-
1
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen CB: Principles that govern the folding of protein chains. Science (New York, NY) 1973, 181:223-230.
-
(1973)
Science (New York, NY)
, vol.181
, pp. 223-230
-
-
Anfinsen, C.B.1
-
2
-
-
24944493938
-
Biochemistry: Toward high-resolution de novo structure prediction for small proteins
-
DOI 10.1126/science.1113801
-
Bradley P, Misura KMS, Baker D: Toward high-resolution de novo structure prediction for small proteins. Science (New York, NY) 2005, 309:1868-1871. (Pubitemid 41325099)
-
(2005)
Science
, vol.309
, Issue.5742
, pp. 1868-1871
-
-
Bradley, P.1
Misura, K.M.S.2
Baker, D.3
-
4
-
-
0345059376
-
Announcing the worldwide Protein Data Bank
-
DOI 10.1038/nsb1203-980
-
Berman H, Henrick K, Nakamura H: Announcing the worldwide protein data bank. Nat Struct Biol 2003, 10:980. (Pubitemid 37500485)
-
(2003)
Nature Structural Biology
, vol.10
, Issue.12
, pp. 980
-
-
Berman, H.1
Henrick, K.2
Nakamura, H.3
-
5
-
-
84873581818
-
Expectation bias and information content
-
Dauter Z, Weiss MS, Einspahr H, Baker EN: Expectation bias and information content. Acta Crystallogr Sect D Struct Biol Cryst 2013, 69:141-141.
-
(2013)
Acta Crystallogr Sect D Struct Biol Cryst
, vol.69
, pp. 141-141
-
-
Dauter, Z.1
Weiss, M.S.2
Einspahr, H.3
Baker, E.N.4
-
6
-
-
0001644632
-
Between objectivity and subjectivity
-
Bränd'en C-I, Alwyn Jones T: Between objectivity and subjectivity. Nature 1990, 343:687-689.
-
(1990)
Nature
, vol.343
, pp. 687-689
-
-
Bränd'En, C.-I.1
Alwyn Jones, T.2
-
7
-
-
84889120137
-
Improved methods for building protein models in electron density maps and the location of errors in these models
-
Jones TA, Zou JY, Cowan SW, Kjeldgaard M: Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr Sect A Found Cryst 1991, 47:110-119.
-
(1991)
Acta Crystallogr Sect A Found Cryst
, vol.47
, pp. 110-119
-
-
Jones, T.A.1
Zou, J.Y.2
Cowan, S.W.3
Kjeldgaard, M.4
-
8
-
-
80054078285
-
A new generation of crystallographic validation tools for the protein data bank
-
Read RJ, Adams PD, Arendall WB, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH: A new generation of crystallographic validation tools for the protein data bank. Structure (London, England: 1993) 2011, 19:1395-1412.
-
(2011)
Structure (London, England: 1993)
, vol.19
, pp. 1395-1412
-
-
Read, R.J.1
Adams, P.D.2
Arendall, W.B.3
Brunger, A.T.4
Emsley, P.5
Joosten, R.P.6
Kleywegt, G.J.7
Krissinel, E.B.8
Lütteke, T.9
Otwinowski, Z.10
Perrakis, A.11
Richardson, J.S.12
Sheffler, W.H.13
Smith, J.L.14
Tickle, I.J.15
Vriend, G.16
Zwart, P.H.17
-
10
-
-
84872815236
-
Studying and polishing the PDB's macromolecules
-
Richardson JS, Richardson DC: Studying and polishing the PDB's macromolecules. Biopolymers 2013. 99:170-182.
-
(2013)
Biopolymers
, vol.99
, pp. 170-182
-
-
Richardson, J.S.1
Richardson, D.C.2
-
11
-
-
84873572846
-
Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures
-
Pozharski E, Weichenberger CX, Rupp B: Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures. Acta Crystallogr Sect D Biol Cryst 2013, 69:150-67.
-
(2013)
Acta Crystallogr Sect D Biol Cryst
, vol.69
, pp. 150-167
-
-
Pozharski, E.1
Weichenberger, C.X.2
Rupp, B.3
-
13
-
-
0033954256
-
The Protein Data Bank
-
Berman HM: The protein data bank. Nucleic Acids Res 2000, 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
-
14
-
-
34447498926
-
PDB improvement starts with data deposition [3]
-
DOI 10.1126/science.317.5835.195
-
Joosten RP, Vriend G: PDB improvement starts with data deposition. Science (New York, NY) 2007, 317:195-196. (Pubitemid 47076180)
-
(2007)
Science
, vol.317
, Issue.5835
, pp. 195-196
-
-
Joosten, R.P.1
Vriend, G.2
-
15
-
-
83355177227
-
Automatic rebuilding and optimization of crystallographic structures in the protein data bank
-
Joosten RP, Joosten K, Cohen SX, Vriend G, Perrakis A: Automatic rebuilding and optimization of crystallographic structures in the protein data bank. Bioinformatics (Oxford, England) 2011, 27:3392-3398.
