-
1
-
-
24944493938
-
Toward high-resolution de novo structure prediction for small proteins
-
Bradley P, Misura KM, Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 2005;309:1868-1871.
-
(2005)
Science
, vol.309
, pp. 1868-1871
-
-
Bradley, P.1
Misura, K.M.2
Baker, D.3
-
2
-
-
78650918983
-
Alternate states of proteins revealed by detailed energy landscape mapping
-
Tyka MD, Keedy DA, Andre I, Dimaio F, Song Y, Richardson DC, Richardson JS, Baker D. Alternate states of proteins revealed by detailed energy landscape mapping. J Mol Biol 2011;405:607-618.
-
(2011)
J Mol Biol
, vol.405
, pp. 607-618
-
-
Tyka, M.D.1
Keedy, D.A.2
Andre, I.3
Dimaio, F.4
Song, Y.5
Richardson, D.C.6
Richardson, J.S.7
Baker, D.8
-
3
-
-
84862225232
-
Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field
-
Xu D, Zhang Y. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins 2012;80:1715-1735.
-
(2012)
Proteins
, vol.80
, pp. 1715-1735
-
-
Xu, D.1
Zhang, Y.2
-
5
-
-
42449146665
-
Consistent blind protein structure generation from NMR chemical shift data
-
Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Wu Y, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A. Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci U S A 2008;105:4685-4690.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 4685-4690
-
-
Shen, Y.1
Lange, O.2
Delaglio, F.3
Rossi, P.4
Aramini, J.M.5
Liu, G.6
Eletsky, A.7
Wu, Y.8
Singarapu, K.K.9
Lemak, A.10
Ignatchenko, A.11
Arrowsmith, C.H.12
Szyperski, T.13
Montelione, G.T.14
Baker, D.15
Bax, A.16
-
6
-
-
58149468410
-
De novo protein structure generation from incomplete chemical shift assignments
-
Shen Y, Vernon R, Baker D, Bax A. De novo protein structure generation from incomplete chemical shift assignments. J Biomol NMR 2009;43:63-78.
-
(2009)
J Biomol NMR
, vol.43
, pp. 63-78
-
-
Shen, Y.1
Vernon, R.2
Baker, D.3
Bax, A.4
-
7
-
-
48449095850
-
CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data
-
Web Server issue
-
Wishart DS, Arndt D, Berjanskii M, Tang P, Zhou J, Lin G. CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucleic Acids Res 2008;36(Web Server issue):W496-W502.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Wishart, D.S.1
Arndt, D.2
Berjanskii, M.3
Tang, P.4
Zhou, J.5
Lin, G.6
-
8
-
-
0141480844
-
TOUCHSTONEX: protein structure prediction with sparse NMR data
-
Li W, Zhang Y, Kihara D, Huang YJ, Zheng D, Montelione GT, Kolinski A, Skolnick J. TOUCHSTONEX: protein structure prediction with sparse NMR data. Proteins 2003;53:290-306.
-
(2003)
Proteins
, vol.53
, pp. 290-306
-
-
Li, W.1
Zhang, Y.2
Kihara, D.3
Huang, Y.J.4
Zheng, D.5
Montelione, G.T.6
Kolinski, A.7
Skolnick, J.8
-
9
-
-
1342306402
-
Protein structure prediction using sparse dipolar coupling data
-
Qu Y, Guo JT, Olman V, Xu Y. Protein structure prediction using sparse dipolar coupling data. Nucleic Acids Res 2004;32:551-561.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 551-561
-
-
Qu, Y.1
Guo, J.T.2
Olman, V.3
Xu, Y.4
-
10
-
-
77149179401
-
NMR structure determination for larger proteins using backbone-only data
-
Raman S, Lange OF, Rossi P, Tyka M, Wang X, Aramini J, Liu G, Ramelot TA, Eletsky A, Szyperski T, Kennedy MA, Prestegard J, Montelione GT, Baker D. NMR structure determination for larger proteins using backbone-only data. Science 2010;327:1014-1018.
-
(2010)
Science
, vol.327
, pp. 1014-1018
-
-
Raman, S.1
Lange, O.F.2
Rossi, P.3
Tyka, M.4
Wang, X.5
Aramini, J.6
Liu, G.7
Ramelot, T.A.8
Eletsky, A.9
Szyperski, T.10
Kennedy, M.A.11
Prestegard, J.12
Montelione, G.T.13
Baker, D.14
-
11
-
-
79851512251
-
RosettaEPR: an integrated tool for protein structure determination from sparse EPR data
-
Hirst SJ, Alexander N, McHaourab HS, Meiler J. RosettaEPR: an integrated tool for protein structure determination from sparse EPR data. J Struct Biol 2011;173:506-514.
