메뉴 건너뛰기




Volumn 77, Issue 1, 2009, Pages 220-234

A novel method for predicting and using distance constraints of high accuracy for refining protein structure prediction

Author keywords

Knowledge based functions; Protein structure prediction; Refinement

Indexed keywords

ARTICLE; BAYES THEOREM; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROBABILITY; PROTEIN STRUCTURE; SIMULATION; STRUCTURE ANALYSIS;

EID: 70349313259     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22434     Document Type: Article
Times cited : (6)

References (50)
  • 1
    • 0032751746 scopus 로고    scopus 로고
    • Predicting protein three-dimensional structure
    • Moult J. Predicting protein three-dimensional structure. Curr Opin Biotechnol 1999;10:583-588.
    • (1999) Curr Opin Biotechnol , vol.10 , pp. 583-588
    • Moult, J.1
  • 3
    • 20444484434 scopus 로고    scopus 로고
    • A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction
    • DOI 10.1016/j.sbi.2005.05.011, PII S0959440X05000953
    • Moult J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol 2005;15:285-289. (Pubitemid 40826447)
    • (2005) Current Opinion in Structural Biology , vol.15 , Issue.3 SPEC. ISS , pp. 285-289
    • Moult, J.1
  • 4
    • 0037264352 scopus 로고    scopus 로고
    • Homology modeling
    • Bourne PE, Weissig H, editors. Hoboken, NJ: Wiley-Liss
    • Krieger E, Nabuurs SB, Vriend G. Homology modeling. In: Bourne PE, Weissig H, editors. Structural bioinformatics. Hoboken, NJ: Wiley-Liss; 2003. pp 509-523.
    • (2003) Structural Bioinformatics , pp. 509-523
    • Krieger, E.1    Nabuurs, S.B.2    Vriend, G.3
  • 5
    • 13744252339 scopus 로고    scopus 로고
    • Accuracy of structure-derived properties in simple comparative models of protein structures
    • DOI 10.1093/nar/gki162
    • Chakravarty S, Wang L, Sanchez R. Accuracy of structure-derived properties in simple comparative models of protein structures. Nucleic Acids Res 2005;33:244-259. (Pubitemid 40276946)
    • (2005) Nucleic Acids Research , vol.33 , Issue.1 , pp. 244-259
    • Chakravarty, S.1    Wang, L.2    Sanchez, R.3
  • 6
    • 10844286440 scopus 로고    scopus 로고
    • Relationship between multiple sequence alignments and quality of protein comparative models
    • DOI 10.1002/prot.20284
    • Cozzetto D, Tramontano A. Relationship between multiple sequence alignments and quality of protein comparative models. Proteins 2005;58:151-157. (Pubitemid 39665626)
    • (2005) Proteins: Structure, Function and Genetics , vol.58 , Issue.1 , pp. 151-157
    • Cozzetto, D.1    Tramontano, A.2
  • 7
    • 24944493938 scopus 로고    scopus 로고
    • Biochemistry: Toward high-resolution de novo structure prediction for small proteins
    • DOI 10.1126/science.1113801
    • Bradley P, Misura KM, Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 2005;309:1868-1871. (Pubitemid 41325099)
    • (2005) Science , vol.309 , Issue.5742 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.S.2    Baker, D.3
  • 8
    • 13844291273 scopus 로고    scopus 로고
    • Protein refinement: A new challenge for CASP in its 10th anniversary
    • DOI 10.1093/bioinformatics/bti249
    • Valencia A. Protein refinement: a new challenge for CASP in its 10th anniversary. Bioinformatics 2005;21:277. (Pubitemid 40246597)
    • (2005) Bioinformatics , vol.21 , Issue.3 , pp. 277
    • Valencia, A.1
  • 10
    • 0025350388 scopus 로고
    • From comparisons of protein sequences and structures to protein modelling and design
    • Sali A, Overington JP, Johnson MS, Blundell TL. From comparisons of protein sequences and structures to protein modelling and design. Trends Biochem Sci 1990;15:235-240. (Pubitemid 20175357)
    • (1990) Trends in Biochemical Sciences , vol.15 , Issue.6 , pp. 235-240
    • Sali, A.1    Overington, J.P.2    Johnson, M.S.3    Blundell, T.L.4
  • 11
    • 0347383758 scopus 로고    scopus 로고
    • MODELLER: Generation and Refinement of Homology-Based Protein Structure Models
    • DOI 10.1016/S0076-6879(03)74020-8
    • Fiser A, Sali A. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 2003;374:461-491. (Pubitemid 37531821)
    • (2003) Methods in Enzymology , vol.374 , pp. 461-491
