메뉴 건너뛰기




Volumn 8, Issue 11, 2013, Pages e201308005-

Structure-based methods for computational protein functional site prediction

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84902169577     PISSN: None     EISSN: 20010370     Source Type: Journal    
DOI: 10.5936/csbj.201308005     Document Type: Short Survey
Times cited : (30)

References (51)
  • 1
    • 36448988254 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structure
    • DOI 10.1038/nrm2281, PII NRM2281
    • Lee D, Redfern O, Orengo C (2007) Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol 8:995-1005. (Pubitemid 350174637)
    • (2007) Nature Reviews Molecular Cell Biology , vol.8 , Issue.12 , pp. 995-1005
    • Lee, D.1    Redfern, O.2    Orengo, C.3
  • 2
    • 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
  • 3
    • 3042681902 scopus 로고    scopus 로고
    • ConSeq: The identification of functionally and structurally important residues in protein sequences
    • DOI 10.1093/bioinformatics/bth070
    • Berezin C, Glaser F, Rosenberg J, Paz I, Pupko T, et al. (2004) ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics 20:1322-1324. (Pubitemid 38807587)
    • (2004) Bioinformatics , vol.20 , Issue.8 , pp. 1322-1324
    • Berezin, C.1    Glaser, F.2    Rosenberg, J.3    Paz, I.4    Pupko, T.5    Fariselli, P.6    Casadio, R.7    Ben-Tal, N.8
  • 4
    • 34548133728 scopus 로고    scopus 로고
    • Predicting functionally important residues from sequence conservation
    • DOI 10.1093/bioinformatics/btm270
    • Capra JA, Singh M (2007) Predicting functionally important residues from sequence conservation. Bioinformatics 23:1875-1882. (Pubitemid 47299827)
    • (2007) Bioinformatics , vol.23 , Issue.15 , pp. 1875-1882
    • Capra, J.A.1    Singh, M.2
  • 6
    • 53749096681 scopus 로고    scopus 로고
    • Improving position-specific predictions of protein functional sites using phylogenetic motifs
    • KC DB, Livesay DR (2008) Improving position-specific predictions of protein functional sites using phylogenetic motifs. Bioinformatics 24:2308-2316.
    • (2008) Bioinformatics , vol.24 , pp. 2308-2316
    • Kc, D.B.1    Livesay, D.R.2
  • 7
    • 78449282705 scopus 로고    scopus 로고
    • Topology improves phylogenetic motif functional site predictions
    • KC DB, Livesay DR (2011) Topology improves phylogenetic motif functional site predictions. IEEE/ACM Trans Comput Biol Bioinform 8:226-233.
    • (2011) IEEE/ACM Trans Comput Biol Bioinform , vol.8 , pp. 226-233
    • Kc, D.B.1    Livesay, D.R.2
  • 8
    • 84902174383 scopus 로고    scopus 로고
    • A spectrum of phylogenetic-based approaches for predicting protein functional sites
    • New York: Humana Press
    • K C D B, R L D (2009) A spectrum of phylogenetic-based approaches for predicting protein functional sites. In Bioinformatics for Systems Biology. New York: Humana Press, pp. 315-337.
    • (2009) Bioinformatics for Systems Biology , pp. 315-337
  • 9
    • 84861463124 scopus 로고    scopus 로고
    • Functional region prediction with a set of appropriate homologous sequences-an index for sequence selection by integrating structure and sequence information with spatial statistics
    • Nemoto W, Toh H (2012) Functional region prediction with a set of appropriate homologous sequences-an index for sequence selection by integrating structure and sequence information with spatial statistics. BMC Struct Biol 12:11.
    • (2012) BMC Struct Biol , vol.12 , pp. 11
    • Nemoto, W.1    Toh, H.2
  • 10
    • 0035838976 scopus 로고    scopus 로고
    • Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
    • DOI 10.1006/jmbi.2001.4870
    • Aloy P, Querol E, Aviles FX, Sternberg MJ (2001) Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J Mol Biol 311:395-408. (Pubitemid 32744549)
    • (2001) Journal of Molecular Biology , vol.311 , Issue.2 , pp. 395-408
    • Aloy, P.1    Querol, E.2    Aviles, F.X.3    Sternberg, M.J.E.4
  • 11
    • 33645024859 scopus 로고    scopus 로고
    • Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins
    • Mihalek I, Res I, Lichtarge O (2006) Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins. Proteins 63:87-99.
