 - Predicting functionally important residues from sequence conservation.
Capra JA, Singh M. Capra JA, et al. Bioinformatics. 2007 Aug 1;23(15):1875-82. doi: 10.1093/bioinformatics/btm270. Epub 2007 May 22. Bioinformatics. 2007. PMID: 17519246 - The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures.
Glaser F, Rosenberg Y, Kessel A, Pupko T, Ben-Tal N. Glaser F, et al. Proteins. 2005 Feb 15;58(3):610-7. doi: 10.1002/prot.20305. Proteins. 2005. PMID: 15614759 - Protein function from sequence and structure data.
Domingues FS, Lengauer T. Domingues FS, et al. Appl Bioinformatics. 2003;2(1):3-12. Appl Bioinformatics. 2003. PMID: 15130830 Review. - Issues in predicting protein function from sequence.
Ponting CP. Ponting CP. Brief Bioinform. 2001 Mar;2(1):19-29. doi: 10.1093/bib/2.1.19. Brief Bioinform. 2001. PMID: 11465059 Review.
Cited by
- Structure, function and inhibition of the two- and three-domain 4Fe-4S IspG proteins.
Liu YL, Guerra F, Wang K, Wang W, Li J, Huang C, Zhu W, Houlihan K, Li Z, Zhang Y, Nair SK, Oldfield E. Liu YL, et al. Proc Natl Acad Sci U S A. 2012 May 29;109(22):8558-63. doi: 10.1073/pnas.1121107109. Epub 2012 May 14. Proc Natl Acad Sci U S A. 2012. PMID: 22586085 Free PMC article. - Unlocking COVID therapeutic targets: A structure-based rationale against SARS-CoV-2, SARS-CoV and MERS-CoV Spike.
Trigueiro-Louro J, Correia V, Figueiredo-Nunes I, Gíria M, Rebelo-de-Andrade H. Trigueiro-Louro J, et al. Comput Struct Biotechnol J. 2020 Jul 31;18:2117-2131. doi: 10.1016/j.csbj.2020.07.017. eCollection 2020. Comput Struct Biotechnol J. 2020. PMID: 32913581 Free PMC article. - Structure and RNA-binding of the helically extended Roquin CCCH-type zinc finger.
Tants JN, Oberstrass L, Weigand JE, Schlundt A. Tants JN, et al. Nucleic Acids Res. 2024 Sep 9;52(16):9838-9853. doi: 10.1093/nar/gkae555. Nucleic Acids Res. 2024. PMID: 38953172 Free PMC article. - The human bitter taste receptor TAS2R10 is tailored to accommodate numerous diverse ligands.
Born S, Levit A, Niv MY, Meyerhof W, Behrens M. Born S, et al. J Neurosci. 2013 Jan 2;33(1):201-13. doi: 10.1523/JNEUROSCI.3248-12.2013. J Neurosci. 2013. PMID: 23283334 Free PMC article. - Sequence variation in ligand binding sites in proteins.
Magliery TJ, Regan L. Magliery TJ, et al. BMC Bioinformatics. 2005 Sep 30;6:240. doi: 10.1186/1471-2105-6-240. BMC Bioinformatics. 2005. PMID: 16194281 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources