-
1
-
-
37549024654
-
The Protein Data Bank: A historical perspective
-
10.1107/S0108767307035623
-
H Berman 2007 The Protein Data Bank: a historical perspective Acta Crystallogr A 64 88 95 10.1107/S0108767307035623
-
(2007)
Acta Crystallogr A
, vol.64
, pp. 88-95
-
-
Berman, H.1
-
2
-
-
0023008905
-
Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination: A model study of crambin
-
DOI 10.1016/0022-2836(86)90146-4
-
GM Clore AT Brunger M Karplus AM Gronenborn 1986 Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination. A model study of crambin J Mol Biol 191 523 551 10.1016/0022-2836(86)90146-4 (Pubitemid 17187239)
-
(1986)
Journal of Molecular Biology
, vol.191
, Issue.3
, pp. 523-551
-
-
Clore, G.M.1
Brunger, A.T.2
Karplus, M.3
Gronenborn, A.M.4
-
3
-
-
12944275687
-
Guidelines for the deposition and release of macromolecular coordinate and experimental data
-
Commission on Biological Macromolecules
-
Commission on Biological Macromolecules 2000 Guidelines for the deposition and release of macromolecular coordinate and experimental data Acta Cryst D56 2
-
(2000)
Acta Cryst
, vol.56
, pp. 2
-
-
-
4
-
-
0032493714
-
Quality assessment of NMR structures: A statistical survey
-
DOI 10.1006/jmbi.1998.1808
-
JF Doreleijers JAC Rullmann R Kaptein 1998 Quality assessment of NMR structures: a statistical survey J Mol Biol 281 149 164 10.1006/jmbi.1998.1808 (Pubitemid 28360678)
-
(1998)
Journal of Molecular Biology
, vol.281
, Issue.1
, pp. 149-164
-
-
Doreleijers, J.F.1
Rullmann, J.A.C.2
Kaptein, R.3
-
5
-
-
0033027208
-
Completeness of NOEs in protein structures: A statistical analysis of NMR data
-
DOI 10.1023/A:1008335423527
-
JF Doreleijers ML Raves T Rullmann R Kaptein 1999 Completeness of NOEs in protein structure: a statistical analysis of NMR data J Biomol NMR 14 123 132 10.1023/A:1008335423527 (Pubitemid 29322966)
-
(1999)
Journal of Biomolecular NMR
, vol.14
, Issue.2
, pp. 123-132
-
-
Doreleijers, J.F.1
Raves, M.L.2
Rullmann, T.3
Kaptein, R.4
-
6
-
-
0037986814
-
BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank
-
DOI 10.1023/A:1023514106644
-
JF Doreleijers S Mading D Maziuk K Sojourner 2003 BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank J Biomol NMR 26 139 146 10.1023/A:1023514106644 (Pubitemid 36609046)
-
(2003)
Journal of Biomolecular NMR
, vol.26
, Issue.2
, pp. 139-146
-
-
Doreleijers, J.F.1
Mading, S.2
Maziuk, D.3
Sojourner, K.4
Yin, L.5
Zhu, J.6
Markley, J.L.7
Ulrich, E.L.8
-
7
-
-
23144441604
-
BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures
-
DOI 10.1007/s10858-005-2195-0
-
JF Doreleijers AJ Nederveen WF Vranken J Lin 2005 BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures J Biomol NMR 32 1 12 10.1007/s10858-005-2195-0 (Pubitemid 41086462)
-
(2005)
Journal of Biomolecular NMR
, vol.32
, Issue.1
, pp. 1-12
-
-
Doreleijers, J.F.1
Nederveen, A.J.2
Vranken, W.3
Lin, J.4
Bonvin, A.M.J.J.5
Kaptein, R.6
Markley, J.L.7
Ulrich, E.L.8
-
8
-
-
0024595937
-
Determination of the three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata: A study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing
-
DOI 10.1021/bi00431a033
