메뉴 건너뛰기




Volumn 12, Issue , 2011, Pages

FunFOLD: An improved automated method for the prediction of ligand binding residues using 3D models of proteins

Author keywords

[No Author keywords available]

Indexed keywords

ACCURATE PREDICTION; AUTOMATIC APPROACHES; CORRELATION COEFFICIENT; FUNCTION PREDICTION; FUNCTIONAL ANNOTATION; LIGAND-BINDING RESIDUES; LIGAND-BINDING SITES; STRUCTURAL SUPERPOSITIONS;

EID: 79955892164     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-160     Document Type: Article
Times cited : (68)

References (38)
  • 1
    • 74249093706 scopus 로고    scopus 로고
    • Assessment of ligand binding residue predictions in CASP8
    • Lopez G, Ezkurdia I, Tress ML. Assessment of ligand binding residue predictions in CASP8. Proteins 2009, 77(Suppl 9):138-146.
    • (2009) Proteins , vol.77 , Issue.SUPPL. 9 , pp. 138-146
    • Lopez, G.1    Ezkurdia, I.2    Tress, M.L.3
  • 3
    • 74249102742 scopus 로고    scopus 로고
    • Protein-binding site prediction based on three-dimensional protein modeling
    • Oh M, Joo K, Lee J. Protein-binding site prediction based on three-dimensional protein modeling. Proteins 2009, 77(Suppl 9):152-156.
    • (2009) Proteins , vol.77 , Issue.SUPPL. 9 , pp. 152-156
    • Oh, M.1    Joo, K.2    Lee, J.3
  • 4
    • 34547575992 scopus 로고    scopus 로고
    • Firestar--prediction of functionally important residues using structural templates and alignment reliability
    • Lopez G, Valencia A, Tress ML. firestar--prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Res 2007, (35 Web Server):W573-577.
    • (2007) Nucleic Acids Res , Issue.35
    • Lopez, G.1    Valencia, A.2    Tress, M.L.3
  • 5
    • 65449148627 scopus 로고    scopus 로고
    • WSsas: a web service for the annotation of functional residues through structural homologues
    • 10.1093/bioinformatics/btp116, 19251774
    • Talavera D, Laskowski RA, Thornton JM. WSsas: a web service for the annotation of functional residues through structural homologues. Bioinformatics 2009, 25(9):1192-1194. 10.1093/bioinformatics/btp116, 19251774.
    • (2009) Bioinformatics , vol.25 , Issue.9 , pp. 1192-1194
    • Talavera, D.1    Laskowski, R.A.2    Thornton, J.M.3
  • 6
    • 40049091146 scopus 로고    scopus 로고
    • Prediction of protein functional residues from sequence by probability density estimation
    • 10.1093/bioinformatics/btm626, 18174181
    • Fischer JD, Mayer CE, Soding J. Prediction of protein functional residues from sequence by probability density estimation. Bioinformatics 2008, 24(5):613-620. 10.1093/bioinformatics/btm626, 18174181.
    • (2008) Bioinformatics , vol.24 , Issue.5 , pp. 613-620
    • Fischer, J.D.1    Mayer, C.E.2    Soding, J.3
  • 7
    • 40749111548 scopus 로고    scopus 로고
    • ConFunc--functional annotation in the twilight zone
    • 10.1093/bioinformatics/btn037, 18263643
    • Wass MN, Sternberg MJ. ConFunc--functional annotation in the twilight zone. Bioinformatics 2008, 24(6):798-806. 10.1093/bioinformatics/btn037, 18263643.
    • (2008) Bioinformatics , vol.24 , Issue.6 , pp. 798-806
    • Wass, M.N.1    Sternberg, M.J.2
  • 8
    • 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. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res 2010, 38 Suppl:W529-533.
    • (2010) Nucleic Acids Res , vol.38 Suppl
    • Ashkenazy, H.1    Erez, E.2    Martz, E.3    Pupko, T.4    Ben-Tal, N.5
  • 9
    • 7244245640 scopus 로고    scopus 로고
    • Sequence patterns derived from the automated prediction of functional residues in structurally-aligned homologous protein families
    • 10.1093/bioinformatics/bth255, 15073006
    • Miguel RN. Sequence patterns derived from the automated prediction of functional residues in structurally-aligned homologous protein families. Bioinformatics 2004, 20(15):2380-2389. 10.1093/bioinformatics/bth255, 15073006.
