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Volumn 51, Issue 7, 2011, Pages 1656-1666

Sampling multiple scoring functions can improve protein loop structure prediction accuracy

Author keywords

[No Author keywords available]

Indexed keywords

DEGREES OF FREEDOM (MECHANICS); FORECASTING; FUNCTIONAL ANALYSIS; LEARNING TO RANK; PARETO PRINCIPLE; PROTEINS;

EID: 79960711882     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200143u     Document Type: Article
Times cited : (18)

References (55)
  • 1
    • 0034567501 scopus 로고    scopus 로고
    • Ab initio loop modeling and its application to homology modeling
    • Bruccoleri, R. E. Ab initio loop modeling and its application to homology modeling Methods Mol. Biol. 2000, 143, 247-264
    • (2000) Methods Mol. Biol. , vol.143 , pp. 247-264
    • Bruccoleri, R.E.1
  • 2
    • 34748913195 scopus 로고    scopus 로고
    • The rigid connecting loop stabilizes hairpin folding of the two helices of the ATP synthase subunit c
    • DOI 10.1110/ps.072776307
    • Dmitriev, O. Y.; Fillingame, R. H. The rigid connecting loop stabilizes hairpin folding of the two helices of the ATP synthase subunit c Protein Sci. 2007, 16 (10) 2118-2122 (Pubitemid 47481647)
    • (2007) Protein Science , vol.16 , Issue.10 , pp. 2118-2122
    • Dmitriev, O.Y.1    Fillingame, R.H.2
  • 4
    • 0031565725 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using patch analysis
    • DOI 10.1006/jmbi.1997.1233
    • Jones, S.; Thornton, J. M. Prediction of protein-protein interaction sites using patch analysis J. Mol. Biol. 1997, 272, 133-143 (Pubitemid 27395543)
    • (1997) Journal of Molecular Biology , vol.272 , Issue.1 , pp. 133-143
    • Jones, S.1    Thornton, J.M.2
  • 5
    • 0032475938 scopus 로고    scopus 로고
    • Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: Identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity
    • DOI 10.1006/jmbi.1998.2061
    • Fetrow, J. S.; Godzik, A.; Skolnick, J. Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: Identification of proteins exhibiting the glutaredoxin0thioredoxin disulfide oxidoreductase activity J. Mol. Biol. 1998, 282, 703-711 (Pubitemid 28442339)
    • (1998) Journal of Molecular Biology , vol.282 , Issue.4 , pp. 703-711
    • Fetrow, J.S.1    Godzik, A.2    Skolnick, J.3
  • 6
    • 26944443142 scopus 로고    scopus 로고
    • Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels
    • Tasneem, A.; Iyer, L. M.; Jakobsson, E.; Aravind, L. Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels Genome Biol. 2005, 6 (1) R4
    • (2005) Genome Biol. , vol.6 , Issue.1 , pp. 4
    • Tasneem, A.1    Iyer, L.M.2    Jakobsson, E.3    Aravind, L.4
  • 10
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • Fiser, A.; Do, R. K. G.; Sali, A. Modeling of loops in protein structures Protein Sci. 2000, 9, 1753-1773
    • (2000) Protein Sci. , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.G.2    Sali, A.3
  • 12
    • 0033135619 scopus 로고    scopus 로고
    • Prediction of loop geometries using a generalized born model of solvation effects
    • DOI 10.1002/(SICI)1097-0134(19990501)35:2<173::AID-PROT4>3.0.CO;2-2
    • Rapp, C. S.; Friesner, R. A. Prediction of loop geometries using a generalized born model of solvation effects Proteins 1999, 35, 173-183 (Pubitemid 29165131)
    • (1999) Proteins: Structure, Function and Genetics , vol.35 , Issue.2 , pp. 173-183
    • Rapp, C.S.1    Friesner, R.A.2
  • 13
    • 0037375615 scopus 로고    scopus 로고
    • Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the generalized born solvation model
    • DOI 10.1002/prot.10235