-
PC Driscoll AM Gronenborn L Beress GM Clore 1989 Determination of the three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata: a study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing Biochemistry 28 2188 2198 10.1021/bi00431a033 (Pubitemid 19084445)
-
(1989)
Biochemistry
, vol.28
, Issue.5
, pp. 2188-2198
-
-
Driscoll, P.C.1
Gronenborn, A.M.2
Beress, L.3
Clore, G.M.4
-
10
-
-
17444420842
-
A framework for scientific data modeling and automated software development
-
DOI 10.1093/bioinformatics/bti234
-
RH Fogh W Boucher WF Vranken A Pajon TJ Stevens TN Bhat J Westbrook J Ionides E Laue 2005 A framework for scientific data modeling and automated software development Bioinformatics 21 1678 1684 10.1093/bioinformatics/bti234 (Pubitemid 40542728)
-
(2005)
Bioinformatics
, vol.21
, Issue.8
, pp. 1678-1684
-
-
Fogh, R.H.1
Boucher, W.2
Vranken, W.F.3
Pajon, A.4
Stevens, T.J.5
Bhat, T.N.6
Westbrook, J.7
Ionides, J.M.C.8
Laue, E.D.9
-
11
-
-
38549176153
-
Remediation of the protein data bank archive
-
DOI 10.1093/nar/gkm937
-
K Henrick Z Feng WF Bluhm D Dimitropoulos JF Doreleijers S Dutta JL Flippen-Anderson J Ionides C Kamada E Krissinel CL Lawson JL Markley H Nakamura R Newman Y Shimizu J Swaminathan S Velankar J Ory EL Ulrich WF Vranken J Westbrook R Yamashita H Yang J Young M Yousufuddin HM Berman 2008 Remediation of the Protein Data Bank archive Nucleic Acids Res 36 D426 D433 10.1093/nar/gkm937 (Pubitemid 351149761)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Henrick, K.1
Feng, Z.2
Bluhm, W.F.3
Dimitropoulos, D.4
Doreleijers, J.F.5
Dutta, S.6
Flippen-Anderson, J.L.7
Ionides, J.8
Kamada, C.9
Krissinel, E.10
Lawson, C.L.11
Markley, J.L.12
Nakamura, H.13
Newman, R.14
Shimizu, Y.15
Swaminathan, J.16
Velankar, S.17
Ory, J.18
Ulrich, E.L.19
Vranken, W.20
Westbrook, J.21
Yamashita, R.22
Yang, H.23
Young, J.24
Yousufuddin, M.25
Berman, H.M.26
more..
-
12
-
-
0030047142
-
Errors in protein structures
-
10.1038/381272a0 1996Natur.381.272H
-
RWW Hooft G Vriend C Sander EE Abola 1996 Errors in protein structures Nature 381 272 10.1038/381272a0 1996Natur.381..272H
-
(1996)
Nature
, vol.381
, pp. 272
-
-
Hooft, R.W.W.1
Vriend, G.2
Sander, C.3
Abola, E.E.4
-
13
-
-
66249103704
-
PDB-REDO: Automated re-refinement of X-ray structure models in the PDB
-
10.1107/S0021889809008784
-
RP Joosten J Salzemann V Bloch H Stockinger A Berglund C Blanchet E Bongcam-Rudloff C Combet ALD Costa G Deleage M Diarena R Fabbretti G Fettahi V Flegel A Gisel V Kasam T Kervinen E Korpelainen K Mattila M Pagni M Reichstadt V Breton IJ Ticklei G Vriend 2009 PDB-REDO: automated re-refinement of X-ray structure models in the PDB J Appl Crystallogr 42 376 384 10.1107/ S0021889809008784
-
(2009)
J Appl Crystallogr
, vol.42
, pp. 376-384
-
-
Joosten, R.P.1
Salzemann, J.2
Bloch, V.3
Stockinger, H.4
Berglund, A.5
Blanchet, C.6
Bongcam-Rudloff, E.7
Combet, C.8
Costa, A.L.D.9
Deleage, G.10
Diarena, M.11
Fabbretti, R.12
Fettahi, G.13
Flegel, V.14
Gisel, A.15
Kasam, V.16
Kervinen, T.17
Korpelainen, E.18
Mattila, K.19
Pagni, M.20
Reichstadt, M.21
Breton, V.22
Ticklei, I.J.23
Vriend, G.24
more..
