메뉴 건너뛰기




Volumn 115, Issue 2-3 SPEC. ISS., 2005, Pages 209-214

Protein structure prediction based on fragment assembly and parameter optimization

Author keywords

Ab initio prediction; Fragment assembly; Global optimization; Parameter optimization; Protein folding; Tertiary structure prediction

Indexed keywords

STAPHYLOCOCCUS PROTEIN A;

EID: 14744276882     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2004.12.046     Document Type: Conference Paper
Times cited : (42)

References (42)
  • 1
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • A. Fiser, R.K.G. Do, and A. Sali Modeling of loops in protein structures Protein Sci. 9 2000 1753 1773
    • (2000) Protein Sci. , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.G.2    Sali, A.3
  • 2
    • 0035427225 scopus 로고    scopus 로고
    • Generalized Comparative Modeling (GENECOMP): A combination of sequence comparison, threading, lattice and off-lattice modeling for protein structure prediction and refinement
    • A. Kolinski, M.R. Betancourt, D. Kihara, P. Rotkiewicz, and J. Skolnick Generalized Comparative Modeling (GENECOMP): a combination of sequence comparison, threading, lattice and off-lattice modeling for protein structure prediction and refinement Proteins 44 2001 133 149
    • (2001) Proteins , vol.44 , pp. 133-149
    • Kolinski, A.1    Betancourt, M.R.2    Kihara, D.3    Rotkiewicz, P.4    Skolnick, J.5
  • 3
    • 0035747672 scopus 로고    scopus 로고
    • Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM
    • P.A. Bates, L.A. Kelley, R.M. MacCallum, and M.J.E. Sternberg Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM Proteins Suppl. 5 2001 39 46
    • (2001) Proteins , Issue.SUPPL. 5 , pp. 39-46
    • Bates, P.A.1    Kelley, L.A.2    MacCallum, R.M.3    Sternberg, M.J.E.4
  • 4
    • 0035748717 scopus 로고    scopus 로고
    • Comparative modeling of CASP4 target proteins: Combining results of sequence search with three-dimensional structure assessment
    • C. Venclovas Comparative modeling of CASP4 target proteins: combining results of sequence search with three-dimensional structure assessment Proteins Suppl. 5 2001 47 54
    • (2001) Proteins , Issue.SUPPL. 5 , pp. 47-54
    • Venclovas, C.1
  • 5
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • D. Baker, and A. Sali Protein structure prediction and structural genomics Science 294 2001 93 96
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 6
    • 0035703313 scopus 로고    scopus 로고
    • Fold recognition from sequence comparisons
    • K.K. Koretke, R.B. Russell, and A.N. Lupas Fold recognition from sequence comparisons Proteins Suppl. 5 2001 68 75
    • (2001) Proteins , Issue.SUPPL. 5 , pp. 68-75
    • Koretke, K.K.1    Russell, R.B.2    Lupas, A.N.3
  • 7
    • 0035747811 scopus 로고    scopus 로고
    • CASP2 knowledge-based approach to distant homology recognition and fold prediction in CASP4
    • A.G. Murzin, and A. Bateman CASP2 knowledge-based approach to distant homology recognition and fold prediction in CASP4 Proteins Suppl. 5 2001 76 85
    • (2001) Proteins , Issue.SUPPL. 5 , pp. 76-85
    • Murzin, A.G.1    Bateman, A.2
  • 10
    • 0035702809 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP): Round III
    • J. Moult, T. Hubbard, K. Fidelis, and J.T. Pedersen Critical assessment of methods of protein structure prediction (CASP): round III Proteins Suppl. 3 1999 2 6
    • (1999) Proteins , Issue.SUPPL. 3 , pp. 2-6
    • Moult, J.1    Hubbard, T.2    Fidelis, K.3    Pedersen, J.T.4
  • 11
    • 0032606039 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP): Round IV
    • J. Moult, K. Fidelis, A. Zemla, and T. Hubbard Critical assessment of methods of protein structure prediction (CASP): round IV Proteins Suppl. 5 2001 2 7