    • de Bakker, P. I. W.; Depristo, M. A.; Burke, D. F.; Blundell, T. L. Ab initio construction of polypeptide fragments: accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model Proteins 2003, 51, 21-40 (Pubitemid 36293030)
    • (2003) Proteins: Structure, Function and Genetics , vol.51 , Issue.1 , pp. 21-40
    • De Bakker, P.I.W.1    DePristo, M.A.2    Burke, D.F.3    Blundell, T.L.4
  • 14
    • 58149157667 scopus 로고    scopus 로고
    • Prediction of Protein Loop Conformation Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling
    • Felts, A. K.; Gallicchio, E.; Chekmarev, D.; Paris, K. A.; Friesner, R. A.; Levy, R. M. Prediction of Protein Loop Conformation Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling J. Chem. Theory Comput. 2008, 4 (5) 855-868
    • (2008) J. Chem. Theory Comput. , vol.4 , Issue.5 , pp. 855-868
    • Felts, A.K.1    Gallicchio, E.2    Chekmarev, D.3    Paris, K.A.4    Friesner, R.A.5    Levy, R.M.6
  • 16
    • 33645923385 scopus 로고    scopus 로고
    • A supersecondary structure library and search algorithm for modeling loops in protein structures
    • DOI 10.1093/nar/gkl156
    • Fernandez-Fuentes, N.; Oliva, B.; Fiser, A. A Supersecondary Structure Library and Search Algorithm for Modeling Loops in Protein Structures Nucleic Acids Res. 2006, 34 (7) 2085-2097 (Pubitemid 44314206)
    • (2006) Nucleic Acids Research , vol.34 , Issue.7 , pp. 2085-2097
    • Fernandez-Fuentes, N.1    Oliva, B.2    Fiser, A.3
  • 17
    • 0023478807 scopus 로고
    • Predicting antobody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures
    • Shenkin, S.; Yarmush, D. L.; Fine, R. M.; Wang, H.; Levinthal, C. Predicting antobody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures Biopolymers 1987, 26, 2053-2085
    • (1987) Biopolymers , vol.26 , pp. 2053-2085
    • Shenkin, S.1    Yarmush, D.L.2    Fine, R.M.3    Wang, H.4    Levinthal, C.5
  • 18
    • 13444304144 scopus 로고    scopus 로고
    • Inverse kinematics in biology: The protein loop closure problem
    • DOI 10.1177/0278364905050352, Robotics Techniques Applied to Computational Biology
    • Kolodny, R.; Guibas, L.; Levitt, M.; Koehl, P. Inverse Kinematics in Biology: The Protein Loop Closure Problem Int. J. Robot. Res. 2005, 24, 151-163 (Pubitemid 40207003)
    • (2005) International Journal of Robotics Research , vol.24 , Issue.2-3 , pp. 151-163
    • Kolodny, R.1    Guibas, L.2    Levitt, M.3    Koehl, P.4
  • 19
    • 0037406075 scopus 로고    scopus 로고
    • Cyclic coordinate descent: A robotics algorithm for protein loop closure
    • DOI 10.1110/ps.0242703
    • Canutescu, A. A.; Dunbrack, R. L. Cyclic Coordinate Descent: A Robotics Algorithm for Protein Loop Closure Protein Sci. 2003, 12, 963-972 (Pubitemid 36505431)
    • (2003) Protein Science , vol.12 , Issue.5 , pp. 963-972
    • Canutescu, A.A.1    Dunbrack Jr., R.L.2
  • 20
    • 68349104348 scopus 로고    scopus 로고
    • Sub-Angstrom Accuracy in Protein Loop Reconstruction by Robotics-Inspired Conformational Sampling
    • Mandell, D. J.; Coutsias, E. A.; Kortemme, T. Sub-Angstrom Accuracy in Protein Loop Reconstruction by Robotics-Inspired Conformational Sampling Nat. Methods 2009, 6, 551-552
    • (2009) Nat. Methods , vol.6 , pp. 551-552
    • Mandell, D.J.1    Coutsias, E.A.2    Kortemme, T.3
  • 21
    • 0031021792 scopus 로고    scopus 로고
    • A Fast and Efficient Program for Modeling Protein Loops
    • Zhang, H.; Lai, L.; Han, Y.; Tang, Y. A Fast and Efficient Program for Modeling Protein Loops Biopolymers 1997, 41, 61-72
    • (1997) Biopolymers , vol.41 , pp. 61-72
    • Zhang, H.1    Lai, L.2    Han, Y.3    Tang, Y.4
  • 22
    • 77149152176 scopus 로고    scopus 로고
    • Backbone statistical potential from local sequence-structure interactions in protein loops
