-
1
-
-
0014116254
-
Minimization of polypeptide energy: I. Preliminary structures of bovine pancreatic ribonuclease S-peptide
-
Gibson KD, Scheraga HA. Minimization of polypeptide energy: I. Preliminary structures of bovine pancreatic ribonuclease S-peptide. Proc Natl Acad Sci USA 1967;58:420-427.
-
(1967)
Proc Natl Acad Sci USA
, vol.58
, pp. 420-427
-
-
Gibson, K.D.1
Scheraga, H.A.2
-
2
-
-
0016399124
-
Energy functions for peptides and proteins: I. Derivation of a consistent force field including the hydrogen bond from amide crystals
-
Hagler AT, Huler E, Lifson S. Energy functions for peptides and proteins: I. Derivation of a consistent force field including the hydrogen bond from amide crystals. J Amer Chem Soc 1974;96:5319-5327.
-
(1974)
J Amer Chem Soc
, vol.96
, pp. 5319-5327
-
-
Hagler, A.T.1
Huler, E.2
Lifson, S.3
-
3
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
-
(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
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
4
-
-
4644328821
-
Empirical force field studies of geometries and conformational transitions of some organic molecules
-
Smith JC, Karplus M. Empirical force field studies of geometries and conformational transitions of some organic molecules. J Am Chem Soc 1992;114:801-812.
-
(1992)
J Am Chem Soc
, vol.114
, pp. 801-812
-
-
Smith, J.C.1
Karplus, M.2
-
5
-
-
0001731773
-
Energy parameters in polypeptides: 10 Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with applications to proline-containing peptides
-
Nemethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A, Rumsey S, Scheraga HA. Energy parameters in polypeptides: 10 improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with applications to proline-containing peptides. J Phys Chem 1992;96:6472-6484.
-
(1992)
J Phys Chem
, 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
Rumsey, S.7
Scheraga, H.A.8
-
6
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
Lindahl E, Hess B, van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 2001;7:306-317.
-
(2001)
J Mol Model
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van Der Spoel, D.3
-
7
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 1998;282:740-744.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
8
-
-
0034718553
-
Folding simulations of a three-stranded antiparallel β-sheet peptide
-
Ferrara P, Caflisch A. Folding simulations of a three-stranded antiparallel β-sheet peptide. Proc Natl Acad Sci USA 2000;97:10780-10785.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 10780-10785
-
-
Ferrara, P.1
Caflisch, A.2
-
9
-
-
0037093655
-
Weak temperature dependence of the free energy surface and folding pathways of structured peptides
-
Cavalli A, Ferrara P, Caflisch A. Weak temperature dependence of the free energy surface and folding pathways of structured peptides. Proteins 2002;47:305-314.
-
(2002)
Proteins
, vol.47
, pp. 305-314
-
-
Cavalli, A.1
Ferrara, P.2
Caflisch, A.3
-
10
-
-
0036892356
-
All-atom fast protein simulations: The villin headpiece
-
Shen M, Freed KF. All-atom fast protein simulations: the villin headpiece. Proteins 2002;49:439-445.
-
(2002)
Proteins
, vol.49
, pp. 439-445
-
-
Shen, M.1
Freed, K.F.2
-
11
-
-
0037038372
-
Absolute comparison of simulated and experimental protein-folding dynamics
-
Snow CD, Nguyen H, Pande VS, Gruebele M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 420:102-106.
-
Nature
, vol.420
, pp. 102-106
-
-
Snow, C.D.1
Nguyen, H.2
Pande, V.S.3
Gruebele, M.4
-
12
-
-
0035698724
-
LiveBench-2: Large-scale automated evaluation of protein structure prediction servers
-
Bujnicki JM, Elofsson A, Fischer D, Rychlewski L. LiveBench-2: Large-scale automated evaluation of protein structure prediction servers. Proteins 2001;Suppl 5:184-191.
-
(2001)
Proteins
, Issue.SUPPL. 5
, pp. 184-191
-
-
Bujnicki, J.M.1
Elofsson, A.2
Fischer, D.3
Rychlewski, L.4
-
13
-
-
3042726390
-
A structural pattern-based method for protein fold recognition
-
Taylor WR, Jonassen I. A structural pattern-based method for protein fold recognition. Proteins 2004;56:222-234.