-
(2011)
Bioinformatics (Oxford, England)
, vol.27
, pp. 3392-3398
-
-
Joosten, R.P.1
Joosten, K.2
Cohen, S.X.3
Vriend, G.4
Perrakis, A.5
-
16
-
-
84860284066
-
PDB-REDO: Constructive validation, more than just looking for errors
-
Joosten RP, Joosten K, Murshudov GN, Perrakis A: PDB-REDO: constructive validation, more than just looking for errors. Acta Crystallographica Section D 2012, 68:484-496.
-
(2012)
Acta Crystallographica Section D
, vol.68
, pp. 484-496
-
-
Joosten, R.P.1
Joosten, K.2
Murshudov, G.N.3
Perrakis, A.4
-
17
-
-
84882387334
-
-
The Jython Project. http://www.jython.org/
-
-
-
-
18
-
-
77957352833
-
Jmol - A paradigm shift in crystallographic visualization
-
Hanson RM: Jmol - a paradigm shift in crystallographic visualization. J Appl Cryst 2010, 43:1250-1260.
-
(2010)
J Appl Cryst
, vol.43
, pp. 1250-1260
-
-
Hanson, R.M.1
-
19
-
-
14644420979
-
The Uppsala Electron-Density Server
-
DOI 10.1107/S0907444904013253
-
Kleywegt GJ, Harris MR, Zou JY, Taylor TC, Wählby A, Jones TA: The Uppsala electron-density server. Acta Crystallogr Sect D Biol Cryst 2004, 60:2240-2249. (Pubitemid 41742776)
-
(2004)
Acta Crystallographica Section D: Biological Crystallography
, vol.60
, Issue.12
, pp. 2240-2249
-
-
Kleywegt, G.J.1
Harris, M.R.2
Zou, J.-Y.3
Taylor, T.C.4
Wahlby, A.5
Jones, T.A.6
-
20
-
-
84882392674
-
-
EDS - Uppsala Electron Density Server. http://eds.bmc.uu.se/eds/
-
-
-
-
21
-
-
79960976768
-
UniProt Knowledgebase: A hub of integrated protein data
-
Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database J Biol Databases Curat 2011, 2011:bar009.
-
(2011)
Database J Biol Databases Curat
, vol.2011
-
-
Magrane, M.1
-
22
-
-
84876574278
-
BioLiP: A semi-manually curated database for biologically relevant ligand-protein interactions
-
Yang J, Roy A, Zhang Y: BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Res 2013, 41:D1096-103.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Yang, J.1
Roy, A.2
Zhang, Y.3
-
23
-
-
33745151060
-
(2S,3S)-3-amino-4-(3,3-difluoropyrrolidin-1-yl)-N,N-dimethyl-4-oxo-2-(4- [1, 2,4]triazolo[1,5-a]-pyridin-6-ylphenyl)butanamide: A selective -amino amide dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes
-
DOI 10.1021/jm060015t
-
Edmondson SD, Mastracchio A, Mathvink RJ, He J, Harper B, Park Y-J, Beconi M, Di Salvo J, Eiermann GJ, He H, Leiting B, Leone JF, Levorse DA, Lyons K, Patel RA, Patel SB, Petrov A, Scapin G, Shang J, Roy RS, Smith A, Wu JK, Xu S, Zhu B, Thornberry NA, Weber AE: (2S,3S)-3-Amino-4-(3,3-difluoropyrrolidin-1- yl)-N, N-dimethyl-4-oxo-2-(4-[1,2,4]triazolo[1,5-a]-pyridin-6-ylphenyl) butanamide: a selective alpha-amino amide dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes. J Med Chem 2006, 49:3614-27. (Pubitemid 43902466)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.12
, pp. 3614-3627
-
-
Edmondson, S.D.1
Mastracchio, A.2
Mathvink, R.J.3
He, J.4
Harper, B.5
Park, Y.-J.6
Beconi, M.7
Di Salvo, J.8
Eiermann, G.J.9
He, H.10
Leiting, B.11
Leone, J.F.12
Levorse, D.A.13
Lyons, K.14
Patel, R.A.15
Patel, S.B.16
Petrov, A.17
Scapin, G.18
Shang, J.19
Roy, R.S.20
Smith, A.21
Wu, J.K.22
Xu, S.23
Zhu, B.24
Thornberry, N.A.25
Weber, A.E.26
more..
