메뉴 건너뛰기




Volumn , Issue , 2007, Pages 225-242

Protein structure prediction

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84894655858     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-0-387-92738-1_11     Document Type: Chapter
Times cited : (6)

References (95)
  • 7
    • 0028328263 scopus 로고
    • An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function
    • Bowie JU, Eisenberg D (1994) An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function. Proc Natl Acad Sci USA 91(10):4436-4440
    • (1994) Proc Natl Acad Sci USA , vol.91 , Issue.10 , pp. 4436-4440
    • Bowie, J.U.1    Eisenberg, D.2
  • 8
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie JU, Luthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164-170
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 9
    • 24944493938 scopus 로고    scopus 로고
    • Toward high-resolution de novo structure prediction for small proteins
    • Bradley P, Misura KM, Baker D (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309(5742):1868-1871
    • (2005) Science , vol.309 , Issue.5742 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.2    Baker, D.3
  • 13
    • 31144467558 scopus 로고    scopus 로고
    • The impact of structural genomics: Expectations and outcomes
    • Chandonia JM, Brenner SE (2006) The impact of structural genomics: expectations and outcomes. Science 311(5759):347-351
    • (2006) Science , vol.311 , Issue.5759 , pp. 347-351
    • Chandonia, J.M.1    Brenner, S.E.2
  • 14
    • 34248549547 scopus 로고    scopus 로고
    • Can molecular dynamics simulations provide high-resolution refinement of protein structure?
    • Chen J, Brooks CL III (2007) Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins 67(4):922-930
    • (2007) Proteins , vol.67 , Issue.4 , pp. 922-930
    • Chen, J.1    Brooks III, C.L.2
  • 15
    • 33745616114 scopus 로고    scopus 로고
    • A machine learning information retrieval approach to protein fold recognition
    • Cheng J, Baldi P (2006) A machine learning information retrieval approach to protein fold recognition. Bioinformatics 22(12):1456-1463
    • (2006) Bioinformatics , vol.22 , Issue.12 , pp. 1456-1463
    • Cheng, J.1    Baldi, P.2
  • 16
    • 36749055649 scopus 로고    scopus 로고
    • Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home
    • Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P et al (2000) Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins 69(S8):118-128
    • (2000) Proteins , vol.69 , Issue.S8 , pp. 118-128
    • Das, R.1    Qian, B.2    Raman, S.3    Vernon, R.4    Thompson, J.5    Bradley, P.6
  • 17
    • 0037079585 scopus 로고    scopus 로고
    • Identifying native-like protein structures using physics-based potentials
    • Dominy BN, Brooks CL (2002) Identifying native-like protein structures using physics-based potentials. J Comput Chem 23(1):147-160
    • (2002) J Comput Chem , vol.23 , Issue.1 , pp. 147-160
    • Dominy, B.N.1    Brooks, C.L.2
  • 18
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsec-ond simulation in aqueous solution
    • Duan Y, Kollman PA (1998) Pathways to a protein folding intermediate observed in a 1-microsec-ond simulation in aqueous solution. Science 282(5389):740-744
    • (1998) Science , vol.282 , Issue.5389 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 19
    • 0347994106 scopus 로고    scopus 로고
    • Refinement of homology-based protein structures by molecular dynamics simulation techniques
    • Fan H, Mark AE (2004) Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Sci 13(1):211-220
    • (2004) Protein Sci , vol.13 , Issue.1 , pp. 211-220
    • Fan, H.1    Mark, A.E.2
  • 20
    • 0036836611 scopus 로고    scopus 로고
    • Evaluating CASP4 predictions with physical energy functions
    • Feig M, Brooks CL, 3rd (2002) Evaluating CASP4 predictions with physical energy functions. Proteins 49(2):232-245
    • (2002) Proteins , vol.49 , Issue.2 , pp. 232-245
    • Feig, M.1    Brooks III, C.L.2
  • 21
    • 0036681394 scopus 로고    scopus 로고
    • Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model
    • Felts AK, Gallicchio E, Wallqvist A, Levy RM (2002) Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model. Proteins 48(2):404-422
    • (2002) Proteins , vol.48 , Issue.2 , pp. 404-422