-
(2011)
J Struct Biol
, vol.173
, pp. 506-514
-
-
Hirst, S.J.1
Alexander, N.2
McHaourab, H.S.3
Meiler, J.4
-
12
-
-
84856803649
-
Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation
-
Lange OF, Baker D. Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation. Proteins 2012;80:884-895.
-
(2012)
Proteins
, vol.80
, pp. 884-895
-
-
Lange, O.F.1
Baker, D.2
-
13
-
-
84857636811
-
Protein structure determination from pseudocontact shifts using ROSETTA
-
Schmitz C, Vernon R, Otting G, Baker D, Huber T. Protein structure determination from pseudocontact shifts using ROSETTA. J Mol Biol 2012;416:668-677.
-
(2012)
J Mol Biol
, vol.416
, pp. 668-677
-
-
Schmitz, C.1
Vernon, R.2
Otting, G.3
Baker, D.4
Huber, T.5
-
14
-
-
79957592606
-
Improved molecular replacement by density- and energy-guided protein structure optimization
-
DiMaio F, Terwilliger TC, Read RJ, Wlodawer A, Oberdorfer G, Wagner U, Valkov E, Alon A, Fass D, Axelrod HL, Das D, Vorobiev SM, Iwai H, Pokkuluri PR, Baker D. Improved molecular replacement by density- and energy-guided protein structure optimization. Nature 2011;473:540-543.
-
(2011)
Nature
, vol.473
, pp. 540-543
-
-
DiMaio, F.1
Terwilliger, T.C.2
Read, R.J.3
Wlodawer, A.4
Oberdorfer, G.5
Wagner, U.6
Valkov, E.7
Alon, A.8
Fass, D.9
Axelrod, H.L.10
Das, D.11
Vorobiev, S.M.12
Iwai, H.13
Pokkuluri, P.R.14
Baker, D.15
-
15
-
-
68949187842
-
Refinement of protein structures into low-resolution density maps using rosetta
-
DiMaio F, Tyka MD, Baker ML, Chiu W, Baker D. Refinement of protein structures into low-resolution density maps using rosetta. J Mol Biol 2009;392:181-190.
-
(2009)
J Mol Biol
, vol.392
, pp. 181-190
-
-
DiMaio, F.1
Tyka, M.D.2
Baker, M.L.3
Chiu, W.4
Baker, D.5
-
16
-
-
84862896208
-
Cryo-electron microscopy modeling by the molecular dynamics flexible fitting method
-
Chan KY, Trabuco LG, Schreiner E, Schulten K. Cryo-electron microscopy modeling by the molecular dynamics flexible fitting method. Biopolymers 2012;97:678-686.
-
(2012)
Biopolymers
, vol.97
, pp. 678-686
-
-
Chan, K.Y.1
Trabuco, L.G.2
Schreiner, E.3
Schulten, K.4
-
17
-
-
82855163967
-
Protein 3D structure computed from evolutionary sequence variation
-
Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C. Protein 3D structure computed from evolutionary sequence variation. PloS one 2011;6:e28766.
-
(2011)
PloS one
, vol.6
-
-
Marks, D.S.1
Colwell, L.J.2
Sheridan, R.3
Hopf, T.A.4
Pagnani, A.5
Zecchina, R.6
Sander, C.7
-
18
-
-
83755178457
-
Direct-coupling analysis of residue coevolution captures native contacts across many protein families
-
Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A 2011;108:E1293-E1301.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
-
-
Morcos, F.1
Pagnani, A.2
Lunt, B.3
Bertolino, A.4
Marks, D.S.5
Sander, C.6
Zecchina, R.7
Onuchic, J.N.8
Hwa, T.9
Weigt, M.10
-
19
-
-
84856090271
-
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
-
Jones DT, Buchan DW, Cozzetto D, Pontil M. PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics 2012;28:184-190.