    • (2001) Proteins , Issue.SUPPL. 5 , pp. 2-7
    • Moult, J.1    Fidelis, K.2    Zemla, A.3    Hubbard, T.4
  • 12
    • 0035703008 scopus 로고    scopus 로고
    • Assessment of novel fold targets in CASP4: Predictions of three-dimensional structures, secondary structures, and interresidue contacts
    • A.M. Lesk, L.L. Conte, and T.J.P. Hubbard Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts Proteins Suppl. 5 2001 98 118
    • (2001) Proteins , Issue.SUPPL. 5 , pp. 98-118
    • Lesk, A.M.1    Conte, L.L.2    Hubbard, T.J.P.3
  • 13
    • 0033514939 scopus 로고    scopus 로고
    • Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein a and to apo calbindin D9K
    • J. Lee, A. Liwo, and H.A. Scheraga Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K Proc. Natl. Acad. Sci. 96 1999 2025 2030
    • (1999) Proc. Natl. Acad. Sci. , vol.96 , pp. 2025-2030
    • Lee, J.1    Liwo, A.2    Scheraga, H.A.3
  • 14
    • 0032605909 scopus 로고    scopus 로고
    • Calculation of protein conformation by global optimization of a potential energy function
    • J. Lee, A. Liwo, D.R. Ripoll, J. Pillardy, and H.A. Scheraga Calculation of protein conformation by global optimization of a potential energy function Proteins Suppl. 3 1999 204 208
    • (1999) Proteins , Issue.SUPPL. 3 , pp. 204-208
    • Lee, J.1    Liwo, A.2    Ripoll, D.R.3    Pillardy, J.4    Scheraga, H.A.5
  • 16
    • 0033545962 scopus 로고    scopus 로고
    • Protein structure prediction by global optimization of a potential energy function
    • A. Liwo, J. Lee, D.R. Ripoll, J. Pillardy, and H.A. Scheraga Protein structure prediction by global optimization of a potential energy function Proc. Natl. Acad. Sci. 96 1999 5482 5485
    • (1999) Proc. Natl. Acad. Sci. , vol.96 , pp. 5482-5485
    • Liwo, A.1    Lee, J.2    Ripoll, D.R.3    Pillardy, J.4    Scheraga, H.A.5
  • 17
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • K.T. Simons, C. Kooperberg, E. Huang, and D. Baker Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions J. Mol. Biol. 268 1997 209 225
    • (1997) J. Mol. Biol. , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 18
    • 0035830958 scopus 로고    scopus 로고
    • Prospects for ab initio protein structural genomics
    • K.T. Simons, C. Strauss, and D. Baker Prospects for ab initio protein structural genomics J. Mol. Biol. 306 2001 1191 1199
    • (2001) J. Mol. Biol. , vol.306 , pp. 1191-1199
    • Simons, K.T.1    Strauss, C.2    Baker, D.3
  • 20
    • 0035698619 scopus 로고    scopus 로고
    • Predicting novel protein folds by using FRAGFOLD
    • D.T. Jones Predicting novel protein folds by using FRAGFOLD Proteins Suppl. 5 2001 127 132
    • (2001) Proteins , Issue.SUPPL. 5 , pp. 127-132
    • Jones, D.T.1
  • 21
    • 0035748356 scopus 로고    scopus 로고
    • Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment
    • D.M. Standley, V.A. Eyrich, Y. An, D.L. Pincus, J.R. Gunn, and R.A. Friesner Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment Proteins Suppl. 5 2001 133 139
    • (2001) Proteins , Issue.SUPPL. 5 , pp. 133-139
    • Standley, D.M.1    Eyrich, V.A.2    An, Y.3    Pincus, D.L.4    Gunn, J.R.5    Friesner, R.A.6
  • 22
    • 0035703315 scopus 로고    scopus 로고
    • Application of PROSPECT in CASP4: Characterizing protein structures with new folds
    • D. Xu, O.H. Crawford, P.F. LoCascio, and Y. Xu Application of PROSPECT in CASP4: characterizing protein structures with new folds Proteins Suppl. 5 2001 140 148
    • (2001) Proteins , Issue.SUPPL. 5 , pp. 140-148
    • Xu, D.1    Crawford, O.H.2    Locascio, P.F.3    Xu, Y.4
  • 23
    • 0035749546 scopus 로고    scopus 로고
    • Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement
    • J. Skolnick, A. Kolinski, D. Kihara, M. Betancourt, P. Rotkiewicz, and M. Boniecki Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement Proteins Suppl. 5 2001 149 156
    • (2001) Proteins , Issue.SUPPL. 5 , pp. 149-156
    • Skolnick, J.1    Kolinski, A.2    Kihara, D.3    Betancourt, M.4    Rotkiewicz, P.5    Boniecki, M.6
  • 24
    • 0035964191 scopus 로고    scopus 로고
    • Touchstone: An ab initio protein structure prediction method that uses threading-based tertiary restraints
    • D. Kihara, H. Lu, A. Kolinski, and J. Skolnick Touchstone: an ab initio protein structure prediction method that uses threading-based tertiary restraints Proc. Natl. Acad. Sci. 98 2001 10125 10130
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 10125-10130
    • Kihara, D.1    Lu, H.2    Kolinski, A.3    Skolnick, J.4
  • 25
    • 4043058565 scopus 로고    scopus 로고
    • Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing
    • J. Lee, S.-Y. Kim, K. Joo, I. Kim, and J. Lee Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing Proteins: Struct., Funct., Bioinform. 56 2004 704 714
    • (2004) Proteins: Struct., Funct., Bioinform. , vol.56 , pp. 704-714
    • Lee, J.1    Kim, S.-Y.2    Joo, K.3    Kim, I.4    Lee, J.5
  • 26
    • 0015859467 scopus 로고
    • Studies on the principles that govern the folding of protein chains
    • C.B. Anfinsen Studies on the principles that govern the folding of protein chains Science 181 1973 223 230
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 28
    • 14744280111 scopus 로고    scopus 로고
    • Prediction of the secondary structures of protein using PREDICT, a nearest neighbor method on pattern space
    • K. Joo, I. Kim, S.-Y. Kim, J. Lee, J. Lee, and S.J. Lee Prediction of the secondary structures of protein using PREDICT, a nearest neighbor method on pattern space J. Korean Phys. Soc. 45 2004 1441
    • (2004) J. Korean Phys. Soc. , vol.45 , pp. 1441
    • Joo, K.1    Kim, I.2    Kim, S.-Y.3    Lee, J.4    Lee, J.5    Lee, S.J.6
  • 29
    • 0001176785 scopus 로고    scopus 로고
    • New optimization method for conformational energy calculations on polypeptides: Conformational space annealing
    • J. Lee, H.A. Scheraga, and S. Rackovsky New optimization method for conformational energy calculations on polypeptides: conformational space annealing J. Comput. Chem. 18 1997 1222 1232
    • (1997) J. Comput. Chem. , vol.18 , pp. 1222-1232
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 30
    • 0032146482 scopus 로고    scopus 로고
    • Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing
    • J. Lee, H.A. Scheraga, and S. Rackovsky Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing Biopolymers 46 1998 103 115
    • (1998) Biopolymers , vol.46 , pp. 103-115
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 31
    • 0000542451 scopus 로고    scopus 로고
    • Conformational space annealing by parallel computations: Extensive conformational search of met-enkephalin and the 20-residue membrane-bound portion of melittin
    • J. Lee, and H.A. Scheraga Conformational space annealing by parallel computations: extensive conformational search of met-enkephalin and the 20-residue membrane-bound portion of melittin Int. J. Quant. Chem. 75 1999 255 265
    • (1999) Int. J. Quant. Chem. , vol.75 , pp. 255-265
    • Lee, J.1    Scheraga, H.A.2
  • 32
    • 0344236093 scopus 로고    scopus 로고
    • Conformational space annealing and an off-lattice frustrated model protein
    • S.-Y. Kim, S.J. Lee, and J. Lee Conformational space annealing and an off-lattice frustrated model protein J. Chem. Phys. 119 2003 10274 10279