    • Rata, I.; Li, Y.; Jakobsson, E. Backbone statistical potential from local sequence-structure interactions in protein loops J. Phys. Chem. B 2010, 114 (5) 1859-1869
    • (2010) J. Phys. Chem. B , vol.114 , Issue.5 , pp. 1859-1869
    • Rata, I.1    Li, Y.2    Jakobsson, E.3
  • 24
    • 15244349255 scopus 로고    scopus 로고
    • Application of MM/PBSA colony free energy to loop decoy discrimination: Toward correlation between energy and root mean square deviation
    • DOI 10.1110/ps.041004105
    • Fogolari, F.; Tosatto, S. C. E. Application of MM/PBSA colony free energy to loop decoy discrimination: Toward correlation between energy and root mean square deviation Protein Sci. 2005, 14 (4) 889-901 (Pubitemid 40389358)
    • (2005) Protein Science , vol.14 , Issue.4 , pp. 889-901
    • Fogolari, F.1    Tosatto, S.C.E.2
  • 25
    • 0028040064 scopus 로고
    • Evaluation of the conformational free energies of loops in proteins
    • Smith, C. S.; Honig, B. Evaluation of the conformational free energies of loops in proteins Proteins 1994, 18 (2) 119-132 (Pubitemid 24055075)
    • (1994) Proteins: Structure, Function and Genetics , vol.18 , Issue.2 , pp. 119-132
    • Smith, K.C.1    Honig, B.2
  • 26
    • 1642575364 scopus 로고    scopus 로고
    • Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential
    • DOI 10.1110/ps.03411904
    • Zhang, C.; Liu, S.; Zhou, Y. Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential Protein Sci. 2004, 13 (2) 391-399 (Pubitemid 38124960)
    • (2004) Protein Science , vol.13 , Issue.2 , pp. 391-399
    • Zhang, C.1    Liu, S.2    Zhou, Y.3
  • 27
    • 77954679017 scopus 로고    scopus 로고
    • Improving predicted protein loop structure ranking using a Pareto-optimality consensus method
    • Li, Y.; Rata, I.; Chiu, S.; Jakobsson, E. Improving predicted protein loop structure ranking using a Pareto-optimality consensus method BMC Struct. Biol. 2010, 10, 22
    • (2010) BMC Struct. Biol. , vol.10 , pp. 22
    • Li, Y.1    Rata, I.2    Chiu, S.3    Jakobsson, E.4
  • 28
    • 67649535959 scopus 로고    scopus 로고
    • Improving Consensus Contact Prediction via Server Correlation Reduction
    • Gao, X.; Bu, D.; Xu, J.; Li, M. Improving Consensus Contact Prediction via Server Correlation Reduction BMC Struct. Biol. 2009, 9, 28-42
    • (2009) BMC Struct. Biol. , vol.9 , pp. 28-42
    • Gao, X.1    Bu, D.2    Xu, J.3    Li, M.4
  • 30
    • 0029011701 scopus 로고
    • A second generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules
    • Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M. A second generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules J. Am. Chem. Soc. 1995, 117, 5179-97
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 5179-5197
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3    Gould, I.R.4    Merz, K.M.5
  • 32
    • 56449101788 scopus 로고    scopus 로고
    • Investigations into the Effect of Multiobjectivization in Protein Structure Prediction
    • Handl, J.; Lovell, S. C.; Knowles, J. Investigations into the Effect of Multiobjectivization in Protein Structure Prediction Lect. Notes Comput. Sci. Eng. 2008, 5199, 702-711
    • (2008) Lect. Notes Comput. Sci. Eng. , vol.5199 , pp. 702-711
    • Handl, J.1    Lovell, S.C.2    Knowles, J.3
  • 33
    • 58149157581 scopus 로고    scopus 로고
    • Improved Energy Selection of Nativelike Protein Loops for Loop Decoys
    • Lin, M. S.; Head-Gordon, T. Improved Energy Selection of Nativelike Protein Loops for Loop Decoys J. Chem. Theory Comput. 2008, 4, 515-521
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 515-521
    • Lin, M.S.1    Head-Gordon, T.2
  • 35
    • 30144441768 scopus 로고    scopus 로고
