-
3
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235-242 (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
4
-
-
0034436062
-
Does NMR mean "not for molecular replacement"? Using NMR-based search models to solve protein crystal structures
-
Chen YW, Dodson EJ, Kleywegt GJ (2000) Does NMR mean "not for molecular replacement"? using NMR-based search models to solve protein crystal structures. Structure 8:213-220
-
(2000)
Structure
, vol.8
, pp. 213-220
-
-
Chen, Y.W.1
Dodson, E.J.2
Kleywegt, G.J.3
-
5
-
-
79953753741
-
Improvement of molecularreplacement models with Sculptor
-
Bunkoczi G, Read RJ (2010) Improvement of molecularreplacement models with Sculptor. Acta Cryst D67:303-312
-
(2010)
Acta Cryst
, vol.D67
, pp. 303-312
-
-
Bunkoczi, G.1
Read, R.J.2
-
6
-
-
79958127392
-
Improved technologies now routinely provide protein NMR structures useful for molecular replacement
-
Mao B, Guan R, Montelione GT (2011) Improved technologies now routinely provide protein NMR structures useful for molecular replacement. Structure 19:757-766
-
(2011)
Structure
, vol.19
, pp. 757-766
-
-
Mao, B.1
Guan, R.2
Montelione, G.T.3
-
7
-
-
16644367949
-
The importance of alignment accuracy for molecular replacement
-
DOI 10.1107/S0907444904010145
-
Schwarzenbacher R, Godzik A, Grzechnik SK, Jaroszewski L (2004) The importance of alignment accuracy for molecular replacement. Acta Cryst D 60:1229-1236 (Pubitemid 41073183)
-
(2004)
Acta Crystallographica Section D: Biological Crystallography
, vol.60
, Issue.7
, pp. 1229-1236
-
-
Schwarzenbacher, R.1
Godzik, A.2
Grzechnik, S.K.3
Jaroszewski, L.4
-
8
-
-
79953730593
-
Evaluating the solution from MrBUMP and BALBES
-
Keegan RM, Long F, Fazio VJ, Winn MD, Murshudov GN, Vagin AA (2011) Evaluating the solution from MrBUMP and BALBES. Acta Cryst D67:313-323
-
(2011)
Acta Cryst
, vol.D67
, pp. 313-323
-
-
Keegan, R.M.1
Long, F.2
Fazio, V.J.3
Winn, M.D.4
Murshudov, G.N.5
Vagin, A.A.6
-
9
-
-
0035788107
-
Pushing the boundaries of molecular replacement with maximum likelihood
-
DOI 10.1107/S0907444901012471
-
Read RJ (2001) Pushing the boundaries of molecular replacement with maximum likelihood. Acta Cryst D 57:1373-1382 (Pubitemid 36117185)
-
(2001)
Acta Crystallographica Section D: Biological Crystallography
, vol.57
, Issue.10
, pp. 1373-1382
-
-
Read, R.J.1
-
10
-
-
37349001709
-
Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis
-
DOI 10.1107/S0907444907053516, PII S0907444907053516
-
Delarue M (2008) Dealing with structural variability in molecular replacement and crystallographic refinement through normalmode analysis. Acta Cryst D64:40-48 (Pubitemid 350308676)
-
(2007)
Acta Crystallographica Section D: Biological Crystallography
, vol.64
, Issue.1
, pp. 40-48
-
-
Delarue, M.1
-
11
-
-
0026663419
-
Normal mode refinement-crystallographic refinement of protein dynamic structure. 1. Theory and test by simulated diffraction data
-
Kidera A, Go N (1992) Normal mode refinement-crystallographic refinement of protein dynamic structure. 1. Theory and test by simulated diffraction data. J Mol Biol 225:457-475
-
(1992)
J Mol Biol
, vol.225
, pp. 457-475
-
-
Kidera, A.1
Go, N.2
-
13
-
-
78650753247
-
Protein structure determination by exhaustive search of Protein Data Bank derived databases
-