-
26
-
-
0030498233
-
XdlMAPMAN and xdlDATAMAN - Programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets
-
DOI 10.1107/S0907444995014983
-
Kleywegt GJ, Jones TA: xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electrondensity maps and reflection data sets. Acta Crystallogr Sect D Biol Cryst 1996, 52:826-828. (Pubitemid 27064307)
-
(1996)
Acta Crystallographica Section D: Biological Crystallography
, vol.52
, Issue.4
, pp. 826-828
-
-
Kleywegt, G.J.1
Jones, T.A.2
-
27
-
-
84860305929
-
Statistical quality indicators for electron-density maps
-
Tickle IJ: Statistical quality indicators for electron-density maps. Acta Crystallogr Sect D Biol Cryst 2012, 68:454-467.
-
(2012)
Acta Crystallogr Sect D Biol Cryst
, vol.68
, pp. 454-467
-
-
Tickle, I.J.1
-
28
-
-
84870308957
-
Essential considerations for using protein-ligand structures in drug discovery
-
Warren GL, Do TD, Kelley BP, Nicholls A, Warren SD: Essential considerations for using protein-ligand structures in drug discovery. Drug Discov Today 2012, 17:1270-1281.
-
(2012)
Drug Discov Today
, vol.17
, pp. 1270-1281
-
-
Warren, G.L.1
Do, T.D.2
Kelley, B.P.3
Nicholls, A.4
Warren, S.D.5
-
29
-
-
84882374936
-
-
UniProtKB. http://www.uniprot.org/help/uniprotkb
-
-
-
-
30
-
-
79953737180
-
Overview of the CCP4 suite and current developments
-
Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AGW, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS: Overview of the CCP4 suite and current developments. Acta Crystallogr Sect D Biol Cryst 2011, 67:235-42.
-
(2011)
Acta Crystallogr Sect D Biol Cryst
, vol.67
, pp. 235-242
-
-
Winn, M.D.1
Ballard, C.C.2
Cowtan, K.D.3
Dodson, E.J.4
Emsley, P.5
Evans, P.R.6
Keegan, R.M.7
Krissinel, E.B.8
Leslie, A.G.W.9
McCoy, A.10
McNicholas, S.J.11
Murshudov, G.N.12
Pannu, N.S.13
Potterton, E.A.14
Powell, H.R.15
Read, R.J.16
Vagin, A.17
Wilson, K.S.18
-
32
-
-
0037093644
-
Increasing the precision of comparative models with YASARA NOVA - A self-parameterizing force field
-
DOI 10.1002/prot.10104
-
Krieger E, Koraimann G, Vriend G: Increasing the precision of comparative models with YASARA NOVA-a self-parameterizing force field. Proteins 2002, 47:393-402. (Pubitemid 34438688)
-
(2002)
Proteins: Structure, Function and Genetics
, vol.47
, Issue.3
, pp. 393-402
-
-
Krieger, E.1
Koraimann, G.2
Vriend, G.3
-
33
-
-
74249090260
-
Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8
-
Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K: Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins 2009, 77(Suppl 9):114-22.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 114-122
-
-
Krieger, E.1
Joo, K.2
Lee, J.3
Lee, J.4
Raman, S.5
Thompson, J.6
Tyka, M.7
Baker, D.8
Karplus, K.9
-
34
-
-
0032475913
-
Structures of free and complexed forms of Escherichia coli xanthine-guanine phosphoribosyltransferase
-
DOI 10.1006/jmbi.1998.2051
-
Vos S, Parry RJ, BurnsMR, De Jersey J, Martin JL: Structures of free and complexed forms of Escherichia coli xanthine-guanine phosphoribosyltransferase. J Mole Biol 1998, 282:875-89. (Pubitemid 28442353)
-
(1998)
Journal of Molecular Biology
, vol.282
, Issue.4
, pp. 875-889
-
-
Vos, S.1
Parry, R.J.2
Burns, M.R.3
De Jersey, J.4
Martin, J.L.5
-
35
-
-
33847347192
-
Diverse, high-quality test set for the validation of protein-ligand docking performance
-
DOI 10.1021/jm061277y
-
Hartshorn MJ, Verdonk ML, Chessari G, Brewerton SC, Mooij WTM, Mortenson PN, Murray CW: Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem 2007, 50:726-41. (Pubitemid 46332985)
-
(2007)
Journal of Medicinal Chemistry
, vol.50
, Issue.4
, pp. 726-741
-
-
Hartshorn, M.J.1
Verdonk, M.L.2
Chessari, G.3
Brewerton, S.C.4
Mooij, W.T.M.5
Mortenson, P.N.6
Murray, C.W.7
|