-
(2004)
Proteins
, vol.56
, pp. 222-234
-
-
Taylor, W.R.1
Jonassen, I.2
-
14
-
-
0036968925
-
De novo prediction of three-dimensional structures for major protein families
-
Bonneau R, Strauss CEM, Rohl CA, Chivian D, Bradley P, Malmström L, Robertson T, Baker D. De novo prediction of three-dimensional structures for major protein families. J Mol Biol 2002;322:65-78.
-
(2002)
J Mol Biol
, vol.322
, pp. 65-78
-
-
Bonneau, R.1
Strauss, C.E.M.2
Rohl, C.A.3
Chivian, D.4
Bradley, P.5
Malmström, L.6
Robertson, T.7
Baker, D.8
-
15
-
-
18344388966
-
The significance of performance ranking in CASP
-
Moult J, Unger R. The significance of performance ranking in CASP. Structure 2002;10:291-293.
-
(2002)
Structure
, vol.10
, pp. 291-293
-
-
Moult, J.1
Unger, R.2
-
16
-
-
0017021957
-
Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
-
Tanaka S, Scheraga HA. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromol 1976;9:945-950.
-
(1976)
Macromol
, vol.9
, pp. 945-950
-
-
Tanaka, S.1
Scheraga, H.A.2
-
17
-
-
33845377127
-
Estimation of effective contact energies from protein crystal structures: Quasi-chemical approximation
-
Miyazawa S, Jernigan RL. Estimation of effective contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985;18:534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
18
-
-
0029919190
-
Residue-residue potentials with a favourable contact pair term and an unfavourable high packing density term, for simulation and threading
-
Miyazawa S, Jernigan RL. Residue-residue potentials with a favourable contact pair term and an unfavourable high packing density term, for simulation and threading. J Mol Biol 1996;256:623-644.
-
(1996)
J Mol Biol
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
19
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force
-
Sippl MJ. Calculation of conformational ensembles from potentials of mean force. J Mol Biol 1990;213:859-883.
-
(1990)
J Mol Biol
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
20
-
-
0000778903
-
A general method for the prediction of the three-dimensional structure and folding pathway of globular proteins: Application to designed helical proteins
-
Kolinski A, Godzik A, Skolnick J. A general method for the prediction of the three-dimensional structure and folding pathway of globular proteins: application to designed helical proteins. J Chem Phys 1993;98:7420-7433.
-
(1993)
J Chem Phys
, vol.98
, pp. 7420-7433
-
-
Kolinski, A.1
Godzik, A.2
Skolnick, J.3
-
21
-
-
0001181898
-
United-residue force field for off-lattice protein structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials
-
Liwo A, Kazmierkiewicz R, Czaplewski C, Groth M, Oldziej S, Wawak RJ, Rackovsky S, Pincus MR, Scheraga HA. United-residue force field for off-lattice protein structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials. J Comput Chem 1998;19:259-276.
-
(1998)
J Comput Chem
, vol.19
, pp. 259-276
-
-
Liwo, A.1
Kazmierkiewicz, R.2
Czaplewski, C.3
Groth, M.4
Oldziej, S.5
Wawak, R.J.6
Rackovsky, S.7
Pincus, M.R.8
Scheraga, H.A.9
-
22
-
-
0031298075
-
Successful ab initio prediction of the tertiary structure of NK-Lysin using multiple sequences and recognized supersecondary structural motifs
-
Jones DT. Successful ab initio prediction of the tertiary structure of NK-Lysin using multiple sequences and recognized supersecondary structural motifs. Proteins 1997;Suppl 1:185-191.
-
(1997)
Proteins
, Issue.SUPPL. 1
, pp. 185-191
-
-
Jones, D.T.1
-
23
-
-
0035342441
-
Lattice protein folding with two and four-body statistical potentials
-
Gan HH, Tropsha A, Schlick T. Lattice protein folding with two and four-body statistical potentials. Proteins 2001;43:161-174.
-
(2001)
Proteins
, vol.43
, pp. 161-174
-
-
Gan, H.H.1
Tropsha, A.2
Schlick, T.3
-
24
-
-
0345411953
-
A reduced protein model with accurate native structure identification ability
-
Betancourt MR. A reduced protein model with accurate native structure identification ability. Proteins 2003;53:889-907.
-
(2003)
Proteins
, vol.53
, pp. 889-907
-
-
Betancourt, M.R.1
-
25
-
-
0033005899
-
Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
-
Betancourt MR, Thirumalai D. Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci 1999;8:361-369.