    • SimFold energy function for de novo protein structure prediction: Consensus with Rosetta
    • DOI 10.1002/prot.20748
    • Fujitsuka, Y.; Chikenji, G.; Takada, S. SimFold Energy Function for de novo protein structure prediction: consensus with Rosetta Proteins 2006, 62 (2) 381-398 (Pubitemid 43054359)
    • (2006) Proteins: Structure, Function and Genetics , vol.62 , Issue.2 , pp. 381-398
    • Fujitsuka, Y.1    Chikenji, G.2    Takada, S.3
  • 36
  • 37
    • 13944275960 scopus 로고    scopus 로고
    • The protein coil library: A structural database of nonhelix, nonstrand fragments derived from the PDB
    • DOI 10.1002/prot.20394
    • Fitzkee, N. C.; Fleming, P. J.; Rose, G. D. The protein coil library: a structural database of non- helix, non-strand fragments derived from the PDB Proteins 2005, 58 (4) 852-854 (Pubitemid 40271250)
    • (2005) Proteins: Structure, Function and Genetics , vol.58 , Issue.4 , pp. 852-854
    • Fitzkee, N.C.1    Fleming, P.J.2    Rose, G.D.3
  • 38
    • 0032612579 scopus 로고    scopus 로고
    • Ab initio protein structure prediction of CASP III targets using ROSETTA
    • DOI 10.1002/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z
    • Simons, K. T.; Bonneau, R.; Ruczinski, I.; Baker, D. Ab initio Protein Structure Prediction of CASP III Targets Using ROSETTA Proteins 1999, 37 (3) 171-176 (Pubitemid 29463528)
    • (1999) Proteins: Structure, Function and Genetics , vol.37 , Issue.SUPPL. 3 , pp. 171-176
    • Simons, K.T.1    Bonneau, R.2    Ruczinski, I.3    Baker, D.4
  • 39
    • 0034604105 scopus 로고    scopus 로고
    • Surprising simplicity to protein folding
    • Baker, D. Surprising simplicity to protein folding Nature 2000, 405, 39-42
    • (2000) Nature , vol.405 , pp. 39-42
    • Baker, D.1
  • 40
    • 27344445735 scopus 로고    scopus 로고
    • Effective and Efficient Algorithm for Multiobjective Optimization of Hydrologic Models
    • Vrugt, J. A.; Gupta, H. V.; Bastidas, L. A.; Boutem, W.; Sorooshian, S. Effective and Efficient Algorithm for Multiobjective Optimization of Hydrologic Models Water Resour. Res. 2002, 39 (8) 1214-1232
    • (2002) Water Resour. Res. , vol.39 , Issue.8 , pp. 1214-1232
    • Vrugt, J.A.1    Gupta, H.V.2    Bastidas, L.A.3    Boutem, W.4    Sorooshian, S.5
  • 41
    • 0142000477 scopus 로고    scopus 로고
    • Differential Evolution - A Simple and Efficient Heuristic for Global Optimization over Continuous Spaces
    • Storn, R.; Price, K. Differential Evolution-A Simple and Efficient Heuristic for Global Optimization over Continuous Spaces J. Global Optim. 1997, 11 (4) 341-359 (Pubitemid 127502202)
    • (1997) Journal of Global Optimization , vol.11 , Issue.4 , pp. 341-359
    • Storn, R.1    Price, K.2
  • 42
    • 0033318858 scopus 로고    scopus 로고
    • Multiobjective evolutionary algorithms a comparative case study and the strength pareto approach
    • DOI 10.1109/4235.797969
    • Zitzler, E.; Thiele, L. Multiobjective Evolutionary Algorithms: A Comparative Case Study and the Strength Pareto Approach IEEE Trans. Evol. Comput. 1999, 3 (4) 257-271 (Pubitemid 30544879)
    • (1999) IEEE Transactions on Evolutionary Computation , vol.3 , Issue.4 , pp. 257-271
    • Zitzler Eckart1    Thiele Lothar2
  • 43
    • 22944453404 scopus 로고    scopus 로고
    • Optimal Allocation of Replicas in Parallel Tempering Simulations
    • Rathore, N.; Chopra, M.; de Pablo, J. J. Optimal Allocation of Replicas in Parallel Tempering Simulations J. Chem. Phys. 2005, 122 (2) 024111
    • (2005) J. Chem. Phys. , vol.122 , Issue.2 , pp. 024111
    • Rathore, N.1    Chopra, M.2    De Pablo, J.J.3
  • 44
    • 20844439932 scopus 로고    scopus 로고