-
(2012)
Bioinformatics
, vol.28
, pp. 184-190
-
-
Jones, D.T.1
Buchan, D.W.2
Cozzetto, D.3
Pontil, M.4
-
20
-
-
77950415030
-
Chemical cross-linking and mass spectrometry as a low-resolution protein structure determination technique
-
Singh P, Panchaud A, Goodlett DR. Chemical cross-linking and mass spectrometry as a low-resolution protein structure determination technique. Anal Chem 2010;82:2636-2642.
-
(2010)
Anal Chem
, vol.82
, pp. 2636-2642
-
-
Singh, P.1
Panchaud, A.2
Goodlett, D.R.3
-
21
-
-
77951961719
-
How significant is a protein structure similarity with TM-score=0.5?
-
Xu J, Zhang Y. How significant is a protein structure similarity with TM-score=0.5? Bioinformatics 2010;26:889-895.
-
(2010)
Bioinformatics
, vol.26
, pp. 889-895
-
-
Xu, J.1
Zhang, Y.2
-
22
-
-
17644392830
-
TM-align: a protein structure alignment algorithm based on the TM-score
-
Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic acids research 2005;33:2302-2309.
-
(2005)
Nucleic acids research
, vol.33
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
23
-
-
79960394811
-
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates
-
Yang Y, Faraggi E, Zhao H, Zhou Y. Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. Bioinformatics 2011;27:2076-2082.
-
(2011)
Bioinformatics
, vol.27
, pp. 2076-2082
-
-
Yang, Y.1
Faraggi, E.2
Zhao, H.3
Zhou, Y.4
-
24
-
-
80052020052
-
Generalized fragment picking in Rosetta: design, protocols and applications
-
Gront D, Kulp DW, Vernon RM, Strauss CE, Baker D. Generalized fragment picking in Rosetta: design, protocols and applications. PloS one 2011;6:e23294.
-
(2011)
PloS one
, vol.6
-
-
Gront, D.1
Kulp, D.W.2
Vernon, R.M.3
Strauss, C.E.4
Baker, D.5
-
25
-
-
33751118503
-
Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation
-
Bradley P, Baker D. Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins 2006;65:922-929.
-
(2006)
Proteins
, vol.65
, pp. 922-929
-
-
Bradley, P.1
Baker, D.2
-
26
-
-
84892970967
-
High resolution comparative modeling with RosettaCM
-
in press.
-
Song Y, DiMaio F, Wang RY, Kim DE, Miles C, Brunette T, Thompson J, Baker D. High resolution comparative modeling with RosettaCM. Structure, in press.
-
Structure
-
-
Song, Y.1
DiMaio, F.2
Wang, R.Y.3
Kim, D.E.4
Miles, C.5
Brunette, T.6
Thompson, J.7
Baker, D.8
-
27
-
-
0020997912
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
29
-
-
36749055649
-
Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home
-
Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmstrom L, Wollacott AM, Wang C, Andre I, Baker D. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins 2007;69(Suppl 8):118-128.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL 8
, pp. 118-128
-
-
Das, R.1
Qian, B.2
Raman, S.3
Vernon, R.4
Thompson, J.5
Bradley, P.6
Khare, S.7
Tyka, M.D.8
Bhat, D.9
Chivian, D.10
Kim, D.E.11
Sheffler, W.H.12
Malmstrom, L.13
Wollacott, A.M.14
Wang, C.15
Andre, I.16
Baker, D.17
-
30
-
-
84867746766
-
Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers
-
Tyka MD, Jung K, Baker D. Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers. J Comput Chem 2012;33:2483-2491.
-
(2012)
J Comput Chem
, vol.33
, pp. 2483-2491
-
-
Tyka, M.D.1
Jung, K.2
Baker, D.3
-
31
-
-
0032929780
-
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
-
Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999;34:82-95.