-
(1999)
Protein Sci
, vol.8
, pp. 361-369
-
-
Betancourt, M.R.1
Thirumalai, D.2
-
26
-
-
0000171351
-
Pairwise contact potentials are unsuitable for protein folding
-
Vendruscolo M, Domany E. Pairwise contact potentials are unsuitable for protein folding. J Chem Phys 1998;109:11101-11108.
-
(1998)
J Chem Phys
, vol.109
, pp. 11101-11108
-
-
Vendruscolo, M.1
Domany, E.2
-
27
-
-
0034141931
-
Can pairwise contact potentials stabilize native protein against decoys obtained by threading?
-
Vendruscolo M, Domany E. Can pairwise contact potentials stabilize native protein against decoys obtained by threading? Proteins 2000;38:134-148.
-
(2000)
Proteins
, vol.38
, pp. 134-148
-
-
Vendruscolo, M.1
Domany, E.2
-
28
-
-
0035943455
-
Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations
-
Carter CW Jr, LeFebvre BC, Cammer SA, Tropsha A, Edgell MH. Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations. J Mol Biol 2001;311:625-638.
-
(2001)
J Mol Biol
, vol.311
, pp. 625-638
-
-
Carter Jr., C.W.1
LeFebvre, B.C.2
Cammer, S.A.3
Tropsha, A.4
Edgell, M.H.5
-
29
-
-
0034829847
-
Conformation-dependent environments in folding proteins
-
Fernandez A. Conformation-dependent environments in folding proteins. J Chem Phys 2001;114:2489-2502.
-
(2001)
J Chem Phys
, vol.114
, pp. 2489-2502
-
-
Fernandez, A.1
-
30
-
-
1242294472
-
Can contact potentials reliably predict stability of proteins?
-
Khatun J, Sagar DK, Dokholyan NV. Can contact potentials reliably predict stability of proteins? J Mol Biol 2004;336:1223-1238.
-
(2004)
J Mol Biol
, vol.336
, pp. 1223-1238
-
-
Khatun, J.1
Sagar, D.K.2
Dokholyan, N.V.3
-
31
-
-
0024395940
-
A 3D building blocks approach to analyzing and predicting structure of proteins
-
Unger R, Harel D, Wherland S, Sussman JL. A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins 1989;5:355-373.
-
(1989)
Proteins
, vol.5
, pp. 355-373
-
-
Unger, R.1
Harel, D.2
Wherland, S.3
Sussman, J.L.4
-
32
-
-
0029860175
-
Local structure motifs of protein backbones are classified by self-organizing neural networks
-
Suchhardt J, Schneider G, Reichelt J, Schomburg D, Wrede P. Local structure motifs of protein backbones are classified by self-organizing neural networks. Prot Eng 1996;9:833-842.
-
(1996)
Prot Eng
, vol.9
, pp. 833-842
-
-
Suchhardt, J.1
Schneider, G.2
Reichelt, J.3
Schomburg, D.4
Wrede, P.5
-
33
-
-
0031301753
-
Blind predictions of local protein structure in CASP2 targets using the I-Sites library
-
Bystroff C, Baker D. Blind predictions of local protein structure in CASP2 targets using the I-Sites library. Proteins 1997;Suppl 1:167-171.
-
(1997)
Proteins
, Issue.SUPPL. 1
, pp. 167-171
-
-
Bystroff, C.1
Baker, D.2
-
34
-
-
0031052447
-
Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme
-
Fetrow JS, Palumbo MJ, Berg G. Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme. Proteins 1997;27:249-271.
-
(1997)
Proteins
, vol.27
, pp. 249-271
-
-
Fetrow, J.S.1
Palumbo, M.J.2
Berg, G.3
-
35
-
-
0033405214
-
Hidden Markov model approach for identifying the modular framework of the protein backbone
-
Camproux AC, Tuffery P, Chevrolat JP, Boisvieux JF, Hazout S. Hidden Markov model approach for identifying the modular framework of the protein backbone. Prot Eng 1999;12:1063-1073.
-
(1999)
Prot Eng
, vol.12
, pp. 1063-1073
-
-
Camproux, A.C.1
Tuffery, P.2
Chevrolat, J.P.3
Boisvieux, J.F.4
Hazout, S.5
-
36
-
-
0034237227
-
A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins
-
Deane CM, Blundell TL. A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins. Proteins 2000;40:135-144.