    • (2006) Proteins , vol.63 , pp. 87-99
    • Mihalek, I.1    Res, I.2    Lichtarge, O.3
  • 12
    • 1242339659 scopus 로고    scopus 로고
    • A family of evolution-entropy hybrid methods for ranking protein residues by importance
    • DOI 10.1016/j.jmb.2003.12.078
    • Mihalek I, Res I, Lichtarge O (2004) A family of evolution-entropy hybrid methods for ranking protein residues by importance. J Mol Biol 336:1265-1282. (Pubitemid 38229712)
    • (2004) Journal of Molecular Biology , vol.336 , Issue.5 , pp. 1265-1282
    • Mihalek, I.1    Res, I.2    Lichtarge, O.3
  • 13
    • 0032475963 scopus 로고    scopus 로고
    • Supersites within superfolds. Binding site similarity in the absence of homology
    • DOI 10.1006/jmbi.1998.2043
    • Russell RB, Sasieni PD, Sternberg MJ (1998) Supersites within superfolds. Binding site similarity in the absence of homology. J Mol Biol 282:903-918. (Pubitemid 28442355)
    • (1998) Journal of Molecular Biology , vol.282 , Issue.4 , pp. 903-918
    • Russell, R.B.1    Sasieni, P.D.2    Sternberg, M.J.E.3
  • 15
    • 77954065271 scopus 로고    scopus 로고
    • I-TASSER: A unified platform for automated protein structure and function prediction
    • Roy A, Kucukural A, Zhang Y (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5:725-738.
    • (2010) Nat Protoc , vol.5 , pp. 725-738
    • Roy, A.1    Kucukural, A.2    Zhang, Y.3
  • 16
    • 78650905964 scopus 로고    scopus 로고
    • ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules
    • Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, et al. (2011) ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol 487:545-574.
    • (2011) Methods Enzymol , vol.487 , pp. 545-574
    • Leaver-Fay, A.1    Tyka, M.2    Lewis, S.M.3    Lange, O.F.4    Thompson, J.5
  • 17
    • 38349100452 scopus 로고    scopus 로고
    • A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
    • Brylinski M, Skolnick J (2008) A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci U S A 105:129-134.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 129-134
    • Brylinski, M.1    Skolnick, J.2
  • 18
    • 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
  • 19
    • 3142764482 scopus 로고    scopus 로고
    • Development and large scale benchmark testing of the PROSPECTOR-3 threading algorithm
    • DOI 10.1002/prot.20106
    • Skolnick J, Kihara D, Zhang Y (2004) Development and large scale benchmark testing of the PROSPECTOR-3 threading algorithm. Proteins 56:502-518. (Pubitemid 38924963)
    • (2004) Proteins: Structure, Function and Genetics , vol.56 , Issue.3 , pp. 502-518
    • Skolnick, J.1    Kihara, D.2    Zhang, Y.3
  • 20
    • 77952849162 scopus 로고    scopus 로고
    • ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment
    • Konc J, Janezic D (2010) ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment. Bioinformatics 26:1160-1168.
    • (2010) Bioinformatics , vol.26 , pp. 1160-1168
    • Konc, J.1    Janezic, D.2
  • 22
    • 84861975365 scopus 로고    scopus 로고
    • Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement
    • Roy A, Zhang Y (2012) Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement. Structure 20:987-997.
    • (2012) Structure , vol.20 , pp. 987-997
    • Roy, A.1    Zhang, Y.2
  • 23
    • 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
  • 24
    • 0027053611 scopus 로고
    • POCKET: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids
    • DOI 10.1016/0263-7855(92)80074-N
    • Levitt DC, Banaszak LJ (1992) POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J Mol Graph 10:229-234. (Pubitemid 23018967)
    • (1992) Journal of Molecular Graphics , vol.10 , Issue.4 , pp. 229-234
    • Levitt, D.G.1    Banaszak, L.J.2
  • 25
    • 0031370977 scopus 로고    scopus 로고
    • LIGSITE: Automatic and efficient detection of potential small molecule-binding sites in proteins
    • DOI 10.1016/S1093-3263(98)00002-3, PII S1093326398000023
    • Hendlich M, Rippmann F, Barnickel G (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graph Model 15:359-363, 389. (Pubitemid 28409807)
    • (1997) Journal of Molecular Graphics and Modelling , vol.15 , Issue.6 , pp. 359-363
    • Hendlich, M.1    Rippmann, F.2    Barnickel, G.3
  • 26
    • 33750029942 scopus 로고    scopus 로고
    • LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation
    • Huang B, Schroeder M (2006) LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol 6:19.