Stokes-Rees I, Sliz P (2010) Protein structure determination by exhaustive search of Protein Data Bank derived databases. Proc Natl Acad Sci USA 107:21476-21481
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 21476-21481
-
-
Stokes-Rees, I.1
Sliz, P.2
-
14
-
-
34447508216
-
Phaser crystallographic software
-
DOI 10.1107/S0021889807021206, PII S0021889807021206
-
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ (2007) Phaser crystallographic software. J Appl Cryst 40:658-674 (Pubitemid 47080256)
-
(2007)
Journal of Applied Crystallography
, vol.40
, Issue.4
, pp. 658-674
-
-
McCoy, A.J.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
Winn, M.D.4
Storoni, L.C.5
Read, R.J.6
-
15
-
-
0033776369
-
Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT
-
Roversi P, Blanc E, Vonrhein C, Evans G, Bricogne G (2000) Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. Acta Cryst D56:1316-1323
-
(2000)
Acta Cryst
, vol.D56
, pp. 1316-1323
-
-
Roversi, P.1
Blanc, E.2
Vonrhein, C.3
Evans, G.4
Bricogne, G.5
-
17
-
-
50249136103
-
Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7
-
Langer G, Cohen SX, Lamzin VS, Perrakis A (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 3:1171-1179
-
(2008)
Nat Protoc
, vol.3
, pp. 1171-1179
-
-
Langer, G.1
Cohen, S.X.2
Lamzin, V.S.3
Perrakis, A.4
-
18
-
-
0032964481
-
Automated protein model building combined with iterative structure refinement
-
DOI 10.1038/8263
-
Perrakis A, Morris R, Lamzin VS (1999) Automated protein model building combined with iterative structure refinement. Nature Struct Biol 6:458-463 (Pubitemid 29218016)
-
(1999)
Nature Structural Biology
, vol.6
, Issue.5
, pp. 458-463
-
-
Perrakis, A.1
Morris, R.2
Lamzin, V.S.3
-
19
-
-
37349103121
-
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
-
DOI 10.1107/S090744490705024X, PII S090744490705024X
-
Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Zwart PH, Hung LW, Read RJ, Adams PD (2008) Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Cryst D 64:61-69 (Pubitemid 350308678)
-
(2007)
Acta Crystallographica Section D: Biological Crystallography
, vol.64
, Issue.1
, pp. 61-69
-
-
Terwilliger, T.C.1
Grosse-Kunstleve, R.W.2
Afonine, P.V.3
Moriarty, N.W.4
Zwart, P.H.5
Hung, L.-W.6
Read, R.J.7
Adams, P.D.8
-
20
-
-
33846061281
-
Identification of secondary structure elements in intermediate resolution density maps
-
DOI 10.1016/j.str.2006.11.008, PII S0969212606004722
-
Baker ML, Ju T, Chiu W (2007) Identification of secondary structure elements in intermediate resolution density maps. Structure 15:7-19 (Pubitemid 46073771)
-
(2007)
Structure
, vol.15
, Issue.1
, pp. 7-19
-
-
Baker, M.L.1
Ju, T.2
Chiu, W.3
-
21
-
-
33748337934
-
The Buccaneer software for automated model building
-
Cowtan K (2006) The Buccaneer software for automated model building. Acta Cryst D62:1002-1011
-
(2006)
Acta Cryst
, vol.D62
, pp. 1002-1011
-
-
Cowtan, K.1
-
22
-
-
36448983552
-
-
Di Maio F, Kondrashov DA, Bitto E, Soni A, Bingman CA, Phillips GN Jr, Shavlik JW (2007) Bioinformatics 23:2851-2858
-
(2007)
Bioinformatics
, vol.23
, pp. 2851-2858
-
-
Di Maio, F.1
Kondrashov, D.A.2
Bitto, E.3
Soni, A.4
Bingman, C.A.5
Phillips Jr., G.N.6
Shavlik, J.W.7
-
23
-
-
0348014440
-
TEXTAL system: Artificial intelligence techniques for automated protein model building
-
DOI 10.1016/S0076-6879(03)74012-9