    • (2004) Bioinformatics , vol.20 , Issue.15 , pp. 2380-2389
    • Miguel, R.N.1
  • 10
    • 67849101184 scopus 로고    scopus 로고
    • INTREPID: a web server for prediction of functionally important residues by evolutionary analysis
    • Sankararaman S, Kolaczkowski B, Sjolander K. INTREPID: a web server for prediction of functionally important residues by evolutionary analysis. Nucleic Acids Res (37 Web Server):W390-395.
    • Nucleic Acids Res , Issue.37
    • Sankararaman, S.1    Kolaczkowski, B.2    Sjolander, K.3
  • 11
    • 38349100452 scopus 로고    scopus 로고
    • A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
    • 10.1073/pnas.0707684105, 2224172, 18165317
    • Brylinski M, Skolnick J. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci USA 2008, 105(1):129-134. 10.1073/pnas.0707684105, 2224172, 18165317.
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.1 , pp. 129-134
    • Brylinski, M.1    Skolnick, J.2
  • 12
    • 77949420656 scopus 로고    scopus 로고
    • Comparison of structure-based and threading-based approaches to protein functional annotation
    • 2804779, 19731377
    • Brylinski M, Skolnick J. Comparison of structure-based and threading-based approaches to protein functional annotation. Proteins 2010, 78(1):118-134. 2804779, 19731377.
    • (2010) Proteins , vol.78 , Issue.1 , pp. 118-134
    • Brylinski, M.1    Skolnick, J.2
  • 13
    • 67849097355 scopus 로고    scopus 로고
    • SITEHOUND-web: a server for ligand binding site identification in protein structures
    • Hernandez M, Ghersi D, Sanchez R. SITEHOUND-web: a server for ligand binding site identification in protein structures. Nucleic Acids Res 2009, (37 Web Server):W413-416.
    • (2009) Nucleic Acids Res , Issue.37
    • Hernandez, M.1    Ghersi, D.2    Sanchez, R.3
  • 14
    • 18744394070 scopus 로고    scopus 로고
    • Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
    • 10.1093/bioinformatics/bti315, 15701681
    • Laurie AT, Jackson RM. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005, 21(9):1908-1916. 10.1093/bioinformatics/bti315, 15701681.
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1908-1916
    • Laurie, A.T.1    Jackson, R.M.2
  • 15
    • 77954299402 scopus 로고    scopus 로고
    • 3DLigandSite: predicting ligand-binding sites using similar structures
    • Wass MN, Kelley LA, Sternberg MJ. 3DLigandSite: predicting ligand-binding sites using similar structures. Nucleic Acids Res 2010, 38 Suppl:W469-473.
    • (2010) Nucleic Acids Res , vol.38 Suppl
    • Wass, M.N.1    Kelley, L.A.2    Sternberg, M.J.3
  • 16
    • 33746267388 scopus 로고    scopus 로고
    • YASSPP: better kernels and coding schemes lead to improvements in protein secondary structure prediction
    • 10.1002/prot.21036, 16763996
    • Karypis G. YASSPP: better kernels and coding schemes lead to improvements in protein secondary structure prediction. Proteins 2006, 64(3):575-586. 10.1002/prot.21036, 16763996.
    • (2006) Proteins , vol.64 , Issue.3 , pp. 575-586
    • Karypis, G.1
  • 17
    • 4143055915 scopus 로고    scopus 로고
    • Predicting metal-binding site residues in low-resolution structural models
    • 10.1016/j.jmb.2004.07.019, 15313626
    • Sodhi JS, Bryson K, McGuffin LJ, Ward JJ, Wernisch L, Jones DT. Predicting metal-binding site residues in low-resolution structural models. J Mol Biol 2004, 342(1):307-320. 10.1016/j.jmb.2004.07.019, 15313626.
    • (2004) J Mol Biol , vol.342 , Issue.1 , pp. 307-320
    • Sodhi, J.S.1    Bryson, K.2    McGuffin, L.J.3    Ward, J.J.4    Wernisch, L.5    Jones, D.T.6
  • 18
    • 33750029942 scopus 로고    scopus 로고
    • LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation
