메뉴 건너뛰기




Volumn 18, Issue 6, 2009, Pages 1306-1315

Evolutionary constraints on structural similarity in orthologs and paralogs

Author keywords

Homology modeling; Orthologs prediction; Orthology; Paralogy; Sequence structure relationship

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; EVOLUTION; LIGAND BINDING; MOLECULAR MODEL; ORTHOLOGY; PARALOGY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURAL GENOMICS;

EID: 66349085886     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.143     Document Type: Article
Times cited : (56)

References (65)
  • 1
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5:823-826.
    • (1986) EMBO J , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 2
    • 0000338489 scopus 로고
    • Comparison of solvent-inaccessible cores of homologous proteins: Definitions useful for protein modelling
    • Hubbard TJ, Blundell TL (1987) Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng 1:159-171. (Pubitemid 18025225)
    • (1987) Protein Engineering , vol.1 , Issue.3 , pp. 159-171
    • Hubbard, T.J.P.1    Blundell, T.L.2
  • 3
    • 0027485083 scopus 로고
    • Comparison of conformational characteristics in structurally similar protein pairs
    • Flores TP, Orengo CA, Moss DS, Thornton JM (1993) Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci 2:1811-1826. (Pubitemid 23328537)
    • (1993) Protein Science , vol.2 , Issue.11 , pp. 1811-1826
    • Flores, T.P.1    Orengo, C.A.2    Moss, D.S.3    Thornton, J.M.4
  • 4
    • 0031566432 scopus 로고    scopus 로고
    • Recognition of analogous and homologous protein folds: Analysis of sequence and structure conservation
    • DOI 10.1006/jmbi.1997.1019
    • Russell RB, Saqi MA, Sayle RA, Bates PA, Sternberg MJ (1997) Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J Mol Biol 269:423-439. (Pubitemid 27267763)
    • (1997) Journal of Molecular Biology , vol.269 , Issue.3 , pp. 423-439
    • Russell, R.B.1    Saqi, M.A.S.2    Sayle, R.A.3    Bates, P.A.4    Sternberg, M.J.E.5
  • 5
    • 0034237578 scopus 로고    scopus 로고
    • Large-scale comparison of protein sequence alignment algorithms with structure alignments
    • DOI 10.1002/(SICI)1097-0134(20000701)40:1<6::AID-PROT30>3.0.CO;2-7
    • Sauder JM, Arthur JW, Dunbrack RL, Jr (2000) Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins 40:6-22. (Pubitemid 30368577)
    • (2000) Proteins: Structure, Function and Genetics , vol.40 , Issue.1 , pp. 6-22
    • Sauder, J.M.1    Arthur, J.W.2    Dunbrack Jr., R.L.3
  • 6
    • 0034677669 scopus 로고    scopus 로고
    • Assessing annotation transfer for genomics: Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
    • Wilson CA, Kreychman J, Gerstein M (2000) Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J Mol Biol 297:233-249.
    • (2000) J Mol Biol , vol.297 , pp. 233-249
    • Wilson, C.A.1    Kreychman, J.2    Gerstein, M.3
  • 7
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost B (1999) Twilight zone of protein sequence alignments. Protein Eng 12:85-94. (Pubitemid 29103686)
    • (1999) Protein Engineering , vol.12 , Issue.2 , pp. 85-94
    • Rost, B.1
  • 8
    • 0034682894 scopus 로고    scopus 로고
    • An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence
    • Yang AS, Honig B (2000) An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence. J Mol Biol 301:679-689.
