-
1
-
-
0033810049
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
8
-
-
0035748354
-
What is the value added by human intervention in protein structure prediction?
-
K. Karplus, R. Karchin, C. Barrett, S. Tu, M. Cline, M. Diekhans, L. Grate, J. Casper, and R. Hughey What is the value added by human intervention in protein structure prediction? Proteins Suppl. 5 2001 86 91
-
(2001)
Proteins
, Issue.SUPPL. 5
, pp. 86-91
-
-
Karplus, K.1
Karchin, R.2
Barrett, C.3
Tu, S.4
Cline, M.5
Diekhans, M.6
Grate, L.7
Casper, J.8
Hughey, R.9
-
9
-
-
0035748718
-
Sequence-structure homology recognition by iterative alignment refinement and comparative modeling
-
M.G. Williams, H. Shirai, J. Shi, H.G. Nagendra, J. Mueller, K. Mizuguchi, R.N. Miguel, S.C. Lovell, C.A. Innis, C.M. Deane, L. Chen, N. Campillo, D.F. Burke, T.L. Blundell, and P.I.W. de Bakker Sequence-structure homology recognition by iterative alignment refinement and comparative modeling Proteins Suppl. 5 2001 92 97
-
(2001)
Proteins
, Issue.SUPPL. 5
, pp. 92-97
-
-
Williams, M.G.1
Shirai, H.2
Shi, J.3
Nagendra, H.G.4
Mueller, J.5
Mizuguchi, K.6
Miguel, R.N.7
Lovell, S.C.8
Innis, C.A.9
Deane, C.M.10
Chen, L.11
Campillo, N.12
Burke, D.F.13
Blundell, T.L.14
De Bakker, P.I.W.15
-
10
-
-
0035702809
-
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
-
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
-
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
-
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
-
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
-
15
-
-
0002001599
-
Hierarchical energy-based approach to protein-structure prediction: Blind-test evaluation with CASP3 targets
-
J. Lee, A. Liwo, D.R. Ripoll, J. Pillardy, J.A. Saunders, K.D. Gibson, and H.A. Scheraga Hierarchical energy-based approach to protein-structure prediction: blind-test evaluation with CASP3 targets Int. J. Quant. Chem. 77 2000 90 117
-
(2000)
Int. J. Quant. Chem.
, vol.77
, pp. 90-117
-
-
Lee, J.1
Liwo, A.2
Ripoll, D.R.3
Pillardy, J.4
Saunders, J.A.5
Gibson, K.D.6
Scheraga, H.A.7
-
16
-
-
0033545962
-
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
-
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
-
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
-
19
-
-
0035703089
-
Rosetta in CASP4: Progress in ab initio protein structure prediction
-
R. Bonneau, J. Tsai, I. Ruczinski, D. Chivian, C. Rohl, C.E.M. Strauss, and D. Baker Rosetta in CASP4: progress in ab initio protein structure prediction Proteins Suppl. 5 2001 119 126
-
(2001)
Proteins
, Issue.SUPPL. 5
, pp. 119-126
-
-
Bonneau, R.1
Tsai, J.2
Ruczinski, I.3
Chivian, D.4
Rohl, C.5
Strauss, C.E.M.6
Baker, D.7
-
20
-
-
0035698619
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
27
-
-
1842817419
-
Profile-based nearest neighbor method for pattern recognition
-
K. Joo, J. Lee, S.-Y. Kim, I. Kim, S.J. Lee, and J. Lee Profile-based nearest neighbor method for pattern recognition J. Korean Phys. Soc. 44 2004 599 604
-
(2004)
J. Korean Phys. Soc.
, vol.44
, pp. 599-604
-
-
Joo, K.1
Lee, J.2
Kim, S.-Y.3
Kim, I.4
Lee, S.J.5
Lee, J.6
-
28
-
-
14744280111
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
35
-
-
0035797740
-
Development of physics-based energy functions that predict medium-resolution structures for proteins of the α, beta, and α/β structural classes
-
J. Pillardy, C. Czaplewski, A. Liwo, W.J. Wedemeyer, J. Lee, D.R. Ripoll, P. Arlukowicz, S. Oldziej, Y.A. Arnautova, and H.A. Scheraga Development of physics-based energy functions that predict medium-resolution structures for proteins of the α, beta, and α/β structural classes J. Phys. Chem., B 105 2001 7299 7311
-
(2001)
J. Phys. Chem., B
, vol.105
, pp. 7299-7311
-
-
Pillardy, J.1
Czaplewski, C.2
Liwo, A.3
Wedemeyer, W.J.4
Lee, J.5
Ripoll, D.R.6
Arlukowicz, P.7
Oldziej, S.8
Arnautova, Y.A.9
Scheraga, H.A.10
-
36
-
-
0037133165
-
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
-
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
-
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
-
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
-
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
-
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
-
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
|