    • (2006) BMC Struct Biol , vol.6 , pp. 19
    • Huang, B.1    Schroeder, M.2
  • 27
    • 0028881975 scopus 로고
    • SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
    • 307-328
    • Laskowski RA (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 13:323-330, 307-328.
    • (1995) J Mol Graph , vol.13 , pp. 323-330
    • Laskowski, R.A.1
  • 28
    • 18744394070 scopus 로고    scopus 로고
    • Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites
    • DOI 10.1093/bioinformatics/bti315
    • Laurie AT, Jackson RM (2005) Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21:1908-1916. (Pubitemid 40668026)
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1908-1916
    • Laurie, A.T.R.1    Jackson, R.M.2
  • 29
    • 52249097805 scopus 로고    scopus 로고
    • Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures
    • Morita M, Nakamura S, Shimizu K (2008) Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures. Proteins 73:468-479.
    • (2008) Proteins , vol.73 , pp. 468-479
    • Morita, M.1    Nakamura, S.2    Shimizu, K.3
  • 30
    • 0031565725 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using patch analysis
    • DOI 10.1006/jmbi.1997.1233
    • Jones S, Thornton JM (1997) Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 272:133-143. (Pubitemid 27395543)
    • (1997) Journal of Molecular Biology , vol.272 , Issue.1 , pp. 133-143
    • Jones, S.1    Thornton, J.M.2
  • 32
    • 0017157584 scopus 로고
    • A simplified representation of protein conformations for rapid simulation of protein folding
    • Levitt M (1976) A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol 104:59-107.
    • (1976) J Mol Biol , vol.104 , pp. 59-107
    • Levitt, M.1
  • 33
    • 0019052221 scopus 로고
    • Hydrophobic basis of packing in globular proteins
    • Rose GD, Roy S (1980) Hydrophobic basis of packing in globular proteins. Proc Natl Acad Sci U S A 77:4643-4647.
    • (1980) Proc Natl Acad Sci U S A , vol.77 , pp. 4643-4647
    • Rose, G.D.1    Roy, S.2
  • 34
    • 27544512084 scopus 로고    scopus 로고
    • The SuMo server: 3D search for protein functional sites
    • DOI 10.1093/bioinformatics/bti645
    • Jambon M, Andrieu O, Combet C, Deleage G, Delfaud F, et al. (2005) The SuMo server: 3D search for protein functional sites. Bioinformatics 21:3929-3930. (Pubitemid 41535510)
    • (2005) Bioinformatics , vol.21 , Issue.20 , pp. 3929-3930
    • Jambon, M.1    Andrieu, O.2    Combet, C.3    Deleage, G.4    Delfaud, F.5    Geourjon, C.6
  • 35
    • 22544441094 scopus 로고    scopus 로고
    • ProFunc: A server for predicting protein function from 3D structure
    • DOI 10.1093/nar/gki414 WEB. SERV. ISS.
    • Laskowski RA, Watson JD, Thornton JM (2005) ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 33:W89-93. (Pubitemid 44529886)
    • (2005) Nucleic Acids Research , vol.33
    • Laskowski, R.A.1    Watson, J.D.2    Thornton, J.M.3
  • 36
    • 84856084072 scopus 로고    scopus 로고
    • FTSite: High accuracy detection of ligand binding sites on unbound protein structures
    • Ngan CH, Hall DR, Zerbe B, Grove LE, Kozakov D, et al. (2012) FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinformatics 28:286-287.
    • (2012) Bioinformatics , vol.28 , pp. 286-287
    • Ngan, C.H.1    Hall, D.R.2    Zerbe, B.3    Grove, L.E.4    Kozakov, D.5
  • 37
    • 17144373303 scopus 로고    scopus 로고
    • Druggability indices for protein targets derived from NMr-based screening data
    • DOI 10.1021/jm049131r
    • Hajduk PJ, Huth JR, Fesik SW (2005) Druggability indices for protein targets derived from NMR-based screening data. J Med Chem 48:2518-2525. (Pubitemid 40516441)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.7 , pp. 2518-2525
    • Hajduk, P.J.1    Huth, J.R.2    Fesik, S.W.3
  • 38
    • 61449104961 scopus 로고    scopus 로고
    • Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques
    • Brenke R, Kozakov D, Chuang GY, Beglov D, Hall D, et al. (2009) Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics 25:621-627.
    • (2009) Bioinformatics , vol.25 , pp. 621-627
    • Brenke, R.1    Kozakov, D.2    Chuang, G.Y.3    Beglov, D.4    Hall, D.5
  • 39
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • DOI 10.1006/jmbi.1996.0167
    • Lichtarge O, Bourne HR, Cohen FE (1996) An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 257:342-358. (Pubitemid 26114038)
    • (1996) Journal of Molecular Biology , vol.257 , Issue.2 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 40
    • 74549149999 scopus 로고    scopus 로고
    • Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
    • Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA (2009) Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput Biol 5:e1000585.