    • Fiser, A.1    Sali, A.2
  • 12
    • 27344449197 scopus 로고    scopus 로고
    • Progress in modeling of protein structures and interactions
    • DOI 10.1126/science.1112160
    • Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D. Progress in modeling of protein structures and interactions. Science 2005;310:638-642. (Pubitemid 41528148)
    • (2005) Science , vol.310 , Issue.5748 , pp. 638-642
    • Schueler-Furman, O.1    Wang, C.2    Bradley, P.3    Misura, K.4    Baker, D.5
  • 13
    • 0021097083 scopus 로고
    • The combinatorial distance geometry method for the calculation of molecular conformation. I. a new approach to an old problem
    • Havel TF, Kuntz ID, Crippen GM. The combinatorial distance geometry method for the calculation of molecular conformation. I. A new approach to an old problem. J Theor Biol 1983;104:359-381.
    • (1983) J Theor Biol , vol.104 , pp. 359-381
    • Havel, T.F.1    Kuntz, I.D.2    Crippen, G.M.3
  • 14
    • 0029097099 scopus 로고
    • Global fold determination from a small number of distance restraints
    • Aszodi A, Gradwell MJ, Taylor WR. Global fold determination from a small number of distance restraints. J Mol Biol 1995;251:308-326.
    • (1995) J Mol Biol , vol.251 , pp. 308-326
    • Aszodi, A.1    Gradwell, M.J.2    Taylor, W.R.3
  • 15
    • 0031303336 scopus 로고    scopus 로고
    • Protein modeling by multiple sequence threading and distance geometry
    • DOI 10.1002/(SICI)1097-0134(1997)1+<38::AID-PROT6>3.0.CO;2-K
    • Aszodi A, Munro RE, Taylor WR. Protein modeling by multiple sequence threading and distance geometry. Proteins 1997;29(Suppl 1):38-42. (Pubitemid 28090479)
    • (1997) Proteins: Structure, Function and Genetics , vol.29 , Issue.SUPPL. 1 , pp. 38-42
    • Aszodi, A.1    Munro, R.E.J.2    Taylor, W.R.3
  • 16
    • 0028238582 scopus 로고
    • Pattern recognition and self-correcting distance geometry calculations applied to myohemerythrin
    • DOI 10.1016/0014-5793(94)00366-1
    • Hanggi G, Braun W. Pattern recognition and self-correcting distance geometry calculations applied to myohemerythrin. FEBS Lett 1994;344:147-153. (Pubitemid 24154628)
    • (1994) FEBS Letters , vol.344 , Issue.2-3 , pp. 147-153
    • Braun, W.1
  • 17
    • 0028955505 scopus 로고
    • Predicting the helix packing of globular proteins by self-correcting distance geometry
    • Mumenthaler C, Braun W. Predicting the helix packing of globular proteins by self-correcting distance geometry. Protein Sci 1995;4:863-871.
    • (1995) Protein Sci , vol.4 , pp. 863-871
    • Mumenthaler, C.1    Braun, W.2
  • 18
    • 0031575423 scopus 로고    scopus 로고
    • MONSSTER: A method for folding globular proteins with a small number of distance restraints
    • DOI 10.1006/jmbi.1996.0720
    • Skolnick J, Kolinski A, Ortiz AR. Monsster: a method for folding globular proteins with a small number of distance restraints. J Mol Biol 1997;265:217-241. (Pubitemid 27110659)
    • (1997) Journal of Molecular Biology , vol.265 , Issue.2 , pp. 217-241
    • Skolnick, J.1    Kolinski, A.2    Ortiz, A.R.3
  • 19
    • 0032571390 scopus 로고    scopus 로고
    • Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments
    • DOI 10.1006/jmbi.1997.1595
    • Ortiz AR, Kolinski A, Skolnick J. Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments. J Mol Biol 1998;277:419-448. (Pubitemid 28174978)
    • (1998) Journal of Molecular Biology , vol.277 , Issue.2 , pp. 419-448
    • Ortiz, A.R.1    Kolinski, A.2    Skolnick, J.3
  • 20
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program DYANA
    • DOI 10.1006/jmbi.1997.1284
    • Guntert P, Mumenthaler C, Wuthrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 1997;273:283-298. (Pubitemid 27460230)
    • (1997) Journal of Molecular Biology , vol.273 , Issue.1 , pp. 283-298
    • Guntert, P.1    Mumenthaler, C.2    Wuthrich, K.3
  • 22
    • 0027168790 scopus 로고
    • Global folding of proteins using a limited number of distance constraints
    • Smith-Brown MJ, Kominos D, Levy RM. Global folding of proteins using a limited number of distance constraints. Protein Eng 1993;6:605-614. (Pubitemid 23246511)