    • Felts, A.K.1    Gallicchio, E.2    Wallqvist, A.3    Levy, R.M.4
  • 22
    • 0037624841 scopus 로고    scopus 로고
    • 3D-SHOTGUN: A novel, cooperative, fold-recognition meta-predictor
    • Fischer D (2003) 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor. Proteins 51(3):434-441
    • (2003) Proteins , vol.51 , Issue.3 , pp. 434-441
    • Fischer, D.1
  • 23
    • 33645972948 scopus 로고    scopus 로고
    • Servers for protein structure prediction
    • Fischer D (2006) Servers for protein structure prediction. Curr Opin Struct Biol 16(2):178-182
    • (2006) Curr Opin Struct Biol , vol.16 , Issue.2 , pp. 178-182
    • Fischer, D.1
  • 24
    • 0242299155 scopus 로고    scopus 로고
    • CAFASP3: The third critical assessment of fully automated structure prediction methods
    • Fischer D, Rychlewski L, Dunbrack RL Jr, Ortiz AR, Elofsson A (2003) CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins 53(Suppl 6): 503-516
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 503-516
    • Fischer, D.1    Rychlewski, L.2    Dunbrack Jr., R.L.3    Ortiz, A.R.4    Elofsson, A.5
  • 26
    • 39149143625 scopus 로고    scopus 로고
    • A comparative study of the reported performance of ab initio protein structure prediction algorithms
    • Helles G (2008) A comparative study of the reported performance of ab initio protein structure prediction algorithms. J R Soc Interface 5(21):387-396
    • (2008) J R Soc Interface , vol.5 , Issue.21 , pp. 387-396
    • Helles, G.1
  • 27
    • 3142680776 scopus 로고    scopus 로고
    • Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction
    • Hsieh MJ, Luo R (2004) Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction. Proteins 56(3):475-486
    • (2004) Proteins , vol.56 , Issue.3 , pp. 475-486
    • Hsieh, M.J.1    Luo, R.2
  • 28
    • 0141956090 scopus 로고    scopus 로고
    • Generalized born model with a simple smoothing function
    • Im W, Lee MS, Brooks CL III (2003) Generalized born model with a simple smoothing function. J Comput Chem 24(14):1691-1702
    • (2003) J Comput Chem , vol.24 , Issue.14 , pp. 1691-1702
    • Im, W.1    Lee, M.S.2    Brooks III, C.L.3
  • 29
    • 23144463912 scopus 로고    scopus 로고
    • FFAS03: A server for profile-profile sequence alignments
    • Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A (2005) FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res 33(Web Server issue):W284-W288
    • (2005) Nucleic Acids Res , vol.33 , Issue.WEB SERVER ISSUE
    • Jaroszewski, L.1    Rychlewski, L.2    Li, Z.3    Li, W.4    Godzik, A.5
  • 30
    • 36749086922 scopus 로고    scopus 로고
    • Assessment of CASP7 structure predictions for template free targets
    • Jauch R, Yeo HC, Kolatkar PR, Clarke ND (2007) Assessment of CASP7 structure predictions for template free targets. Proteins 69(Suppl 8):57-67
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 57-67
    • Jauch, R.1    Yeo, H.C.2    Kolatkar, P.R.3    Clarke, N.D.4
  • 31
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • Jones DT (1999) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 287(4):797-815
    • (1999) J Mol Biol , vol.287 , Issue.4 , pp. 797-815
    • Jones, D.T.1
  • 32
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones DT, Taylor WR, Thornton JM (1992) A new approach to protein fold recognition. Nature 358(6381):86-89
    • (1992) Nature , vol.358 , Issue.6381 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 34
    • 33645941402 scopus 로고
    • The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin
    • Jorgensen WL, Tirado-Rives J (1988) The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc 110:1657-1666
    • (1988) J Am Chem Soc , vol.110 , pp. 1657-1666
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 35
    • 0035913529 scopus 로고    scopus 로고
    • Evaluation and reparametriza-tion of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
    • Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) Evaluation and reparametriza-tion of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105:6474-6487
    • (2001) J Phys Chem B , vol.105 , pp. 6474-6487
    • Kaminski, G.A.1    Friesner, R.A.2    Tirado-Rives, J.3    Jorgensen, W.L.4
  • 36
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • Karplus K, Barrett C, Hughey R (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics 14:846-856