-
(2000)
Proteins
, vol.40
, pp. 135-144
-
-
Deane, C.M.1
Blundell, T.L.2
-
37
-
-
0034669774
-
Bayesian probabilistic approach for predicting structures in terms of protein blocks
-
de Brevern AG, Etchebest C, Hazout S. Bayesian probabilistic approach for predicting structures in terms of protein blocks. Proteins 2000;41:271-287.
-
(2000)
Proteins
, vol.41
, pp. 271-287
-
-
De Brevern, A.G.1
Etchebest, C.2
Hazout, S.3
-
38
-
-
0036893073
-
Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship
-
de Brevern AG, Valadie H, Hazout S, Etchebest C. Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship. Protein Sci 2002;11:2871-2886.
-
(2002)
Protein Sci
, vol.11
, pp. 2871-2886
-
-
De Brevern, A.G.1
Valadie, H.2
Hazout, S.3
Etchebest, C.4
-
39
-
-
0037312528
-
A pentapeptide-based method for protein secondary structure prediction
-
Figureau A, Soto MA, Toha J. A pentapeptide-based method for protein secondary structure prediction. Protein Eng 2003;16:103-108.
-
(2003)
Protein Eng
, vol.16
, pp. 103-108
-
-
Figureau, A.1
Soto, M.A.2
Toha, J.3
-
40
-
-
0025326949
-
Automatic definition of recurrent local structure motif in proteins
-
Rooman MJ, Rodriguez J, Wodak SJ. Automatic definition of recurrent local structure motif in proteins. J Mol Biol 1990;213:327-336.
-
(1990)
J Mol Biol
, vol.213
, pp. 327-336
-
-
Rooman, M.J.1
Rodriguez, J.2
Wodak, S.J.3
-
41
-
-
0001194908
-
Discretized model of proteins: I. Monte Carlo study of cooperativity in homopolypeptides
-
Kolinski A, Skolnick J. Discretized model of proteins: I. Monte Carlo study of cooperativity in homopolypeptides. J Chem Phys 1992;97:9412-9426.
-
(1992)
J Chem Phys
, vol.97
, pp. 9412-9426
-
-
Kolinski, A.1
Skolnick, J.2
-
42
-
-
0036971123
-
Dynamics of hydrogen bond desolvation in protein folding
-
Fernandez A, Sosnick TR, Colubri A. Dynamics of hydrogen bond desolvation in protein folding. J Mol Biol 2002;321:659-675.
-
(2002)
J Mol Biol
, vol.321
, pp. 659-675
-
-
Fernandez, A.1
Sosnick, T.R.2
Colubri, A.3
-
43
-
-
0030806961
-
Statistical significance of hierarchical multibody potentials based on Delaunay tessellation and their application in sequence-structure alignment
-
Munson PJ, Singh RJ. Statistical significance of hierarchical multibody potentials based on Delaunay tessellation and their application in sequence-structure alignment. Protein Sci 1997;6:1467-1481.
-
(1997)
Protein Sci
, vol.6
, pp. 1467-1481
-
-
Munson, P.J.1
Singh, R.J.2
-
44
-
-
0030054951
-
Delaunay tessellation of proteins: Four-body nearest neighbour propensities of amino acids
-
Singh RK, Tropsha A, Vaisman I. Delaunay tessellation of proteins: Four-body nearest neighbour propensities of amino acids. J Comput Biol 1996;3:213-221.
-
(1996)
J Comput Biol
, vol.3
, pp. 213-221
-
-
Singh, R.K.1
Tropsha, A.2
Vaisman, I.3
-
45
-
-
0029738719
-
Characterization of diverse residue clusters in protein three-dimensional structures
-
Karlin S, Zhu Z. Characterization of diverse residue clusters in protein three-dimensional structures. Proc Natl Acad Sci USA 1996;93:8344-8349.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 8344-8349
-
-
Karlin, S.1
Zhu, Z.2
-
46
-
-
0029775624
-
Clusters of charged residues in protein three-dimensional structures
-
Zhu Z, Karlin S. Clusters of charged residues in protein three-dimensional structures. Proc Natl Acad Sci USA 1996;93:8350-8355.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 8350-8355
-
-
Zhu, Z.1
Karlin, S.2
-
47
-
-
0033081985
-
Discovery of local packing motifs in protein structures
-
Jonassen I, Eidhammer I, Taylor WR. Discovery of local packing motifs in protein structures. Proteins 1999;34:206-219.