    • (2000) J Mol Biol , vol.301 , pp. 679-689
    • Yang, A.S.1    Honig, B.2
  • 9
    • 0037397439 scopus 로고    scopus 로고
    • Definitions of enzyme function for the structural genomics era
    • DOI 10.1016/S1367-5931(03)00028-0
    • Babbitt PC (2003) Definitions of enzyme function for the structural genomics era. Curr Opin Chem Biol 7:230-237. (Pubitemid 36514955)
    • (2003) Current Opinion in Chemical Biology , vol.7 , Issue.2 , pp. 230-237
    • Babbitt, P.C.1
  • 10
    • 0034033261 scopus 로고    scopus 로고
    • History of the enzyme nomenclature system
    • Tipton K, Boyce S (2000) History of the enzyme nomenclature system. Bioinformatics 16:34-40. (Pubitemid 30204199)
    • (2000) Bioinformatics , vol.16 , Issue.1 , pp. 34-40
    • Tipton, K.1    Boyce, S.2
  • 11
    • 0034308142 scopus 로고    scopus 로고
    • Practical limits of function prediction
    • DOI 10.1002/1097-0134(20001001)41:1<98::AID-PROT120>3.0.CO;2-S
    • Devos D, Valencia A (2000) Practical limits of function prediction. Proteins 41:98-107. (Pubitemid 30666916)
    • (2000) Proteins: Structure, Function and Genetics , vol.41 , Issue.1 , pp. 98-107
    • Devos, D.1    Valencia, A.2
  • 12
    • 0036308741 scopus 로고    scopus 로고
    • Enzyme function less conserved than anticipated
    • DOI 10.1016/S0022-2836(02)00016-5
    • Rost B (2002) Enzyme function less conserved than anticipated. J Mol Biol 318:595-608. (Pubitemid 34734850)
    • (2002) Journal of Molecular Biology , vol.318 , Issue.2 , pp. 595-608
    • Rost, B.1
  • 13
    • 0142106373 scopus 로고    scopus 로고
    • How well is enzyme function conserved as a function of pairwise sequence identity?
    • Tian W, Skolnick J (2003) How well is enzyme function conserved as a function of pairwise sequence identity? J Mol Biol 333:863-882.
    • (2003) J Mol Biol , vol.333 , pp. 863-882
    • Tian, W.1    Skolnick, J.2
  • 14
    • 34548130064 scopus 로고    scopus 로고
    • Quantitative assessment of relationship between sequence similarity and function similarity
    • DOI 10.1186/1471-2164-8-222
    • Joshi T, Xu D (2007) Quantitative assessment of relationship between sequence similarity and function similarity. BMC Genomics 8:222. (Pubitemid 47296536)
    • (2007) BMC Genomics , vol.8 , pp. 222
    • Joshi, T.1    Xu, D.2
  • 15
    • 34548655343 scopus 로고    scopus 로고
    • Quantitative sequence-function relationships in proteins based on gene ontology
    • DOI 10.1186/1471-2105-8-294
    • Sangar V, Blankenberg DJ, Altman N, Lesk AM (2007) Quantitative sequence-function relationships in proteins based on gene ontology. BMC Bioinformatics 8:294. (Pubitemid 47399349)
    • (2007) BMC Bioinformatics , vol.8 , pp. 294
    • Sangar, V.1    Blankenberg, D.J.2    Altman, N.3    Lesk, A.M.4
  • 16
    • 0033597176 scopus 로고    scopus 로고
    • The relationship between protein structure and function: A comprehensive survey with application to the yeast genome
    • DOI 10.1006/jmbi.1999.2661
    • Hegyi H, Gerstein M (1999) The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J Mol Biol 288:147-164. (Pubitemid 29201511)
    • (1999) Journal of Molecular Biology , vol.288 , Issue.1 , pp. 147-164
    • Hegyi, H.1    Gerstein, M.2
  • 17
    • 0035815113 scopus 로고    scopus 로고
    • Evolution of function in protein superfamilies, from a structural perspective
    • DOI 10.1006/jmbi.2001.4513
    • Todd AE, Orengo CA, Thornton JM (2001) Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 307:1113-1143. (Pubitemid 33029957)
    • (2001) Journal of Molecular Biology , vol.307 , Issue.4 , pp. 1113-1143
    • Todd, A.E.1    Orengo, C.A.2    Thornton, J.M.3
  • 19
    • 0346799108 scopus 로고    scopus 로고
    • Prediction of protein function from protein sequence and structure