    • (1998) Bioinformatics , vol.14 , pp. 846-856
    • Karplus, K.1    Barrett, C.2    Hughey, R.3
  • 37
    • 0035964191 scopus 로고    scopus 로고
    • TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints
    • Kihara D, Lu H, Kolinski A, Skolnick J (2001) TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc Natl Acad Sci USA 98:10125-10130
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 10125-10130
    • Kihara, D.1    Lu, H.2    Kolinski, A.3    Skolnick, J.4
  • 38
    • 0141642142 scopus 로고    scopus 로고
    • ASTRO-FOLD: A combinatorial and global optimization framework for Ab initio prediction of three-dimensional structures of proteins from the amino acid sequence
    • Klepeis JL, Floudas CA (2003) ASTRO-FOLD: a combinatorial and global optimization framework for Ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. Biophys J 85(4):2119-2146
    • (2003) Biophys J , vol.85 , Issue.4 , pp. 2119-2146
    • Klepeis, J.L.1    Floudas, C.A.2
  • 39
    • 12944263648 scopus 로고    scopus 로고
    • Ab initio prediction of the three-dimensional structure of a de novo designed protein: A double-blind case study
    • Klepeis JL, Wei Y, Hecht MH, Floudas CA (2005) Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study. Proteins 58(3):560-570
    • (2005) Proteins , vol.58 , Issue.3 , pp. 560-570
    • Klepeis, J.L.1    Wei, Y.2    Hecht, M.H.3    Floudas, C.A.4
  • 40
    • 36749099341 scopus 로고    scopus 로고
    • Assessment of CASP7 predictions for template-based modeling targets
    • Kopp J, Bordoli L, Battey JN, Kiefer F, Schwede T (2007) Assessment of CASP7 predictions for template-based modeling targets. Proteins 6(S8):38-56
    • (2007) Proteins , vol.6 , Issue.S8 , pp. 38-56
    • Kopp, J.1    Bordoli, L.2    Battey, J.N.3    Kiefer, F.4    Schwede, T.5
  • 42
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis T, Karplus M (1999) Effective energy function for proteins in solution. Proteins 35(2):133-152
    • (1999) Proteins , vol.35 , Issue.2 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 43
    • 0035914481 scopus 로고    scopus 로고
    • Molecular dynamics in the endgame of protein structure prediction
    • Lee MR, Tsai J, Baker D, Kollman PA (2001) Molecular dynamics in the endgame of protein structure prediction. J Mol Biol 313(2):417-430
    • (2001) J Mol Biol , vol.313 , Issue.2 , pp. 417-430
    • Lee, M.R.1    Tsai, J.2    Baker, D.3    Kollman, P.A.4
  • 44
    • 2442480826 scopus 로고    scopus 로고
    • Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model
    • Lee MC, Duan Y (2004) Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model. Proteins 55(3):620-634
    • (2004) Proteins , vol.55 , Issue.3 , pp. 620-634
    • Lee, M.C.1    Duan, Y.2
  • 45
    • 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 (1995) Potential-energy function and parameters for simulations of the molecular-dynamics of proteins and nucleic-acids in solution. Comput Phys Commun 91(1-3):215-231
    • (1995) Comput Phys Commun , vol.91 , Issue.1-3 , pp. 215-231
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Daggett, V.4
  • 46
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: A package for molecular simulation and trajectory analysis. J Mol Modeling 7:306-317
    • (2001) J Mol Modeling , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 47
    • 0033545962 scopus 로고    scopus 로고
    • Protein structure prediction by global optimization of a potential energy function
    • Liwo A, Lee J, Ripoll DR, Pillardy J, Scheraga HA (1999) Protein structure prediction by global optimization of a potential energy function. Proc Natl Acad Sci USA 96(10):5482-5485
    • (1999) Proc Natl Acad Sci USA , vol.96 , Issue.10 , pp. 5482-5485
    • Liwo, A.1    Lee, J.2    Ripoll, D.R.3    Pillardy, J.4    Scheraga, H.A.5
  • 48
    • 0027524668 scopus 로고
    • Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment
    • Liwo A, Pincus MR, Wawak RJ, Rackovsky S, Scheraga HA (1993) Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment. Protein Sci 2(10):1697-1714
    • (1993) Protein Sci , vol.2 , Issue.10 , pp. 1697-1714
    • Liwo, A.1    Pincus, M.R.2    Wawak, R.J.3    Rackovsky, S.4    Scheraga, H.A.5
  • 52