-
(1999)
Proteins
, vol.34
, pp. 206-219
-
-
Jonassen, I.1
Eidhammer, I.2
Taylor, W.R.3
-
49
-
-
0025789054
-
Side-chain clusters in protein structures and their role in protein folding
-
Herringa J, Argos P. Side-chain clusters in protein structures and their role in protein folding. J Mol Biol 1991;220:151-171.
-
(1991)
J Mol Biol
, vol.220
, pp. 151-171
-
-
Herringa, J.1
Argos, P.2
-
50
-
-
0041319042
-
The origin and extent of coarse-grained regularities in protein internal packing
-
Bagci Z, Kloczkowski A, Jernigan RL, Bahar I. The origin and extent of coarse-grained regularities in protein internal packing. Proteins 2003;53:56-67.
-
(2003)
Proteins
, vol.53
, pp. 56-67
-
-
Bagci, Z.1
Kloczkowski, A.2
Jernigan, R.L.3
Bahar, I.4
-
51
-
-
0021118508
-
Principles that determine the structure of proteins
-
Chothia C. Principles that determine the structure of proteins. Ann Rev Biochem 1984;53:537-572.
-
(1984)
Ann Rev Biochem
, vol.53
, pp. 537-572
-
-
Chothia, C.1
-
52
-
-
0019997016
-
Analysis and prediction of the packing of alpha-helices against a beta-sheet in the tertiary structure of globular proteins
-
Cohen FE, Sternberg MJE, Taylor WR. Analysis and prediction of the packing of alpha-helices against a beta-sheet in the tertiary structure of globular proteins. J Mol Biol 1982;156:821-862.
-
(1982)
J Mol Biol
, vol.156
, pp. 821-862
-
-
Cohen, F.E.1
Sternberg, M.J.E.2
Taylor, W.R.3
-
53
-
-
0019505121
-
Analysis of the tertiary structure of protein beta-sheet sandwiches
-
Cohen FE, Sternberg MJE, Taylor WR. Analysis of the tertiary structure of protein beta-sheet sandwiches. J Mol Biol 1981;148:253-277.
-
(1981)
J Mol Biol
, vol.148
, pp. 253-277
-
-
Cohen, F.E.1
Sternberg, M.J.E.2
Taylor, W.R.3
-
54
-
-
0026671355
-
Structural principles for the propeller assembly of beta-sheets: The preference for seven-fold symmetry
-
Murzin A. Structural principles for the propeller assembly of beta-sheets: the preference for seven-fold symmetry. Proteins 1992;14:191-201.
-
(1992)
Proteins
, vol.14
, pp. 191-201
-
-
Murzin, A.1
-
55
-
-
0020485895
-
Orthogonal packing of beta-pleated sheets in proteins
-
Chothia C, Janin J. Orthogonal packing of beta-pleated sheets in proteins. Biochem 1982;21:3955-3965.
-
(1982)
Biochem
, vol.21
, pp. 3955-3965
-
-
Chothia, C.1
Janin, J.2
-
57
-
-
0018350099
-
Gene duplications in the structural evolution of chymotrypsin
-
McClachlan AD. Gene duplications in the structural evolution of chymotrypsin. J Mol Biol 1979;128:49-79.
-
(1979)
J Mol Biol
, vol.128
, pp. 49-79
-
-
McClachlan, A.D.1
-
58
-
-
0030581145
-
The use of amino acid patterns of classified helices and strands in secondary structure prediction
-
Zhu Z, Blundell TL. The use of amino acid patterns of classified helices and strands in secondary structure prediction. J Mol Biol 1996;260:261-276.
-
(1996)
J Mol Biol
, vol.260
, pp. 261-276
-
-
Zhu, Z.1
Blundell, T.L.2
-
59
-
-
0028566270
-
A revised set of potentials for beta-turn formation in protein
-
Hutchinson E, Thornton JM. A revised set of potentials for beta-turn formation in protein. Prot Sci 1994;3:2207-2216.
-
(1994)
Prot Sci
, vol.3
, pp. 2207-2216
-
-
Hutchinson, E.1
Thornton, J.M.2
-
60
-
-
0017709445
-
Beta-turns in proteins
-
Chou PY, Fasman GD. Beta-turns in proteins. J Mol Biol 1977;115:135-175.