-
Ioerger TR, Sacchettini JC (2003) TEXTAL system: artificial intelligence techniques for automated protein model building. Methods Enzymol 374:244-270 (Pubitemid 37531813)
-
(2003)
Methods in Enzymology
, vol.374
, pp. 244-270
-
-
Ioerger, T.R.1
Sacchettini, J.C.2
-
24
-
-
0034929414
-
A new software routine that automates the fitting of protein X-ray crystallographic electron-density maps
-
DOI 10.1107/S0907444901006394
-
Levitt DG (2001) A new software routine that automates the fitting of protein X-ray crystallographic electron density maps. Acta Cryst D57:1013-1019 (Pubitemid 32620894)
-
(2001)
Acta Crystallographica Section D: Biological Crystallography
, vol.57
, Issue.7
, pp. 1013-1019
-
-
Levitt, D.G.1
-
25
-
-
0036006267
-
Pattern-recognition methods to identify secondary structure within X-ray crystallographic electron-density maps
-
Oldfield TJ (2002) Pattern-recognition methods to identify secondary structure within X-ray crystallographic electron-density maps. Acta Cryst D58:487-493
-
(2002)
Acta Cryst
, vol.D58
, pp. 487-493
-
-
Oldfield, T.J.1
-
27
-
-
77649119465
-
Rapid model-building of alpha-helices in electron density maps
-
Terwilliger TC (2010) Rapid model-building of alpha-helices in electron density maps. Acta Cryst D66:268-275
-
(2010)
Acta Cryst
, vol.D66
, pp. 268-275
-
-
Terwilliger, T.C.1
-
28
-
-
79957592606
-
Improving molecular replacement by density and energy guided protein structure optimization
-
Di Maio 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 (2011) Improving molecular replacement by density and energy guided protein structure optimization. Nature 473:540-543
-
(2011)
Nature
, vol.473
, pp. 540-543
-
-
Di Maio, 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
-
29
-
-
36049029967
-
High-resolution structure prediction and the crystallographic phase problem
-
DOI 10.1038/nature06249, PII NATURE06249
-
Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D (2007) High resolution structure prediction and the crystallographic phase problem. Nature 450:259-264 (Pubitemid 350100534)
-
(2007)
Nature
, vol.450
, Issue.7167
, pp. 259-264
-
-
Qian, B.1
Raman, S.2
Das, R.3
Bradley, P.4
McCoy, A.J.5
Read, R.J.6
Baker, D.7
-
30
-
-
62949126043
-
Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study
-
Ramelot TA, Raman S, Kuzin AP, Xiao R, Ma LC, Acton TB, Hunt JF, Montelione GT, Baker D, Kennedy MA (2009) Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study. Proteins 75:147-167
-
(2009)
Proteins
, vol.75
, pp. 147-167
-
-
Ramelot, T.A.1
Raman, S.2
Kuzin, A.P.3
Xiao, R.4
Ma, L.C.5
Acton, T.B.6
Hunt, J.F.7
Montelione, G.T.8
Baker, D.9
Kennedy, M.A.10
-
31
-
-
58849144738
-
Prospects for de novo phasing with de novo protein models
-
Das R, Baker D (2009) Prospects for de novo phasing with de novo protein models. Acta Cryst D65:169-175
-
(2009)
Acta Cryst
, vol.D65
, pp. 169-175
-
-
Das, R.1
Baker, D.2
-
32
-
-
76449098262
-
PHENIX: A comprehensive Python-based system for macromolecular structure solution
-
Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst D66:213-221
-
(2010)
Acta Cryst
, vol.D66
, pp. 213-221
-
-
Adams, P.D.1
Afonine, P.V.2
Bunkoczi, G.3
Chen, V.B.4
Davis, I.W.5
Echols, N.6
Headd, J.J.7
Hung, L.W.8
Kapral, G.J.9
Grosse-Kunstleve, R.W.10
McCoy, A.J.11
Moriarty, N.W.12
Oeffner, R.13