    • 10.1186/1472-6807-6-19, 1601958, 16995956
    • Huang B, Schroeder M. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol 2006, 6:19. 10.1186/1472-6807-6-19, 1601958, 16995956.
    • (2006) BMC Struct Biol , vol.6 , pp. 19
    • Huang, B.1    Schroeder, M.2
  • 19
    • 77951210909 scopus 로고    scopus 로고
    • Mapping of ligand-binding cavities in proteins
    • 2957484, 20034113
    • Andersson CD, Chen BY, Linusson A. Mapping of ligand-binding cavities in proteins. Proteins 2010, 78(6):1408-1422. 2957484, 20034113.
    • (2010) Proteins , vol.78 , Issue.6 , pp. 1408-1422
    • Andersson, C.D.1    Chen, B.Y.2    Linusson, A.3
  • 20
    • 30344440806 scopus 로고    scopus 로고
    • The prediction of protein function at CASP6
    • Soro S, Tramontano A. The prediction of protein function at CASP6. Proteins 2005, 61(Suppl 7):201-213.
    • (2005) Proteins , vol.61 , Issue.SUPPL. 7 , pp. 201-213
    • Soro, S.1    Tramontano, A.2
  • 21
    • 36748998785 scopus 로고    scopus 로고
    • Assessment of predictions submitted for the CASP7 function prediction category
    • Lopez G, Rojas A, Tress M, Valencia A. Assessment of predictions submitted for the CASP7 function prediction category. Proteins 2007, 69(Suppl 8):165-174.
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 165-174
    • Lopez, G.1    Rojas, A.2    Tress, M.3    Valencia, A.4
  • 22
    • 74249093489 scopus 로고    scopus 로고
    • Prediction of ligand binding sites using homologous structures and conservation at CASP8
    • 2814558, 19626715
    • Wass MN, Sternberg MJ. Prediction of ligand binding sites using homologous structures and conservation at CASP8. Proteins 2009, 77(Suppl 9):147-151. 2814558, 19626715.
    • (2009) Proteins , vol.77 , Issue.SUPPL. 9 , pp. 147-151
    • Wass, M.N.1    Sternberg, M.J.2
  • 23
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: a simple approach to improve protein structure predictions
    • 10.1093/bioinformatics/btg124, 12761065
    • Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003, 19(8):1015-1018. 10.1093/bioinformatics/btg124, 12761065.
    • (2003) Bioinformatics , vol.19 , Issue.8 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 24
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the Web: a case study using the Phyre server
    • 10.1038/nprot.2009.2, 19247286
    • Kelley LA, Sternberg MJ. Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 2009, 4(3):363-371. 10.1038/nprot.2009.2, 19247286.
    • (2009) Nat Protoc , vol.4 , Issue.3 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.2
  • 25
    • 0036839162 scopus 로고    scopus 로고
    • MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison
    • 2373724, 12381844
    • Ortiz AR, Strauss CE, Olmea O. MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci 2002, 11(11):2606-2621. 2373724, 12381844.
    • (2002) Protein Sci , vol.11 , Issue.11 , pp. 2606-2621
    • Ortiz, A.R.1    Strauss, C.E.2    Olmea, O.3
  • 26
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • 10.1093/nar/25.17.3389, 146917, 9254694
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
    • (1997) Nucleic Acids Res , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 27
    • 84888283026 scopus 로고    scopus 로고
    • CASP9 function prediction assessment
    • CASP9 function prediction assessment. , http://www.predictioncenter.org/casp9/doc/presentations/CASP9_FN.pdf
  • 28
    • 77950478720 scopus 로고    scopus 로고
    • Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments
    • 10.1093/bioinformatics/btp629, 19897565
    • McGuffin LJ, Roche DB. Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments. Bioinformatics 2010, 26(2):182-188. 10.1093/bioinformatics/btp629, 19897565.
    • (2010) Bioinformatics , vol.26 , Issue.2 , pp. 182-188