-
(1977)
J Mol Biol
, vol.115
, pp. 135-175
-
-
Chou, P.Y.1
Fasman, G.D.2
-
61
-
-
0024290472
-
Amino acid preferences for specific locations at the ends of alpha helices
-
Richardson JS, Richardson DC. Amino acid preferences for specific locations at the ends of alpha helices. Science 1988;240:1648-1652.
-
(1988)
Science
, vol.240
, pp. 1648-1652
-
-
Richardson, J.S.1
Richardson, D.C.2
-
62
-
-
0025272940
-
Alpha-helical coiled coils and bundles: How to design an alpha-helical protein
-
Cohen C, Parry DAD. Alpha-helical coiled coils and bundles: how to design an alpha-helical protein. Proteins 1990;7:1-15.
-
(1990)
Proteins
, vol.7
, pp. 1-15
-
-
Cohen, C.1
Parry, D.A.D.2
-
63
-
-
0026356891
-
Predicting coiled coils from protein sequences
-
Lupas A, van Dyke M, Stock J. Predicting coiled coils from protein sequences. Science 1991;252:1162-1164.
-
(1991)
Science
, vol.252
, pp. 1162-1164
-
-
Lupas, A.1
Van Dyke, M.2
Stock, J.3
-
64
-
-
0027049823
-
Relationships between sequence and structure for the four-alpha-helix bundle tertiary motif in proteins
-
Paliakasis CD, Kokkinidis M. Relationships between sequence and structure for the four-alpha-helix bundle tertiary motif in proteins. Protein Eng 1992;5:739-748.
-
(1992)
Protein Eng
, vol.5
, pp. 739-748
-
-
Paliakasis, C.D.1
Kokkinidis, M.2
-
65
-
-
0029083811
-
Predicting oligomerization states of coiled coils
-
Woolfson DN, Alber T. Predicting oligomerization states of coiled coils. Protein Sci 1995;4:1596-1607.
-
(1995)
Protein Sci
, vol.4
, pp. 1596-1607
-
-
Woolfson, D.N.1
Alber, T.2
-
66
-
-
2642670311
-
Design of a 20-amino acid, three-stranded beta-sheet protein
-
Kortemme T, Ramirez-Alvarado M, Serrano L. Design of a 20-amino acid, three-stranded beta-sheet protein. Science 1998;281:253-256.
-
(1998)
Science
, vol.281
, pp. 253-256
-
-
Kortemme, T.1
Ramirez-Alvarado, M.2
Serrano, L.3
-
67
-
-
0032917075
-
De novo design of a monomeric three-stranded antiparallel beta-sheet
-
de Alba E, Santoro J, Rico M, Jimenez MA. De novo design of a monomeric three-stranded antiparallel beta-sheet. Protein Sci 1999;8:854-865.
-
(1999)
Protein Sci
, vol.8
, pp. 854-865
-
-
De Alba, E.1
Santoro, J.2
Rico, M.3
Jimenez, M.A.4
-
68
-
-
0033824762
-
Structure, folding, and energetics of cooperative interactions between the beta-strands of a de novo designed three-stranded antiparallel beta-sheet peptide
-
Griffiths-Jones SR, Searle MS. Structure, folding, and energetics of cooperative interactions between the beta-strands of a de novo designed three-stranded antiparallel beta-sheet peptide. J Amer Chem Soc 2000;122:8350-8356.
-
(2000)
J Amer Chem Soc
, vol.122
, pp. 8350-8356
-
-
Griffiths-Jones, S.R.1
Searle, M.S.2
-
69
-
-
0029013417
-
Ice-binding structure and mechanism of an antifreeze protein from winter flounder
-
Sicheri F, Yang DSC. Ice-binding structure and mechanism of an antifreeze protein from winter flounder. Nature 1995;375:427-431.
-
(1995)
Nature
, vol.375
, pp. 427-431
-
-
Sicheri, F.1
Yang, D.S.C.2
-
70
-
-
0030880591
-
Solution structure of alpha-T-alpha, a helical hairpin peptide of de novo design
-
Fezoui Y, Connolly PJ, Osterhout JJ. Solution structure of alpha-T-alpha, a helical hairpin peptide of de novo design. Protein Sci 1997;6:1869-1877.
-
(1997)
Protein Sci
, vol.6
, pp. 1869-1877
-
-
Fezoui, Y.1
Connolly, P.J.2
Osterhout, J.J.3
-
71
-
-
5744249209
-
Equation of state calculation by fast computing machines
-
Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller EJ. Equation of state calculation by fast computing machines. Chem Phys 1952;21:1087-1092.