    • DOI 10.1017/S0033583503003901
    • Whisstock JC, Lesk AM (2003) Prediction of protein function from protein sequence and structure. Q Rev Biophys 36:307-340. (Pubitemid 38268660)
    • (2003) Quarterly Reviews of Biophysics , vol.36 , Issue.3 , pp. 307-340
    • Whisstock, J.C.1    Lesk, A.M.2
  • 20
    • 1642277108 scopus 로고    scopus 로고
    • Quantifying structure-function uncertainty: A graph theoretical exploration into the origins and limitations of protein annotation
    • DOI 10.1016/j.jmb.2004.02.009, PII S0022283604001548
    • Shakhnovich BE, Harvey JM (2004) Quantifying structure-function uncertainty: a graph theoretical exploration into the origins and limitations of protein annotation. J Mol Biol 337:933-949. (Pubitemid 38368936)
    • (2004) Journal of Molecular Biology , vol.337 , Issue.4 , pp. 933-949
    • Shakhnovich, B.E.1    Harvey, J.M.2
  • 21
    • 0036408311 scopus 로고    scopus 로고
    • Sequence variations within protein families are linearly related to structural variations
    • DOI 10.1016/S0022-2836(02)00971-3
    • Koehl P, Levitt M (2002) Sequence variations within protein families are linearly related to structural variations. J Mol Biol 323:551-562. (Pubitemid 35283679)
    • (2002) Journal of Molecular Biology , vol.323 , Issue.3 , pp. 551-562
    • Koehl, P.1    Levitt, M.2
  • 22
    • 0033609902 scopus 로고    scopus 로고
    • Evolution of protein sequences and structures
    • DOI 10.1006/jmbi.1999.2972
    • Wood TC, Pearson WR (1999) Evolution of protein sequences and structures. J Mol Biol 291:977-995. (Pubitemid 29403625)
    • (1999) Journal of Molecular Biology , vol.291 , Issue.4 , pp. 977-995
    • Wood, T.C.1    Pearson, W.R.2
  • 23
    • 0014800108 scopus 로고
    • Distinguishing homologous from analogous proteins
    • Fitch WM (1970) Distinguishing homologous from analogous proteins. Syst Zool 19:99-113.
    • (1970) Syst Zool , vol.19 , pp. 99-113
    • Fitch, W.M.1
  • 24
    • 0036889686 scopus 로고    scopus 로고
    • Orthology, paralogy and proposed classification for paralog subtypes
    • DOI 10.1016/S0168-9525(02)02793-2, PII S0168952502027932
    • Sonnhammer EL, Koonin EV (2002) Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet 18:619-620. (Pubitemid 35346684)
    • (2002) Trends in Genetics , vol.18 , Issue.12 , pp. 619-620
    • Sonnhammer, E.L.L.1    Koonin, E.V.2
  • 25
    • 27644472372 scopus 로고    scopus 로고
    • Orthologs, paralogs, and evolutionary genomics
    • DOI 10.1146/annurev.genet.39.073003.114725
    • Koonin EV (2005) Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 39:309-338. (Pubitemid 43011118)
    • (2005) Annual Review of Genetics , vol.39 , pp. 309-338
    • Koonin, E.V.1
  • 26
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • DOI 10.1126/science.278.5338.631
    • Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278:631-637. (Pubitemid 27464953)
    • (1997) Science , vol.278 , Issue.5338 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 27
    • 33745022802 scopus 로고    scopus 로고
    • Benchmarking ortholog identification methods using functional genomics data
    • DOI 10.1186/gb-2006-7-4-r31
    • Hulsen T, Huynen MA, de Vlieg J, Groenen PM (2006) Benchmarking ortholog identification methods using functional genomics data. Genome Biol 7:R31. (Pubitemid 43871879)
    • (2006) Genome Biology , vol.7 , Issue.4
    • Hulsen, T.1    Huynen, M.A.2    De Vlieg, J.3    Groenen, P.M.A.4
  • 28
    • 37849023306 scopus 로고    scopus 로고
    • Assessing performance of orthology detection strategies applied to eukaryotic genomes
    • Chen F, Mackey AJ, Vermunt JK, Roos DS (2007) Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLo S ONE 2:e383.