Read, R.J.14
Richardson, D.C.15
Richardson, J.S.16
Terwilliger, T.C.17
Zwart, P.H.18
-
33
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
DOI 10.1093/bioinformatics/bti125
-
Söding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960 (Pubitemid 40467915)
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 951-960
-
-
Soding, J.1
-
34
-
-
10744230917
-
Automated prediction of CASP-5 structures using the robetta server
-
DOI 10.1002/prot.10529
-
Chivian D, Kim DE, Malmstrom L, Bradley P, Robertson T, Murphy P, Strauss CEM, Bonneau R, Rohl CA, Baker D (2003) Automated prediction of CASP-5 structures using the Robetta server. Proteins 53(Suppl 6):524-533 (Pubitemid 37352212)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.53
, Issue.SUPPL. 6
, pp. 524-533
-
-
Chivian, D.1
Kim, D.E.2
Malmstrom, L.3
Bradley, P.4
Robertson, T.5
Murphy, P.6
Strauss, C.E.M.7
Bonneau, R.8
Rohl, C.A.9
Baker, D.10
-
37
-
-
68949187842
-
Refinement of protein structures into low-resolution density maps using Rosetta
-
Di Maio F, Tyka MD, Baker ML, Chiu W, Baker D (2009) Refinement of protein structures into low-resolution density maps using Rosetta. J Mol Biol 392:181-190
-
(2009)
J Mol Biol
, vol.392
, pp. 181-190
-
-
Di Maio, F.1
Tyka, M.D.2
Baker, M.L.3
Chiu, W.4
Baker, D.5
-
38
-
-
79955672567
-
Cloning, expression, purification, crystallization and preliminary X-ray diffraction data of the Pyrococcus horikoshii RadA intein
-
Lyskowski A, Oeemig JS, Jaakonen A, Rommi K, Di Maio F, Zhou D, Kajander T, Baker D, Wlodawer A, Goldman A, Iwaï H (2011) Cloning, expression, purification, crystallization and preliminary X-ray diffraction data of the Pyrococcus horikoshii RadA intein. Acta Cryst F67:623-626
-
(2011)
Acta Cryst
, vol.F67
, pp. 623-626
-
-
Lyskowski, A.1
Oeemig, J.S.2
Jaakonen, A.3
Rommi, K.4
Di Maio, F.5
Zhou, D.6
Kajander, T.7
Baker, D.8
Wlodawer, A.9
Goldman, A.10
Iwaï, H.11
-
39
-
-
79551646228
-
Crystal structure of XMRV protease differs from the structures of other retropepsins
-
Li M, Di Maio F, Zhou D, Gustchina A, Lubkowski J, Dauter Z, Baker D, Wlodawer A (2011) Crystal structure of XMRV protease differs from the structures of other retropepsins. Nat Struct Mol Biol 18:227-229
-
(2011)
Nat Struct Mol Biol
, vol.18
, pp. 227-229
-
-
Li, M.1
Di Maio, F.2
Zhou, D.3
Gustchina, A.4
Lubkowski, J.5
Dauter, Z.6
Baker, D.7
Wlodawer, A.8
-
40
-
-
33748955158
-
Ultra-high resolution crystal structure of HIV-1 protease mutant reveals two binding sites for clinical inhibitor TMC114
-
DOI 10.1016/j.jmb.2006.08.007, PII S0022283606009958
-
Kovalevsky AY, Liu F, Leshchenko S, Ghosh AK, Louis JM, Harrison RW, Weber IT (2006) Ultra-high resolution crystal structure of HIV-1 protease mutant reveals two binding sites for clinical inhibitor TMC114. J Mol Biol 363:161-173 (Pubitemid 44437563)
-
(2006)
Journal of Molecular Biology
, vol.363
, Issue.1
, pp. 161-173
-
-
Kovalevsky, A.Y.1
Liu, F.2
Leshchenko, S.3
Ghosh, A.K.4
Louis, J.M.5
Harrison, R.W.6
Weber, I.T.7
-
41
-
-
77951623055
-
Super-resolution biomolecular crystallography with low-resolution data
-
Schröder G, Levitt M, Brünger AT (2010) Super-resolution biomolecular crystallography with low-resolution data. Nature 464:1218-1222
-
(2010)
Nature
, vol.464
, pp. 1218-1222
-
-
Schröder, G.1
Levitt, M.2
Brünger, A.T.3
|