Substitution scoring matrices for proteins - An overview.
amino acid substitution matrix
general purpose matrix
sequence alignments
sequence analysis
specialized matrix
Journal
Protein science : a publication of the Protein Society
ISSN: 1469-896X
Titre abrégé: Protein Sci
Pays: United States
ID NLM: 9211750
Informations de publication
Date de publication:
11 2020
11 2020
Historique:
received:
17
08
2020
revised:
17
09
2020
accepted:
18
09
2020
pubmed:
22
9
2020
medline:
29
1
2021
entrez:
21
9
2020
Statut:
ppublish
Résumé
Sequence analysis is the primary and simplest approach to discover structural, functional and evolutionary details of related proteins. All the alignment based approaches of sequence analysis make use of amino acid substitution matrices, and the accuracy of the results largely depends on the type of scoring matrices used to perform alignment tasks. An amino acid substitution matrix is a 20 × 20 matrix in which the individual elements encapsulate the rates at which each of the 20 amino acid residues in proteins are substituted by other amino acid residues over time. In contrast to most globular/ordered proteins whose amino acids composition is considered as standard, there are several classes of proteins (e.g., transmembrane proteins) in which certain types of amino acid (e.g., hydrophobic residues) are enriched. These compositional differences among various classes of proteins are manifested in their underlying residue substitution frequencies. Therefore, each of the compositionally distinct class of proteins or protein segments should be studied using specific scoring matrices that reflect their distinct residue substitution pattern. In this review, we describe the development and application of various substitution scoring matrices peculiar to proteins with standard and biased compositions. Along with most commonly used standard matrices (PAM, BLOSUM, MD and VTML) that act as default parameters in various homologs search and alignment tools, different substitution scoring matrices specific to compositionally distinct class of proteins are discussed in detail.
Identifiants
pubmed: 32954566
doi: 10.1002/pro.3954
pmc: PMC7586916
doi:
Substances chimiques
Membrane Proteins
0
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
2150-2163Informations de copyright
© 2020 The Protein Society.
Références
J Comput Biol. 2000;7(6):761-76
pubmed: 11382360
BMC Bioinformatics. 2017 Jun 5;18(1):293
pubmed: 28583067
J Mol Biol. 1995 Jun 16;249(4):816-31
pubmed: 7602593
Proc Natl Acad Sci U S A. 1987 Jan;84(1):166-9
pubmed: 3467347
Bioinformatics. 2001;17 Suppl 1:S182-9
pubmed: 11473008
Adv Exp Med Biol. 2014;796:15-33
pubmed: 24158799
Comput Chem. 2000 Jan;24(1):71-94
pubmed: 10642881
Nucleic Acids Res. 2002 Jan 1;30(1):260-3
pubmed: 11752310
Protein Eng. 1994 Nov;7(11):1323-32
pubmed: 7700864
Mol Biol Evol. 2006 Feb;23(2):421-36
pubmed: 16251508
Science. 2008 Jun 20;320(5883):1632-5
pubmed: 18566285
Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10915-9
pubmed: 1438297
Bioinformatics. 2000 Sep;16(9):760-6
pubmed: 11108698
Pac Symp Biocomput. 2002;:589-600
pubmed: 11928510
Nucleic Acids Res. 2000 Jan 1;28(1):254-6
pubmed: 10592239
Bioinformatics. 2007 Nov 1;23(21):2947-8
pubmed: 17846036
BMC Bioinformatics. 2015 Jul 02;16:206
pubmed: 26134144
J Mol Biol. 1996 Mar 15;256(5):924-38
pubmed: 8601843
Bioinformatics. 2005 Jan 1;21(1):137-40
pubmed: 15310560
Mol Syst Biol. 2011 Oct 11;7:539
pubmed: 21988835
Nucleic Acids Res. 2002 Jul 15;30(14):3059-66
