-
1
-
-
67349189383
-
The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain
-
Anfinsen CB, Haber E, Sela M, White FH, (1961) The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc Natl Acad Sci U S A 47: 1309-14.
-
(1961)
Proc Natl Acad Sci U S A
, vol.47
, pp. 1309-1314
-
-
Anfinsen, C.B.1
Haber, E.2
Sela, M.3
White, F.H.4
-
2
-
-
70349241497
-
Sampling bottlenecks in de novo protein structure prediction
-
Kim DE, Blum B, Bradley P, Baker D, (2009) Sampling bottlenecks in de novo protein structure prediction. J Mol Biol 393: 249-60.
-
(2009)
J Mol Biol
, vol.393
, pp. 249-260
-
-
Kim, D.E.1
Blum, B.2
Bradley, P.3
Baker, D.4
-
3
-
-
0028328263
-
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 U S A 91: 4436-40.
-
(1994)
Proc Natl Acad Sci U S A
, vol.91
, pp. 4436-4440
-
-
Bowie, J.U.1
Eisenberg, D.2
-
4
-
-
0031585984
-
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: 209-25.
-
(1997)
J Mol Biol
, vol.268
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
5
-
-
0032612579
-
Ab initio protein structure prediction of CASP III targets using ROSETTA
-
Simons KT, Bonneau R, Ruczinski I, Baker D, (1999) Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins Suppl 3: 171-6.
-
(1999)
Proteins
, Issue.SUPPL. 3
, pp. 171-176
-
-
Simons, K.T.1
Bonneau, R.2
Ruczinski, I.3
Baker, D.4
-
6
-
-
1642464839
-
Protein structure prediction using Rosetta
-
Rohl CA, Strauss CEM, Misura KMS, Baker D, (2004) Protein structure prediction using Rosetta. Methods Enzymol 383: 66-93.
-
(2004)
Methods Enzymol
, vol.383
, pp. 66-93
-
-
Rohl, C.A.1
Strauss, C.E.M.2
Misura, K.M.S.3
Baker, D.4
-
7
-
-
78650905964
-
ROSETTA3: an objectoriented software suite for the simulation and design of macromolecules
-
Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, et al. (2011) ROSETTA3: an objectoriented software suite for the simulation and design of macromolecules. Methods Enzymol 487: 545-74.
-
(2011)
Methods Enzymol
, vol.487
, pp. 545-574
-
-
Leaver-Fay, A.1
Tyka, M.2
Lewis, S.M.3
Lange, O.F.4
Thompson, J.5
-
8
-
-
80855133462
-
CASP9 assessment of free modeling target predictions
-
Kinch L, Yong Shi S, Cong Q, Cheng H, Liao Y, et al. (2011) CASP9 assessment of free modeling target predictions. Proteins: Structure, Function, and Bioinformatics 79: 59-73.
-
(2011)
Proteins: Structure, Function, and Bioinformatics
, vol.79
, pp. 59-73
-
-
Kinch, L.1
Yong Shi, S.2
Cong, Q.3
Cheng, H.4
Liao, Y.5
-
9
-
-
84862225232
-
Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field
-
Xu D, Zhang Y, (2012) Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins 80: 1715-1735.
-
(2012)
Proteins
, vol.80
, pp. 1715-1735
-
-
Xu, D.1
Zhang, Y.2
-
10
-
-
4043058565
-
Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing
-
Lee J, Kim SY, Joo K, Kim I, Lee J, (2004) Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing. Proteins 56: 704-14.
-
(2004)
Proteins
, vol.56
, pp. 704-714
-
-
Lee, J.1
Kim, S.Y.2
Joo, K.3
Kim, I.4
Lee, J.5
-
11
-
-
0142116211
-
A reversible fragment assembly method for de novo protein structure prediction
-
Chikenji G, Fujitsuka Y, Takada S, (2003) A reversible fragment assembly method for de novo protein structure prediction. The Journal of Chemical Physics 119: 6895-6903.
-
(2003)
The Journal of Chemical Physics
, vol.119
, pp. 6895-6903
-
-
Chikenji, G.1
Fujitsuka, Y.2
Takada, S.3
-
12
-
-
0242362161
-
Combining localstructure, fold-recognition, and new fold methods for protein structure prediction
-
Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, et al. (2003) Combining localstructure, fold-recognition, and new fold methods for protein structure prediction. Proteins 53 Suppl 6: 491-6.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL.