    • 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(14):5361-5366
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.14 , pp. 5361-5366
    • Misura, K.M.1    Chivian, D.2    Rohl, C.A.3    Kim, D.E.4    Baker, D.5
  • 55
    • 0035702809 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP): Round i v
    • Moult J, Fidelis K, Zemla A, Hubbard T (2001) Critical assessment of methods of protein structure prediction (CASP): round I V. Proteins Suppl 5:2-7
    • (2001) Proteins Suppl , vol.5 , pp. 2-7
    • Moult, J.1    Fidelis, K.2    Zemla, A.3    Hubbard, T.4
  • 56
    • 0001731773 scopus 로고
    • Energy Parameters in Polypeptides. 10. Improved geometric parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
    • Nemethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A et al (1992) Energy Parameters in Polypeptides. 10. Improved geometric parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J Phys Chem B 96:6472-6484
    • (1992) J Phys Chem B , vol.96 , pp. 6472-6484
    • Nemethy, G.1    Gibson, K.D.2    Palmer, K.A.3    Yoon, C.N.4    Paterlini, G.5    Zagari, A.6
  • 57
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular systems
    • Neria E, Fischer S, Karplus M (1996) Simulation of activation free energies in molecular systems. J Chem Phys 105(5):1902-1921
    • (1996) J Chem Phys , vol.105 , Issue.5 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 58
    • 0025913646 scopus 로고
    • Automated modeling of coiled coils: Application to the GCN4 dimerization region
    • Nilges M, Brunger AT (1991) Automated modeling of coiled coils: application to the GCN4 dimerization region. Protein Eng 4(6):649-659
    • (1991) Protein Eng , vol.4 , Issue.6 , pp. 649-659
    • Nilges, M.1    Brunger, A.T.2
  • 59
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near native folds from well-constructed decoys
    • Park B, Levitt M (1996) Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol 258(2):367-392
    • (1996) J Mol Biol , vol.258 , Issue.2 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 60
    • 9144244232 scopus 로고    scopus 로고
    • MODBASE, a database of annotated comparative protein structure models, and associated resources
    • Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC et al (2004) MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 32(Database issue):D217-D222
    • (2004) Nucleic Acids Res , vol.32 , Issue.DATABASE ISSUE
    • Pieper, U.1    Eswar, N.2    Braberg, H.3    Madhusudhan, M.S.4    Davis, F.P.5    Stuart, A.C.6
  • 61
    • 33644874394 scopus 로고    scopus 로고
    • MODBASE: A database of annotated comparative protein structure models and associated resources
    • Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A et al (2006) MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 34(Database issue):D291-D295
    • (2006) Nucleic Acids Res , vol.34 , Issue.DATABASE ISSUE
    • Pieper, U.1    Eswar, N.2    Davis, F.P.3    Braberg, H.4    Madhusudhan, M.S.5    Rossi, A.6
  • 62
    • 11144241105 scopus 로고    scopus 로고
    • LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction
    • Rychlewski L, Fischer D (2005) LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction. Protein Sci 14(1):240-245
    • (2005) Protein Sci , vol.14 , Issue.1 , pp. 240-245
    • Rychlewski, L.1    Fischer, D.2
  • 63
    • 0037423702 scopus 로고    scopus 로고
    • COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance
    • Sadreyev R, Grishin N (2003) COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol 326(1):317-336
    • (2003) J Mol Biol , vol.326 , Issue.1 , pp. 317-336
    • Sadreyev, R.1    Grishin, N.2
  • 64
    • 0031787022 scopus 로고    scopus 로고
    • 100, 000 protein structures for the biologist
    • Sali A (1998) 100, 000 protein structures for the biologist. Nat Struct Biol 5(12):1029-1032
    • (1998) Nat Struct Biol , vol.5 , Issue.12 , pp. 1029-1032
    • Sali, A.1
  • 65
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234(3):779-815
    • (1993) J Mol Biol , vol.234 , Issue.3 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 66
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    • Shi J, Blundell TL, Mizuguchi K (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 310(1):243-257
    • (2001) J Mol Biol , vol.310 , Issue.1 , pp. 243-257