pubmed: 12136088
Int J Pept Protein Res. 1987 Feb;29(2):276-81
pubmed: 3570667
Mol Biol Evol. 2000 Nov;17(11):1581-8
pubmed: 11070046
J Biosci. 2010 Jun;35(2):295-314
pubmed: 20689185
J Mol Biol. 2001 Jun 29;310(1):243-57
pubmed: 11419950
BMC Bioinformatics. 2008 May 16;9:236
pubmed: 18485187
Proteins. 2005 Oct 1;61(1):127-36
pubmed: 16044462
Mol Biol Evol. 2010 Mar;27(3):609-21
pubmed: 19923193
Science. 1966 Jul 1;153(3731):34-7
pubmed: 17730601
J Mol Evol. 1979 Mar 15;12(3):219-36
pubmed: 439147
Mol Biol Evol. 2002 Jan;19(1):8-13
pubmed: 11752185
Nucleic Acids Res. 2003 Apr 1;31(7):1838-44
pubmed: 12654999
Annu Int Conf IEEE Eng Med Biol Soc. 2008;2008:1347-50
pubmed: 19162917
Nucleic Acids Res. 2014 Jan;42(Database issue):D191-8
pubmed: 24253303
J Mol Biol. 2000 Sep 8;302(1):205-17
pubmed: 10964570
Genome Biol Evol. 2016 Jul 03;8(6):2044-64
pubmed: 27289099
Bioinformatics. 2005 Apr 1;21(7):902-11
pubmed: 15509610
Bioinformatics. 1998 Jun;14(5):430-8
pubmed: 9682056
Trends Genet. 2000 Jun;16(6):276-7
pubmed: 10827456
Bioinformatics. 2006 Feb 15;22(4):413-22
pubmed: 16352653
Nucleic Acids Res. 2009 Jan;37(Database issue):D539-43
pubmed: 18957442
Genomics. 1991 Nov;11(3):635-50
pubmed: 1774068
Protein Sci. 1992 Feb;1(2):216-26
pubmed: 1304904
Proteins. 2007 May 15;67(3):695-708
pubmed: 17299747
J Mol Biol. 1970 Mar;48(3):443-53
pubmed: 5420325
BMC Bioinformatics. 2005 Jan 10;6:4
pubmed: 15638949
J Proteome Res. 2006 Nov;5(11):2985-95
pubmed: 17081050
Nature. 2002 Oct 3;419(6906):498-511
pubmed: 12368864
Proc Biol Sci. 1990 Aug 22;241(1301):132-45
pubmed: 1978340
Syst Synth Biol. 2008 Dec;2(3-4):75-82
pubmed: 19399641
J Mol Biol. 1993 Oct 20;233(4):716-38
pubmed: 8411177
Bioinformatics. 1999 Jun;15(6):471-9
pubmed: 10383472
PLoS One. 2011;6(5):e20488
pubmed: 21647374
Genome Biol. 2001;2(4):RESEARCH0010
pubmed: 11305938
Nucleic Acids Res. 2014 Jan;42(Database issue):D422-5
pubmed: 24304901
J Mol Biol. 2005 Apr 8;347(4):827-39
pubmed: 15769473
BMC Bioinformatics. 2003 Oct 10;4:47
pubmed: 14552658
Science. 1974 Sep 6;185(4154):862-4
pubmed: 4843792
J Mol Biol. 2001 Jan 19;305(3):567-80
pubmed: 11152613
BMC Bioinformatics. 2004 Aug 19;5:113
pubmed: 15318951
Nucleic Acids Res. 2008 Dec;36(21):6664-75
pubmed: 18948281
IEEE/ACM Trans Comput Biol Bioinform. 2015 May-Jun;12(3):686-94
pubmed: 26357279
Bioinformation. 2011;7(4):163-8
pubmed: 22102772
Science. 1992 Jun 5;256(5062):1443-5
pubmed: 1604319
J Mol Biol. 1997 Jun 13;269(3):423-39
pubmed: 9199410
FEBS Lett. 1994 Feb 21;339(3):269-75
pubmed: 8112466
BMC Bioinformatics. 2006 Apr 17;7:208
pubmed: 16618368
Protein Eng. 2000 Aug;13(8):545-50
pubmed: 10964983
Nucleic Acids Res. 2000 Jan 1;28(1):228-30
pubmed: 10592233
J Mol Biol. 1988 Dec 20;204(4):1019-29
pubmed: 3221397
Nucleic Acids Res. 1998 Jan 1;26(1):275-9
pubmed: 9399852
Proteins. 2002 May 1;47(2):228-35
pubmed: 11933069
Protein Sci. 2020 Nov;29(11):2150-2163
pubmed: 32954566
Bioinformatics. 2004 Apr 12;20(6):847-53
pubmed: 14764567
J Mol Biol. 1997 Apr 11;267(4):1026-38
pubmed: 9135128
FEMS Microbiol Rev. 2012 Mar;36(2):408-34
pubmed: 22092310
J Mol Evol. 1986;24(1-2):1-11
pubmed: 3104608
Bioinformatics. 2005 Apr 1;21(7):1267-8
pubmed: 15333456
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
pubmed: 15034147
Proteins. 2000 Dec 1;41(4):498-503
pubmed: 11056037
Comput Appl Biosci. 1992 Jun;8(3):275-82
pubmed: 1633570
Proc Natl Acad Sci U S A. 1988 Apr;85(8):2653-7
pubmed: 3357886
Sci Rep. 2019 Nov 8;9(1):16380
pubmed: 31704957