-
(1952)
Chem Phys
, vol.21
, pp. 1087-1092
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.J.5
-
72
-
-
0029863769
-
Automatic classification and analysis of alpha-alpha-turn motifs in proteins
-
Wintjens RT, Rooman MJ, Wodak SJ. Automatic classification and analysis of alpha-alpha-turn motifs in proteins. J Mol Biol 1996;255:235-253.
-
(1996)
J Mol Biol
, vol.255
, pp. 235-253
-
-
Wintjens, R.T.1
Rooman, M.J.2
Wodak, S.J.3
-
73
-
-
0029563695
-
Are database-derived potentials valid for coring forward and inverted protein folding?
-
Rooman MJ, Wodak SJ. Are database-derived potentials valid for coring forward and inverted protein folding? Protein Eng 1995;8:849-858.
-
(1995)
Protein Eng
, vol.8
, pp. 849-858
-
-
Rooman, M.J.1
Wodak, S.J.2
-
74
-
-
0029976427
-
Statistical potentials extracted from protein structures: How accurate are they?
-
Thomas PD, Dill KA. Statistical potentials extracted from protein structures: How accurate are they? J Mol Biol 1996;257:457-469.
-
(1996)
J Mol Biol
, vol.257
, pp. 457-469
-
-
Thomas, P.D.1
Dill, K.A.2
-
75
-
-
0001064488
-
Statistical potentials extracted from protein structures: Are these meaningful potentials?
-
Ben-Naim A. Statistical potentials extracted from protein structures: Are these meaningful potentials? J Chem Phys 1997;107:3698-3706.
-
(1997)
J Chem Phys
, vol.107
, pp. 3698-3706
-
-
Ben-Naim, A.1
-
76
-
-
0031557390
-
Factors affecting the ability of energy functions to discriminate correct from incorrect folds
-
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.
-
(1997)
J Mol Biol
, vol.266
, pp. 831-846
-
-
Park, B.H.1
Huang, E.S.2
Levitt, M.3
-
77
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002;11:2714-2726.
-
(2002)
Protein Sci
, vol.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
78
-
-
0037133165
-
A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: Application to the UNRES force field
-
Liwo A, Arlukowicz P, Czaplewski C, Oldziej S, Pillardy J, Scheraga HA. 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 USA 2002;99:1937-1942.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 1937-1942
-
-
Liwo, A.1
Arlukowicz, P.2
Czaplewski, C.3
Oldziej, S.4
Pillardy, J.5
Scheraga, H.A.6
-
79
-
-
0032053525
-
Prediction of the three-dimensional structure of proteins using the electrostatic screening model and hierarchic condensation
-
Avbelj F, Fele L. Prediction of the three-dimensional structure of proteins using the electrostatic screening model and hierarchic condensation. Proteins 1998;31:74-96.
-
(1998)
Proteins
, vol.31
, pp. 74-96
-
-
Avbelj, F.1
Fele, L.2
-
80
-
-
0019042107
-
Prediction of the surface-interior diagram of globular proteins by an empirical method
-
Nishikawa K, Ooi T. Prediction of the surface-interior diagram of globular proteins by an empirical method. Int J Protein Peptide Res 1980;16:19-32.
-
(1980)
Int J Protein Peptide Res
, vol.16
, pp. 19-32
-
-
Nishikawa, K.1
Ooi, T.2
-
81
-
-
0024818499
-
Stereochemical modelling of disulfide bridges: Criteria for introduction into proteins by site-directed mutagenesis
-
Sowdhamini R, Srinivasan N, Shoichet B, Santi DV, Ramakrishnan C, Balaram P. Stereochemical modelling of disulfide bridges: criteria for introduction into proteins by site-directed mutagenesis. Prot Eng 1989;3:95-103.
-
(1989)
Prot Eng
, vol.3
, pp. 95-103
-
-
Sowdhamini, R.1
Srinivasan, N.2
Shoichet, B.3
Santi, D.V.4
Ramakrishnan, C.5
Balaram, P.6
-
82
-
-
0017872911
-
A survey of amino acid side-chain interactions in 21 proteins
-
Warme PK, Morgan RS. A survey of amino acid side-chain interactions in 21 proteins. J Mol Biol 1978;118:289-304.
-
(1978)
J Mol Biol
, vol.118
, pp. 289-304
-
-
Warme, P.K.1
Morgan, R.S.2
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