    • Shi, J.1    Blundell, T.L.2    Mizuguchi, K.3
  • 67
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons KT, Kooperberg C, Huang E, Baker D (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268(1):209-225
    • (1997) J Mol Biol , vol.268 , Issue.1 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 68
    • 0034060287 scopus 로고    scopus 로고
    • Structural genomics and its importance for gene function analysis
    • Skolnick J, Fetrow JS, Kolinski A (2000) Structural genomics and its importance for gene function analysis. Nat Biotechnol 18(3):283-287
    • (2000) Nat Biotechnol , vol.18 , Issue.3 , pp. 283-287
    • Skolnick, J.1    Fetrow, J.S.2    Kolinski, A.3
  • 69
    • 3142764482 scopus 로고    scopus 로고
    • Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm
    • Skolnick J, Kihara D, Zhang Y (2004) Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm. Protein 56:502-518
    • (2004) Protein , vol.56 , pp. 502-518
    • Skolnick, J.1    Kihara, D.2    Zhang, Y.3
  • 70
    • 0034677504 scopus 로고    scopus 로고
    • Protein structure groups seek to draft common ground rules
    • Smaglik P (2000) Protein structure groups seek to draft common ground rules. Nature 403(6771):691
    • (2000) Nature , vol.403 , Issue.6771 , pp. 691
    • Smaglik, P.1
  • 71
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21(7):951-960
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 951-960
    • Soding, J.1
  • 72
    • 20544435097 scopus 로고    scopus 로고
    • Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
    • Sorin EJ, Pande VS (2005) Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys J 88(4):2472-2493
    • (2005) Biophys J , vol.88 , Issue.4 , pp. 2472-2493
    • Sorin, E.J.1    Pande, V.S.2
  • 73
    • 0035812704 scopus 로고    scopus 로고
    • Global efforts in structural genomics
    • Stevens RC, Yokoyama S, Wilson IA (2001) Global efforts in structural genomics. Science 294(5540):89-92
    • (2001) Science , vol.294 , Issue.5540 , pp. 89-92
    • Stevens, R.C.1    Yokoyama, S.2    Wilson, I.A.3
  • 74
    • 33847673583 scopus 로고    scopus 로고
    • Near-native structure refinement using in vacuo energy minimization
    • Summa CM, Levitt M (2007) Near-native structure refinement using in vacuo energy minimization. Proc Natl Acad Sci USA 104(9):3177-3182
    • (2007) Proc Natl Acad Sci USA , vol.104 , Issue.9 , pp. 3177-3182
    • Summa, C.M.1    Levitt, M.2
  • 75
    • 0031665755 scopus 로고    scopus 로고
    • Class-directed structure determination: Foundation for a protein structure initiative
    • Terwilliger TC, Waldo G, Peat TS, Newman JM, Chu K, Berendzen J (1998) Class-directed structure determination: foundation for a protein structure initiative. Protein Sci 7(9):1851-1856
    • (1998) Protein Sci , vol.7 , Issue.9 , pp. 1851-1856
    • Terwilliger, T.C.1    Waldo, G.2    Peat, T.S.3    Newman, J.M.4    Chu, K.5    Berendzen, J.6
  • 76
    • 0038008976 scopus 로고    scopus 로고
    • An improved protein decoy set for testing energy functions for protein structure prediction
    • Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D (2003) An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 53(1):76-87
    • (2003) Proteins , vol.53 , Issue.1 , pp. 76-87
    • Tsai, J.1    Bonneau, R.2    Morozov, A.V.3    Kuhlman, B.4    Rohl, C.A.5    Baker, D.6
  • 79
    • 0028290433 scopus 로고
    • Prediction of the folding pathways and structure of the GCN4 leucine zipper
    • Vieth M, Kolinski A, Brooks CL III, Skolnick J (1994) Prediction of the folding pathways and structure of the GCN4 leucine zipper. J Mol Biol 237(4):361-367
    • (1994) J Mol Biol , vol.237 , Issue.4 , pp. 361-367
    • Vieth, M.1    Kolinski, A.2    Iii B.Cl3    Skolnick, J.4
  • 81
    • 36749049687 scopus 로고    scopus 로고
    • Prediction of global and local model quality in CASP7 using Pcons and ProQ
    • Wallner B, Elofsson A (2007) Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins 69(S8):184-193
    • (2007) Proteins , vol.69 , Issue.S8 , pp. 184-193
    • Wallner, B.1    Elofsson, A.2
  • 82
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang JM, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21(12):1049-1074
    • (2000) J Comput Chem , vol.21 , Issue.12 , pp. 1049-1074
    • Wang, J.M.1    Cieplak, P.2    Kollman, P.A.3