    • (2007) PLo S ONE , vol.2
    • Chen, F.1    Mackey, A.J.2    Vermunt, J.K.3    Roos, D.S.4
  • 29
    • 0029448349 scopus 로고
    • A biologically consistent model for comparing molecular phylogenies
    • Mirkin B, Muchnik I, Smith TF (1995) A biologically consistent model for comparing molecular phylogenies. J Comput Biol 2:493-507.
    • (1995) J Comput Biol , vol.2 , pp. 493-507
    • Mirkin, B.1    Muchnik, I.2    Smith, T.F.3
  • 30
    • 0031110886 scopus 로고    scopus 로고
    • From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem
    • DOI 10.1006/mpev.1996.0390, PII S1055790396903905
    • Page RDM, Charleston MA (1997) From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol Phylogenet Evol 7:231-240. (Pubitemid 127345887)
    • (1997) Molecular Phylogenetics and Evolution , vol.7 , Issue.2 , pp. 231-240
    • Page, R.D.M.1    Charleston, M.A.2
  • 31
    • 0030762443 scopus 로고    scopus 로고
    • On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies
    • Zhang L (1997) On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies. J Comput Biol 2:177-187. (Pubitemid 27318314)
    • (1997) Journal of Computational Biology , vol.4 , Issue.2 , pp. 177-187
    • Zhang, L.1
  • 32
    • 0031949306 scopus 로고    scopus 로고
    • Duplication-based measures of difference between gene and species trees
    • Eulenstein O, Mirkin B, Vingron M (1998) Duplication-based measures of difference between gene and species trees. J Comput Biol 5:135-148. (Pubitemid 28153011)
    • (1998) Journal of Computational Biology , vol.5 , Issue.1 , pp. 135-148
    • Eulenstein, O.1    Mirkin, B.2    Vingron, M.3
  • 36
    • 33644787447 scopus 로고    scopus 로고
    • OrthoMCL-DB: Querying a comprehensive multi-species collection of ortholog groups
    • Chen F, Mackey AJ, Stoeckert CJ, Jr, Roos DS (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 34:D363-D368.
    • (2006) Nucleic Acids Res , vol.34
    • Chen, F.1    Mackey, A.J.2    Stoeckert Jr., C.J.3    Roos, D.S.4
  • 37
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • DOI 10.1126/science.1065659
    • Baker D, Sali A (2001) Protein structure prediction and structural genomics. Science 294:93-96. (Pubitemid 32952955)
    • (2001) Science , vol.294 , Issue.5540 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 38
    • 29144526714 scopus 로고    scopus 로고
    • Protein structure prediction: Inroads to biology
    • DOI 10.1016/j.molcel.2005.12.005, PII S1097276505018472
    • Petrey D, Honig B (2005) Protein structure prediction: inroads to biology. Mol Cell 20:811-819. (Pubitemid 41814871)
    • (2005) Molecular Cell , vol.20 , Issue.6 , pp. 811-819
    • Petrey, D.1    Honig, B.2
  • 39
    • 33646002994 scopus 로고    scopus 로고
    • Comparative modeling for protein structure prediction
    • Ginalski K (2006) Comparative modeling for protein structure prediction. Curr Opin Struct Biol 16:172-177.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 172-177
    • Ginalski, K.1
  • 40
    • 33645792604 scopus 로고    scopus 로고
    • Physically realistic homology models built with ROSETTA can be more accurate than their templates
    • Misura KM, Chivian D, Rohl CA, Kim DE, Baker D (2006) Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci USA 103:5361-5366.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 5361-5366
    • Misura, K.M.1    Chivian, D.2    Rohl, C.A.3    Kim, D.E.4    Baker, D.5
  • 42
    • 0031928367 scopus 로고    scopus 로고
    • Shining a light on structural genomics
    • DOI 10.1038/1334
    • Kim SH (1998) Shining a light on structural genomics. Nat Struct Biol 5 (Suppl):643-645. (Pubitemid 28363645)
    • (1998) Nature Structural Biology , vol.5 , Issue.8 SUPPL. , pp. 643-645
    • Kim, S.-H.1
  • 44
    • 5044251904 scopus 로고    scopus 로고
    • A practical and robust sequence search strategy for structural genomics target selection