, pp. 491-496
-
-
Karplus, K.1
Karchin, R.2
Draper, J.3
Casper, J.4
Mandel-Gutfreund, Y.5
-
13
-
-
0242267507
-
Assembling novel protein folds from super-secondary structural fragments
-
Jones DT, McGuffin LJ, (2003) Assembling novel protein folds from super-secondary structural fragments. Proteins 53 Suppl 6: 480-5.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL.
, pp. 480-485
-
-
Jones, D.T.1
McGuffin, L.J.2
-
14
-
-
33749368323
-
Sampling realistic protein conformations using local structural bias
-
Hamelryck T, Kent JT, Krogh A, (2006) Sampling realistic protein conformations using local structural bias. PLoS Comput Biol 2: e131.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Hamelryck, T.1
Kent, J.T.2
Krogh, A.3
-
15
-
-
55549086519
-
Fragment-HMM: a new approach to protein structure prediction
-
Li SC, Bu D, Xu J, Li M, (2008) Fragment-HMM: a new approach to protein structure prediction. Protein Sci 17: 1925-34.
-
(2008)
Protein Sci
, vol.17
, pp. 1925-1934
-
-
Li, S.C.1
Bu, D.2
Xu, J.3
Li, M.4
-
16
-
-
62649111500
-
Mimicking the folding pathway to improve homology-free protein structure prediction
-
DeBartolo J, Colubri A, Jha AK, Fitzgerald JE, Freed KF, et al. (2009) Mimicking the folding pathway to improve homology-free protein structure prediction. Proc Natl Acad Sci U S A 106: 3734-3739.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 3734-3739
-
-
DeBartolo, J.1
Colubri, A.2
Jha, A.K.3
Fitzgerald, J.E.4
Freed, K.F.5
-
17
-
-
84867907201
-
De novo prediction of protein folding pathways and structure using the principle of sequential stabilization
-
Adhikari AN, Freed KF, Sosnick TR, (2012) De novo prediction of protein folding pathways and structure using the principle of sequential stabilization. Proc Natl Acad Sci U S A 109: 17442-17447.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 17442-17447
-
-
Adhikari, A.N.1
Freed, K.F.2
Sosnick, T.R.3
-
19
-
-
0000578485
-
The single isomorphous replacement method
-
Blow DM, Rossmann MG, (1961) The single isomorphous replacement method. Acta Crystallographica 14: 1195-1202.
-
(1961)
Acta Crystallographica
, vol.14
, pp. 1195-1202
-
-
Blow, D.M.1
Rossmann, M.G.2
-
20
-
-
80052020052
-
Generalized fragment picking in Rosetta: design, protocols and applications
-
Gront D, Kulp DW, Vernon RM, Strauss CEM, Baker D, (2011) Generalized fragment picking in Rosetta: design, protocols and applications. PLoS One 6: e23294.
-
(2011)
PLoS One
, vol.6
-
-
Gront, D.1
Kulp, D.W.2
Vernon, R.M.3
Strauss, C.E.M.4
Baker, D.5
-
22
-
-
0005386585
-
Iterated Local Search
-
Ed F Glover and G Kochenberger, ISORMS 57, (2002), Kluwer
-
Lourenco H, Martin O, Stutzle T (2001) Iterated Local Search. In "Handbook of Metaheuristics", Ed F Glover and G Kochenberger, ISORMS 57, p 321-353 (2002), Kluwer.
-
(2001)
In "Handbook of Metaheuristics"
, pp. 321-353
-
-
Lourenco, H.1
Martin, O.2
Stutzle, T.3
-
23
-
-
79953299184
-
Entropy-accelerated exact clustering of protein decoys
-
Berenger F, Zhou Y, Shrestha R, Zhang KYJ, (2011) Entropy-accelerated exact clustering of protein decoys. Bioinformatics 27: 939-45.
-
(2011)
Bioinformatics
, vol.27
, pp. 939-945
-
-
Berenger, F.1
Zhou, Y.2
Shrestha, R.3
Zhang, K.Y.J.4
-
24
-
-
79953737180
-
Overview of the CCP4 suite and current developments
-
Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, et al. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67: 235-42.
-
(2011)
Acta Crystallogr D Biol Crystallogr
, vol.67
, pp. 235-242
-
-
Winn, M.D.1
Ballard, C.C.2
Cowtan, K.D.3
Dodson, E.J.4
Emsley, P.5
-
25
-
-
84893482610
-
A solution of the best rotation to relate two sets of vectors
-
Kabsch W, (1976) A solution of the best rotation to relate two sets of vectors. Acta Crystallographica A32: 922-923.
-
(1976)
Acta Crystallographica
, vol.A32
, pp. 922-923
-
-
Kabsch, W.1
|