  • 83
    • 0021757436 scopus 로고
    • A new force field for molecular mechanical simulation of nucleic acids and proteins
    • Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G et al (1984) A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 106:765-784
    • (1984) J Am Chem Soc , vol.106 , pp. 765-784
    • Weiner, S.J.1    Kollman, P.A.2    Case, D.A.3    Singh, U.C.4    Ghio, C.5    Alagona, G.6
  • 84
    • 34547298869 scopus 로고    scopus 로고
    • Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking
    • Wroblewska L, Skolnick J (2007) Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking. J Comput Chem 28(12):2059-2066
    • (2007) J Comput Chem , vol.28 , Issue.12 , pp. 2059-2066
    • Wroblewska, L.1    Skolnick, J.2
  • 85
    • 34249869832 scopus 로고    scopus 로고
    • Ab initio modeling of small proteins by iterative TASSER simulations
    • Wu S, Skolnick J, Zhang Y (2007) Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 5:17
    • (2007) BMC Biol , vol.5 , pp. 17
    • Wu, S.1    Skolnick, J.2    Zhang, Y.3
  • 86
    • 34250851687 scopus 로고    scopus 로고
    • LOMETS: A local meta-threading-server for protein structure prediction
    • Wu S, Zhang Y (2007) LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res 35(10):3375-3382
    • (2007) Nucleic Acids Res , vol.35 , Issue.10 , pp. 3375-3382
    • Wu, S.1    Zhang, Y.2
  • 87
    • 46449123146 scopus 로고    scopus 로고
    • MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information
    • Wu S, Zhang Y (2008) MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins 72(2):547-556
    • (2008) Proteins , vol.72 , Issue.2 , pp. 547-556
    • Wu, S.1    Zhang, Y.2
  • 88
    • 0036428782 scopus 로고    scopus 로고
    • Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing
    • Zagrovic B, Snow CD, Shirts MR, Pande VS (2002) Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J Mol Biol 323(5):927-937
    • (2002) J Mol Biol , vol.323 , Issue.5 , pp. 927-937
    • Zagrovic, B.1    Snow, C.D.2    Shirts, M.R.3    Pande, V.S.4
  • 89
    • 36749061828 scopus 로고    scopus 로고
    • Template-based modeling and free modeling by I-TASSER in CASP7
    • Zhang Y (2007) Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 69(Suppl 8):108-117
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 108-117
    • Zhang, Y.1
  • 90
    • 0041843696 scopus 로고    scopus 로고
    • TOUCHSTONE II: A new approach to ab initio protein structure prediction
    • Zhang Y, Kolinski A, Skolnick J (2003) TOUCHSTONE II: A new approach to ab initio protein structure prediction. Biophys J 85:1145-1164
    • (2003) Biophys J , vol.85 , pp. 1145-1164
    • Zhang, Y.1    Kolinski, A.2    Skolnick, J.3
  • 91
    • 2442676589 scopus 로고    scopus 로고
    • Automated structure prediction of weakly homologous proteins on a genomic scale
    • Zhang Y, Skolnick J (2004a) Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci USA 101:7594-7599
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7594-7599
    • Zhang, Y.1    Skolnick, J.2
  • 92
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • Zhang Y, Skolnick J (2004b) Scoring function for automated assessment of protein structure template quality. Proteins 57(4):702-710
    • (2004) Proteins , vol.57 , Issue.4 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 93
    • 12844288890 scopus 로고    scopus 로고
    • The protein structure prediction problem could be solved using the current PDB library
    • Zhang Y, Skolnick J (2005a) The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci USA 102:1029-1034
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 1029-1034
    • Zhang, Y.1    Skolnick, J.2
  • 94
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • Zhang Y, Skolnick J (2005b) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33(7):2302-2309
    • (2005) Nucleic Acids Res , vol.33 , Issue.7 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 95
    • 11344292852 scopus 로고    scopus 로고
    • Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments
    • Zhou H, Zhou Y (2005) Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins 58(2):321-328
    • (2005) Proteins , vol.58 , Issue.2 , pp. 321-328
    • Zhou, H.1    Zhou, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.