    • DOI 10.1093/bioinformatics/bth240
    • Bray JE, Marsden RL, Rison SC, Savchenko A, Edwards AM, Thornton JM, Orengo CA (2004) A practical and robust sequence search strategy for structural genomics target selection. Bioinformatics 20:2288-2295. (Pubitemid 39341618)
    • (2004) Bioinformatics , vol.20 , Issue.14 , pp. 2288-2295
    • Bray, J.E.1    Marsden, R.L.2    Rison, S.C.G.3    Savchenko, A.4    Edwards, A.M.5    Thornton, J.M.6    Orengo, C.A.7
  • 45
    • 18044397545 scopus 로고    scopus 로고
    • Progress of structural genomics initiatives: An analysis of solved target structures
    • DOI 10.1016/j.jmb.2005.03.037
    • Todd AE, Marsden RL, Thornton JM, Orengo CA (2005) Progress of structural genomics initiatives: an analysis of solved target structures. J Mol Biol 348:1235-1260. (Pubitemid 40602364)
    • (2005) Journal of Molecular Biology , vol.348 , Issue.5 , pp. 1-26
    • Todd, A.E.1    Marsden, R.L.2    Thornton, J.M.3    Orengo, C.A.4
  • 46
    • 31144467558 scopus 로고    scopus 로고
    • The impact of structural genomics: Expectations and outcomes
    • DOI 10.1126/science.1121018
    • Chandonia JM, Brenner SE (2006) The impact of structural genomics: expectations and outcomes. Science 311:347-351. (Pubitemid 43132652)
    • (2006) Science , vol.311 , Issue.5759 , pp. 347-351
    • Chandonia, J.-M.1    Brenner, S.E.2
  • 47
    • 0036169142 scopus 로고    scopus 로고
    • LigBase: A database of families of aligned ligand binding sites in known protein sequences and structures
    • Stuart AC, Ilyin VA, Sali A (2002) LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics 18:200-201. (Pubitemid 34145052)
    • (2002) Bioinformatics , vol.18 , Issue.1 , pp. 200-201
    • Stuart, A.C.1    Llyin, V.A.2    Sali, A.3
  • 51
    • 11144323163 scopus 로고    scopus 로고
    • Virtual screening of chemical libraries
    • DOI 10.1038/nature03197
    • Shoichet BK (2004) Virtual screening of chemical libraries. Nature 432:862-865. (Pubitemid 40037142)
    • (2004) Nature , vol.432 , Issue.7019 , pp. 862-865
    • Shoichet, B.K.1
  • 56
    • 37349020962 scopus 로고    scopus 로고
    • Probing Protein Fold Space with a Simplified Model
    • DOI 10.1016/j.jmb.2007.10.087, PII S0022283607014581
    • Minary P, Levitt M (2008) Probing protein fold space with a simplified model. J Mol Biol 375:920-933. (Pubitemid 350309392)
    • (2008) Journal of Molecular Biology , vol.375 , Issue.4 , pp. 920-933
    • Minary, P.1    Levitt, M.2
  • 57
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 58
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: Identification of ortholog groups for eukaryotic genomes
    • DOI 10.1101/gr.1224503
    • Li L, Stoeckert CJ, Jr, Roos DS (2003). OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178-2189. (Pubitemid 37161775)
    • (2003) Genome Research , vol.13 , Issue.9 , pp. 2178-2189
    • Li, L.1    Stoeckert Jr., C.J.2    Roos, D.S.3
  • 60
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89:10915-10919.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 62
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. JMol Biol 234:779-815. (Pubitemid 223006096)
    • (1993) Journal of Molecular Biology , vol.234 , Issue.3 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 63
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov IN, Bourne PE (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 11:739-747. (Pubitemid 28434482)
    • (1998) Protein Engineering , vol.11 , Issue.9 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 64
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • DOI 10.1093/nar/gki524
    • Zhang Y, Skolnick J (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33:2302-2309. (Pubitemid 41439897)
    • (2005) Nucleic Acids Research , vol.33 , Issue.7 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.