    • Selection of Temperature Intervals for Parallel Tempering Simulations
    • Kone, A.; Kofke, D. A. Selection of Temperature Intervals for Parallel Tempering Simulations J. Chem. Phys. 2005, 122 (20) 206101
    • (2005) J. Chem. Phys. , vol.122 , Issue.20 , pp. 206101
    • Kone, A.1    Kofke, D.A.2
  • 46
    • 0002336164 scopus 로고
    • Ring Closure and Local Conformational Deformations of Chain Molecules
    • Go, N.; Scheraga, H. A. Ring Closure and Local Conformational Deformations of Chain Molecules Macromolecules 1970, 3 (2) 178-187
    • (1970) Macromolecules , vol.3 , Issue.2 , pp. 178-187
    • Go, N.1    Scheraga, H.A.2
  • 47
    • 0000781576 scopus 로고    scopus 로고
    • Exact analytical loop closure in proteins using polynomial equations
    • Wedemeyer, W. J.; Scheraga, H. A. Exact Analytical Loop Closure in Proteins Using Polynomial Equations J. Comput. Chem. 1999, 20 (8) 819-844 (Pubitemid 129656130)
    • (1999) Journal of Computational Chemistry , vol.20 , Issue.8 , pp. 819-844
    • Wedemeyer, W.J.1    Scheraga, H.A.2
  • 48
    • 56549099908 scopus 로고    scopus 로고
    • Prediction of Protein Loop Structures using a Local Move Monte Carlo Approach and a Grid-based Force Field
    • Cui, M.; Mezei, M.; Osman, R. Prediction of Protein Loop Structures using a Local Move Monte Carlo Approach and a Grid-based Force Field Protein Eng. Des. Sel. 2008, 21 (12) 729-735
    • (2008) Protein Eng. Des. Sel. , vol.21 , Issue.12 , pp. 729-735
    • Cui, M.1    Mezei, M.2    Osman, R.3
  • 49
    • 84986431515 scopus 로고
    • Acceleration of Convergence in Monte Carlo Simulations of Aqueous Solutions using the Metropolis Algorithm
    • Kincaid, R. H.; Scheraga, H. A. Acceleration of Convergence in Monte Carlo Simulations of Aqueous Solutions using the Metropolis Algorithm J. Comput. Chem. 1982, 3, 525-547
    • (1982) J. Comput. Chem. , vol.3 , pp. 525-547
    • Kincaid, R.H.1    Scheraga, H.A.2
  • 50
    • 1542295220 scopus 로고    scopus 로고
    • The Good of the Many Outweights the Good of the One: Evolutionary Multiobjective Optimization
    • Corne, D. W.; Deb, K.; Fleming, P. J.; Knowles, J. D. The Good of the Many Outweights the Good of the One: Evolutionary Multiobjective Optimization IEEE Newsletter: connections 2003, 1 (1) 9-13
    • (2003) IEEE Newsletter: Connections , vol.1 , Issue.1 , pp. 9-13
    • Corne, D.W.1    Deb, K.2    Fleming, P.J.3    Knowles, J.D.4
  • 52
    • 0028947257 scopus 로고
    • Funnels, pathways, and the energy landscape of protein folding: A synthesis
    • Bryngelson, J. D.; Onuchic, J. N.; Socci, N. D.; Wolynes, P. G. Funnels, pathways, and the energy landscape of protein folding: A synthesis Proteins 1994, 21 (3) 167-195
    • (1994) Proteins , vol.21 , Issue.3 , pp. 167-195
    • Bryngelson, J.D.1    Onuchic, J.N.2    Socci, N.D.3    Wolynes, P.G.4
  • 54
    • 33745603720 scopus 로고    scopus 로고
    • A Markov Chain Monte Carlo version of the genetic algorithm Differential Evolution: Easy Bayesian computing for real parameter spaces
    • DOI 10.1007/s11222-006-8769-1
    • Ter Braak, C. J. F. A Markov chain Monte Carlo version of the genetic algorithm differential evolution: easy Bayesian computing for real parameter spaces Stat. Comput. 2006, 16, 239-249 (Pubitemid 43992692)
    • (2006) Statistics and Computing , vol.16 , Issue.3 , pp. 239-249
    • Ter Braak, C.J.F.1
  • 55
    • 0013941871 scopus 로고
    • The intraclass correlation coefficient as a measure of reliability
    • Bartko, J. J. The intraclass correlation coefficient as a measure of reliability Psychol. Rep. 1966, 19, 3-11
    • (1966) Psychol. Rep. , vol.19 , pp. 3-11
    • Bartko, J.J.1


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