-
(1999)
Proteins
, vol.34
, pp. 82-95
-
-
Simons, K.T.1
Ruczinski, I.2
Kooperberg, C.3
Fox, B.A.4
Bystroff, C.5
Baker, D.6
-
32
-
-
73149111493
-
Simultaneous prediction of protein folding and docking at high resolution
-
Das R, Andre I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T, Baker D. Simultaneous prediction of protein folding and docking at high resolution. Proc Natl Acad Sci U S A 2009;106:18978-18983.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 18978-18983
-
-
Das, R.1
Andre, I.2
Shen, Y.3
Wu, Y.4
Lemak, A.5
Bansal, S.6
Arrowsmith, C.H.7
Szyperski, T.8
Baker, D.9
-
33
-
-
67849110427
-
Structure prediction for CASP8 with all-atom refinement using Rosetta
-
Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim BH, Das R, Grishin NV, Baker D. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins 2009;77(Suppl 9):89-99.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL 9
, pp. 89-99
-
-
Raman, S.1
Vernon, R.2
Thompson, J.3
Tyka, M.4
Sadreyev, R.5
Pei, J.6
Kim, D.7
Kellogg, E.8
DiMaio, F.9
Lange, O.10
Kinch, L.11
Sheffler, W.12
Kim, B.H.13
Das, R.14
Grishin, N.V.15
Baker, D.16
-
34
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
-
(1999)
J Mol Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
35
-
-
79959458821
-
Modeling symmetric macromolecular structures in Rosetta3
-
DiMaio F, Leaver-Fay A, Bradley P, Baker D, Andre I. Modeling symmetric macromolecular structures in Rosetta3. PloS one 2011;6:e20450.
-
(2011)
PloS one
, vol.6
-
-
DiMaio, F.1
Leaver-Fay, A.2
Bradley, P.3
Baker, D.4
Andre, I.5
-
36
-
-
0032502839
-
Contact order, transition state placement and the refolding rates of single domain proteins
-
Plaxco KW, Simons KT, Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 1998;277:985-994.
-
(1998)
J Mol Biol
, vol.277
, pp. 985-994
-
-
Plaxco, K.W.1
Simons, K.T.2
Baker, D.3
-
37
-
-
0036968925
-
De novo prediction of three-dimensional structures for major protein families
-
Bonneau R, Strauss CE, Rohl CA, Chivian D, Bradley P, Malmstrom 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.2
Rohl, C.A.3
Chivian, D.4
Bradley, P.5
Malmstrom, L.6
Robertson, T.7
Baker, D.8
-
38
-
-
38549153238
-
Data growth and its impact on the SCOP database: new developments
-
Database issue
-
Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 2008;36(Database issue):D419-D425.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Andreeva, A.1
Howorth, D.2
Chandonia, J.M.3
Brenner, S.E.4
Hubbard, T.J.5
Chothia, C.6
Murzin, A.G.7
-
39
-
-
78651338019
-
Extending CATH: increasing coverage of the protein structure universe and linking structure with function
-
Database issue
-
Cuff AL, Sillitoe I, Lewis T, Clegg AB, Rentzsch R, Furnham N, Pellegrini-Calace M, Jones D, Thornton J, Orengo CA. Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Res 2011;39(Database issue):D420-D426.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Cuff, A.L.1
Sillitoe, I.2
Lewis, T.3
Clegg, A.B.4
Rentzsch, R.5
Furnham, N.6
Pellegrini-Calace, M.7
Jones, D.8
Thornton, J.9
Orengo, C.A.10
-
40
-
-
0042622381
-
LGA: a method for finding 3D similarities in protein structures
-
Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res 2003;31:3370-3374.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3370-3374
-
-
Zemla, A.1
-
41
-
-
0034306307
-
The REPRO server: finding protein internal sequence repeats through the Web
-
George RA, Heringa J. The REPRO server: finding protein internal sequence repeats through the Web. Trends Biochem Sci 2000;25:515-517.
-
(2000)
Trends Biochem Sci
, vol.25
, pp. 515-517
-
-
George, R.A.1
Heringa, J.2
-
42
-
-
35648943768
-
Toward high-resolution prediction and design of transmembrane helical protein structures
-
Barth P, Schonbrun J, Baker D. Toward high-resolution prediction and design of transmembrane helical protein structures. Proc Natl Acad Sci U S A 2007;104:15682-15687.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 15682-15687
-
-
Barth, P.1
Schonbrun, J.2
Baker, D.3
-
43
-
-
84862270506
-
Atomic model of the type III secretion system needle
-
Loquet A, Sgourakis NG, Gupta R, Giller K, Riedel D, Goosmann C, Griesinger C, Kolbe M, Baker D, Becker S, Lange A. Atomic model of the type III secretion system needle. Nature 2012;486:276-279.
-
(2012)
Nature
, vol.486
, pp. 276-279
-
-
Loquet, A.1
Sgourakis, N.G.2
Gupta, R.3
Giller, K.4
Riedel, D.5
Goosmann, C.6
Griesinger, C.7
Kolbe, M.8
Baker, D.9
Becker, S.10
Lange, A.11
|