    • (2009) PLoS Comput Biol , vol.5
    • Capra, J.A.1    Laskowski, R.A.2    Thornton, J.M.3    Singh, M.4    Funkhouser, T.A.5
  • 41
    • 77954257799 scopus 로고    scopus 로고
    • ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
    • Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res 38:W529-533.
    • (2010) Nucleic Acids Res , vol.38
    • Ashkenazy, H.1    Erez, E.2    Martz, E.3    Pupko, T.4    Ben-Tal, N.5
  • 42
    • 77955019084 scopus 로고    scopus 로고
    • Parallelization of the MAFFT multiple sequence alignment program
    • Katoh K, Toh H (2010) Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics 26:1899-1900.
    • (2010) Bioinformatics , vol.26 , pp. 1899-1900
    • Katoh, K.1    Toh, H.2
  • 43
    • 0002218484 scopus 로고    scopus 로고
    • Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
    • Pupko T, Bell RE, Mayrose I, Glaser F, 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 Suppl 1:S71-77. (Pubitemid 41185639)
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Pupko, T.1    Bell, R.E.2    Mayrose, I.3    Glaser, F.4    Ben-Tal, N.5
  • 45
    • 2542445427 scopus 로고    scopus 로고
    • ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
    • DOI 10.1093/bioinformatics/19.1.163
    • Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, et al. (2003) ConSurf: identification of functional regions in proteins by surfacemapping of phylogenetic information. Bioinformatics 19:163-164. (Pubitemid 36150199)
    • (2003) Bioinformatics , vol.19 , Issue.1 , pp. 163-164
    • Glaser, F.1    Pupko, T.2    Paz, I.3    Bell, R.E.4    Bechor-Shental, D.5    Martz, E.6    Ben-Tal, N.7
  • 46
    • 12944257228 scopus 로고    scopus 로고
    • The ConSurf-HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures
    • DOI 10.1002/prot.20305
    • Glaser F, Rosenberg Y, Kessel A, Pupko T, Ben-Tal N (2005) The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures. Proteins 58:610-617. (Pubitemid 40176033)
    • (2005) Proteins: Structure, Function and Genetics , vol.58 , Issue.3 , pp. 610-617
    • Glaser, F.1    Rosenberg, Y.2    Kessel, A.3    Pupko, T.4    Ben-Tal, N.5
  • 48
    • 69249150494 scopus 로고    scopus 로고
    • MetaPocket: A meta approach to improve protein ligand binding site prediction
    • Huang B (2009) MetaPocket: a meta approach to improve protein ligand binding site prediction. OMICS 13:325-330.
    • (2009) OMICS , vol.13 , pp. 325-330
    • Huang, B.1
  • 49
    • 0342424187 scopus 로고    scopus 로고
    • Fast prediction and visualization of protein binding pockets with PASS
    • DOI 10.1023/A:1008124202956
    • Brady GP, Jr., Stouten PF (2000) Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided Mol Des 14:383-401. (Pubitemid 30219399)
    • (2000) Journal of Computer-Aided Molecular Design , vol.14 , Issue.4 , pp. 383-401
    • Brady Jr., G.P.1    Stouten, P.F.W.2
  • 50
    • 4544230537 scopus 로고    scopus 로고
    • Distinguishing structural and functional restraints in evolution in order to identify interaction sites
    • DOI 10.1016/j.jmb.2004.08.022, PII S0022283604009830
    • Chelliah V, Chen L, Blundell TL, Lovell SC (2004) Distinguishing structural and functional restraints in evolution in order to identify interaction sites. J Mol Biol 342:1487-1504. (Pubitemid 39213963)
    • (2004) Journal of Molecular Biology , vol.342 , Issue.5 , pp. 1487-1504
    • Chelliah, V.1    Chen, L.2    Blundell, T.L.3    Lovell, S.C.4
  • 51
    • 27144551715 scopus 로고    scopus 로고
    • Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design
    • DOI 10.1093/nar/gki894
    • Cheng G, Qian B, Samudrala R, Baker D (2005) Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Res 33:5861-5867. (Pubitemid 41742605)
    • (2005) Nucleic Acids Research , vol.33 , Issue.18 , pp. 5861-5867
    • Cheng, G.1    Qian, B.2    Samudrala, R.3    Baker, D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.