    • (1993) Protein Engineering , vol.6 , Issue.6 , pp. 605-614
    • Smith-Brown, M.J.1    Kominos, D.2    Levy, R.M.3
  • 23
    • 0031855094 scopus 로고    scopus 로고
    • Assembly of protein structure from sparse experimental data: An efficient Monte Carlo model
    • DOI 10.1002/(SICI)1097-0134(19980901)32:4<475::AID-PROT6>3.0.CO;2-F
    • Kolinski A, Skolnick J. Assembly of protein structure from sparse experimental data: an efficient monte carlo model. Proteins 1998;32:475-494. (Pubitemid 28380787)
    • (1998) Proteins: Structure, Function and Genetics , vol.32 , Issue.4 , pp. 475-494
    • Kolinski, A.1    Skolnick, J.2
  • 24
    • 0031687654 scopus 로고    scopus 로고
    • Distance geometry generates native-like folds for small helical proteins using the consensus distances of predicted protein structures
    • Huang ES, Samudrala R, Ponder JW. Distance geometry generates native-like folds for small helical proteins using the consensus distances of predicted protein structures. Protein Sci 1998;7:1998-2003. (Pubitemid 28432441)
    • (1998) Protein Science , vol.7 , Issue.9 , pp. 1998-2003
    • Huang, E.S.1    Samudrala, R.2    Ponder, J.W.3
  • 25
    • 0033516514 scopus 로고    scopus 로고
    • Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions
    • DOI 10.1006/jmbi.1999.2861
    • Huang ES, Samudrala R, Ponder JW. Ab initio fold prediction of small helical proteins using distance geometry and knowledge based scoring functions. J Mol Biol 1999;290:267-281. (Pubitemid 29308590)
    • (1999) Journal of Molecular Biology , vol.290 , Issue.1 , pp. 267-281
    • Huang, E.S.1    Samudrala, R.2    Ponder, J.W.3
  • 26
    • 36049029967 scopus 로고    scopus 로고
    • High-resolution structure prediction and the crystallographic phase problem
    • DOI 10.1038/nature06249, PII NATURE06249
    • Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D. High-resolution structure prediction and the crystallographic phase problem. Nature 2007;450:259-264. (Pubitemid 350100534)
    • (2007) Nature , vol.450 , Issue.7167 , pp. 259-264
    • Qian, B.1    Raman, S.2    Das, R.3    Bradley, P.4    McCoy, A.J.5    Read, R.J.6    Baker, D.7
  • 27
    • 33750967051 scopus 로고    scopus 로고
    • An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data
    • DOI 10.1007/s10858-006-9082-1
    • Hung LH, Samudrala R. An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data. J Biomol NMR 2006;36:189-198. (Pubitemid 44740882)
    • (2006) Journal of Biomolecular NMR , vol.36 , Issue.3 , pp. 189-198
    • Hung, L.-H.1    Samudrala, R.2
  • 29
    • 50849144042 scopus 로고    scopus 로고
    • Contact prediction in protein modeling: Scoring, folding and refinement of coarse-grained models
    • Latek D, Kolinski A. Contact prediction in protein modeling: scoring, folding and refinement of coarse-grained models. BMC Struct Biol 2008;8:36.
    • (2008) BMC Struct Biol , vol.8 , pp. 36
    • Latek, D.1    Kolinski, A.2
  • 31
    • 0029982530 scopus 로고    scopus 로고
    • The structural alignment between two proteins: Is there a unique answer?
    • Godzik A. The structural alignment between two proteins: is there a unique answer? Protein Sci 1996;5:1325-1338.
    • (1996) Protein Sci , vol.5 , pp. 1325-1338
    • Godzik, A.1
  • 32
    • 17744387920 scopus 로고    scopus 로고
    • All are not equal: A benchmark of different homology modeling programs
    • DOI 10.1110/ps.041253405
    • Wallner B, Elofsson A. All are not equal: a benchmark of different homology modeling programs. Protein Sci 2005;14:1315-1327. (Pubitemid 40577811)
    • (2005) Protein Science , vol.14 , Issue.5 , pp. 1315-1327
    • Wallner, B.1    Elofsson, A.2
  • 33
    • 0026244229 scopus 로고
    • Molscript: A program to produce both detailed and schematic plots of protein structures
    • Kraulis P. Molscript: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24:946-950.
    • (1991) J Appl Crystallogr , vol.24 , pp. 946-950
    • Kraulis, P.1
  • 34
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D: Photorealistic molecular graphics
    • Merritt EA, Bacon DJ. Raster3D: photorealistic molecular graphics. Methods Enzymol 1997;277:505-524.