    • McGuffin, L.J.1    Roche, D.B.2
  • 29
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: a protein structure alignment algorithm based on the TM-score
    • 10.1093/nar/gki524, 1084323, 15849316
    • Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005, 33(7):2302-2309. 10.1093/nar/gki524, 1084323, 15849316.
    • (2005) Nucleic Acids Res , vol.33 , Issue.7 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 30
    • 33846088140 scopus 로고    scopus 로고
    • FireDB--a database of functionally important residues from proteins of known structure
    • Lopez G, Valencia A, Tress M. FireDB--a database of functionally important residues from proteins of known structure. Nucleic Acids Res 2007, (35 Database):D219-223.
    • (2007) Nucleic Acids Res , Issue.35
    • Lopez, G.1    Valencia, A.2    Tress, M.3
  • 31
    • 77951961719 scopus 로고    scopus 로고
    • How significant is a protein structure similarity with TM-score = 0.5?
    • 10.1093/bioinformatics/btq066, 2913670, 20164152
    • Xu J, Zhang Y. How significant is a protein structure similarity with TM-score = 0.5?. Bioinformatics 2010, 26(7):889-895. 10.1093/bioinformatics/btq066, 2913670, 20164152.
    • (2010) Bioinformatics , vol.26 , Issue.7 , pp. 889-895
    • Xu, J.1    Zhang, Y.2
  • 32
    • 84888285205 scopus 로고    scopus 로고
    • CASP downloads
    • CASP downloads. , http://predictioncenter.org/download_area/
  • 33
    • 79959564695 scopus 로고    scopus 로고
    • The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction
    • Roche DB, Buenavista MT, Tetchner SJ, McGuffin LJ. The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction. Nucleic Acids Res 2011,
    • (2011) Nucleic Acids Res
    • Roche, D.B.1    Buenavista, M.T.2    Tetchner, S.J.3    McGuffin, L.J.4
  • 34
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • 10.1073/pnas.85.8.2444, 280013, 3162770
    • Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988, 85(8):2444-2448. 10.1073/pnas.85.8.2444, 280013, 3162770.
    • (1988) Proc Natl Acad Sci USA , vol.85 , Issue.8 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 35
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Matthews BW. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 1975, 405(2):442-451.
    • (1975) Biochim Biophys Acta , vol.405 , Issue.2 , pp. 442-451
    • Matthews, B.W.1
  • 36
    • 78149275853 scopus 로고    scopus 로고
    • The binding site distance test score: a robust method for the assessment of predicted protein binding sites
    • 10.1093/bioinformatics/btq543, 20861025
    • Roche DB, Tetchner SJ, McGuffin LJ. The binding site distance test score: a robust method for the assessment of predicted protein binding sites. Bioinformatics 2010, 26(22):2920-2921. 10.1093/bioinformatics/btq543, 20861025.
    • (2010) Bioinformatics , vol.26 , Issue.22 , pp. 2920-2921
    • Roche, D.B.1    Tetchner, S.J.2    McGuffin, L.J.3
  • 37
    • 74249087111 scopus 로고    scopus 로고
    • Prediction of global and local model quality in CASP8 using the ModFOLD server
    • McGuffin LJ. Prediction of global and local model quality in CASP8 using the ModFOLD server. Proteins 2009, 77(Suppl 9):185-190.
    • (2009) Proteins , vol.77 , Issue.SUPPL. 9 , pp. 185-190
    • McGuffin, L.J.1
  • 38
    • 49549111841 scopus 로고    scopus 로고
    • Intrinsic disorder prediction from the analysis of multiple protein fold recognition models
    • 10.1093/bioinformatics/btn326, 18579567
    • McGuffin LJ. Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. Bioinformatics 2008, 24(16):1798-1804. 10.1093/bioinformatics/btn326, 18579567.
    • (2008) Bioinformatics , vol.24 , Issue.16 , pp. 1798-1804
    • McGuffin, L.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.