    • (2003) J. Chem. Phys. , vol.119 , pp. 10274-10279
    • Kim, S.-Y.1    Lee, S.J.2    Lee, J.3
  • 33
    • 0141904480 scopus 로고    scopus 로고
    • Unbiased global optimization of Lennard-Jones clusters for N≤201 using conformational space annealing method
    • J. Lee, I.H. Lee, and J. Lee Unbiased global optimization of Lennard-Jones clusters for N≤201 using conformational space annealing method Phys. Rev. Lett. 91 2003 0802011 0802014
    • (2003) Phys. Rev. Lett. , vol.91 , pp. 0802011-0802014
    • Lee, J.1    Lee, I.H.2    Lee, J.3
  • 34
    • 0035797727 scopus 로고    scopus 로고
    • Optimization of parameters in macromolecular potential energy functions by conformational space annealing
    • J. Lee, D.R. Ripoll, C. Czaplewski, J. Pillardy, W.J. Wedemeyer, and H.A. Scheraga Optimization of parameters in macromolecular potential energy functions by conformational space annealing J. Phys. Chem., B 105 2001 7291 7298
    • (2001) J. Phys. Chem., B , vol.105 , pp. 7291-7298
    • Lee, J.1    Ripoll, D.R.2    Czaplewski, C.3    Pillardy, J.4    Wedemeyer, W.J.5    Scheraga, H.A.6
  • 36
    • 0037133165 scopus 로고    scopus 로고
    • A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: Application to the UNRES force field
    • A. Liwo, P. Arlukowicz, C. Czaplewski, S. Oldziej, J. Pillardy, and H.A. Scheraga A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field Proc. Natl. Acad. Sci. U. S. A. 99 2002 1937 1942
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , pp. 1937-1942
    • Liwo, A.1    Arlukowicz, P.2    Czaplewski, C.3    Oldziej, S.4    Pillardy, J.5    Scheraga, H.A.6
  • 37
    • 0037038520 scopus 로고    scopus 로고
    • Full optimization of linear parameters of a united residue protein potential
    • J. Lee, K. Park, and J. Lee Full optimization of linear parameters of a united residue protein potential J. Phys. Chem., B 106 2002 11647 11657
    • (2002) J. Phys. Chem., B , vol.106 , pp. 11647-11657
    • Lee, J.1    Park, K.2    Lee, J.3
  • 38
    • 2342421001 scopus 로고    scopus 로고
    • Design of a protein potential energy landscape by parameter optimization
    • J. Lee, S.-Y. Kim, and J. Lee Design of a protein potential energy landscape by parameter optimization J. Phys. Chem., B 108 2004 4525 4534
    • (2004) J. Phys. Chem., B , vol.108 , pp. 4525-4534
    • Lee, J.1    Kim, S.-Y.2    Lee, J.3
  • 39
    • 33845377127 scopus 로고
    • Estimation of effective inter-residue contact energies from protein crystal structures: Quasi-chemical approximation
    • S. Miyazawa, and R.L. Jernigan Estimation of effective inter-residue contact energies from protein crystal structures: quasi-chemical approximation Macromolecules 18 1985 534 552
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 40
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term for simulation and threading
    • S. Miyazawa, and R.L. Jernigan Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term for simulation and threading J. Mol. Biol. 256 1996 623 644
    • (1996) J. Mol. Biol. , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 41
    • 0030080729 scopus 로고    scopus 로고
    • Fast cholesky factorization for interior point methods of linear programming
    • C.A. Mészáros Fast cholesky factorization for interior point methods of linear programming Comput. Math. Appl. 31 1996 49 51
    • (1996) Comput. Math. Appl. , vol.31 , pp. 49-51
    • Mészáros, C.A.1
  • 42
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • R. Koradi, M. Billeter, and K. Wuthrich MOLMOL: a program for display and analysis of macromolecular structures J. Mol. Graph. 14 1996 51 55
    • (1996) J. Mol. Graph. , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.