    • (1997) Methods Enzymol , vol.277 , pp. 505-524
    • Merritt, E.A.1    Bacon, D.J.2
  • 35
    • 0031576989 scopus 로고    scopus 로고
    • Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool
    • Bower MJ, Cohen FE, Dunbrack RL, Jr. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 1997;267:1268-1282.
    • (1997) J Mol Biol , vol.267 , pp. 1268-1282
    • Bower, M.J.1    Cohen, F.E.2    Dunbrack Jr., R.L.3
  • 36
    • 0031557390 scopus 로고    scopus 로고
    • Factors affecting the ability of energy functions to discriminate correct from incorrect folds
    • DOI 10.1006/jmbi.1996.0809
    • Park BH, Huang ES, Levitt M. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J Mol Biol 1997;266:831-846. (Pubitemid 27113219)
    • (1997) Journal of Molecular Biology , vol.266 , Issue.4 , pp. 831-846
    • Park, B.H.1    Huang, E.S.2    Levitt, M.3
  • 37
    • 0029633167 scopus 로고
    • Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
    • Levitt M, Hirshberg M, Sharon R, Daggett V. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comput Phys Commun 1995;91:215-231.
    • (1995) Comput Phys Commun , vol.91 , pp. 215-231
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Daggett, V.4
  • 38
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    • DOI 10.1006/jmbi.1997.1479
    • Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998;275:895-916. (Pubitemid 28077703)
    • (1998) Journal of Molecular Biology , vol.275 , Issue.5 , pp. 895-916
    • Samudrala, R.1    Moult, J.2
  • 39
    • 33748121754 scopus 로고    scopus 로고
    • The effect of experimental resolution on the performance of knowledge-based discriminatory functions for protein structure selection
    • DOI 10.1093/protein/gzl027
    • Liu T, Samudrala R. The effect of experimental resolution on the performance of knowledge based discriminatory functions for protein structure selection. Protein Eng Des Sel 2006;19:431-437. (Pubitemid 44306061)
    • (2006) Protein Engineering, Design and Selection , vol.19 , Issue.9 , pp. 431-437
    • Liu, T.1    Samudrala, R.2
  • 42
    • 25444446805 scopus 로고    scopus 로고
    • A resistant molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles
    • DOI 10.1186/1471-2105-6-91
    • Moglich A, Weinfurtner D, Maurer T, Gronwald W, Kalbitzer HR. A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles. BMC Bioinformatics 2005;6:91. (Pubitemid 41363573)
    • (2005) BMC Bioinformatics , vol.6 , pp. 91
    • Moglich, A.1    Weinfurtner, D.2    Maurer, T.3    Gronwald, W.4    Kalbitzer, H.R.5
  • 44
    • 52949098360 scopus 로고    scopus 로고
    • Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information
    • Wang K, Horst JA, Cheng G, Nickle DC, Samudrala R. Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information. PLoS Comput Biol 2008;4:e1000181.
    • (2008) PLoS Comput Biol , vol.4
    • Wang, K.1    Horst, J.A.2    Cheng, G.3    Nickle, D.C.4    Samudrala, R.5
  • 45
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: A simple approach to improve protein structure predictions
    • DOI 10.1093/bioinformatics/btg124
    • Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003;19:1015-1018. (Pubitemid 36675823)
    • (2003) Bioinformatics , vol.19 , Issue.8 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 46
    • 0031308498 scopus 로고    scopus 로고
    • Handling context-sensitivity in protein structures using graph theory: Bona fide prediction
    • Samudrala R,Moult J. Handling context-sensitivity in protein structures using graph theory: bona fide prediction. Proteins 1997;(Suppl 1):43-49.
    • (1997) Proteins , Issue.SUPPL. 1 , pp. 43-49
    • Samudrala, R.1    Moult, J.2
  • 47
    • 21444448763 scopus 로고    scopus 로고
    • PROTINFO: New algorithms for enhanced protein structure predictions
    • DOI 10.1093/nar/gki403
    • Hung LH, Ngan SC, Liu T, Samudrala R. Protinfo: new algorithms for enhanced protein structure predictions. Nucleic Acids Res 2005;33:W77-W80. (Pubitemid 44529883)
    • (2005) Nucleic Acids Research , vol.33 , Issue.WEB. SERV. ISS
    • Hung, L.-H.1    Ngan, S.-C.2    Liu, T.3    Samudrala, R.4
  • 50
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.