-
14
-
-
0022419169
-
A protein structure from nuclear magnetic resonance data. Lac repressor headpiece
-
10.1016/0022-2836(85)90036-1
-
R Kaptein ERP Zuiderweg RM Scheek R Boelens WF van Gunsteren 1985 A protein structure from nuclear magnetic resonance data. Lac repressor headpiece J Mol Biol 182 179 182 10.1016/0022-2836(85)90036-1
-
(1985)
J Mol Biol
, vol.182
, pp. 179-182
-
-
Kaptein, R.1
Zuiderweg, E.R.P.2
Scheek, R.M.3
Boelens, R.4
Van Gunsteren, W.F.5
-
15
-
-
0242322928
-
Architecture of a protein molecule
-
10.1038/182764a0 1958Natur.182.764K
-
JC Kendrew 1958 Architecture of a protein molecule Nature 182 764 767 10.1038/182764a0 1958Natur.182..764K
-
(1958)
Nature
, vol.182
, pp. 764-767
-
-
Kendrew, J.C.1
-
16
-
-
0000243829
-
PROCHECK: A program to check the stereochemical quality of protein structures
-
10.1107/S0021889892009944
-
RA Laskowski MW MacArthur DS Moss JM Thornton 1993 PROCHECK: a program to check the stereochemical quality of protein structures J Appl Cryst 26 283 291 10.1107/S0021889892009944
-
(1993)
J Appl Cryst
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
MacArthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
17
-
-
0032110340
-
Recommendations for the presentation of NMR structures of proteins and nucleic acids: IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy
-
JL Markley A Bax Y Arata CW Hilbers R Kaptein BD Sykes PE Wright K Wüthrich 1998 Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB inter-union task group on the standardization of data bases of protein and nucleic acid structures determined by NMR spectroscopy J Biomol NMR 12 1 23 10.1023/A:1008290618449 (Pubitemid 128512831)
-
(1998)
Journal of Biomolecular NMR
, vol.12
, Issue.1
, pp. 1-23
-
-
Markley, J.L.1
Bax, A.2
Arata, Y.3
Hilbers, C.W.4
Kaptein, R.5
Sykes, B.D.6
Wright, P.E.7
Wuthrich, K.8
-
18
-
-
41149116500
-
BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): New policies affecting biomolecular NMR depositions
-
10.1007/s10858-008-9221-y
-
JL Markley EL Ulrich HM Berman K Henrick H Nakamura H Akutsu 2008 BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions J Biomol NMR 40 153 155 10.1007/s10858-008-9221-y
-
(2008)
J Biomol NMR
, vol.40
, pp. 153-155
-
-
Markley, J.L.1
Ulrich, E.L.2
Berman, H.M.3
Henrick, K.4
Nakamura, H.5
Akutsu, H.6
-
19
-
-
2442610955
-
DRESS: A Database of REfined Solution NMR Structures
-
DOI 10.1002/prot.20118
-
SB Nabuurs AJ Nederveen WF Vranken JF Doreleijers AM Bonvin GW Vuister G Vriend CA Spronk 2004 DRESS: a database of REfined solution NMR structures Proteins 55 483 486 10.1002/prot.20118 (Pubitemid 38620072)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.55
, Issue.3
, pp. 483-486
-
-
Nabuurs, S.B.1
Nederveen, A.J.2
Vranken, W.3
Doreleijers, J.F.4
Bonvin, A.M.J.J.5
Vuister, G.W.6
Vriend, G.7
Spronk, C.A.E.M.8
-
20
-
-
21044449889
-
RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
-
DOI 10.1002/prot.20408
-
AJ Nederveen JF Doreleijers WF Vranken Z Miller CA Spronk SB Nabuurs P Güntert M Livny JL Markley M Nilges EL Ulrich R Kaptein AM Bonvin 2005 RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank Proteins 59 662 672 10.1002/prot.20408 (Pubitemid 40695843)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.59
, Issue.4
, pp. 662-672
-
-
Nederveen, A.J.1
Doreleijers, J.F.2
Vranken, W.3
Miller, Z.4
Spronk, C.A.E.M.5
Nabuurs, S.B.6
Guntert, P.7
Livny, M.8
Markley, J.L.9
Nilges, M.10
Ulrich, E.L.11
Kaptein, R.12
Bonvin, A.M.J.J.13
-
21
-
-
0024285896
-
Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations
-
10.1016/0014-5793(88)81148-7
-
M Nilges GM Clore AM Gronenborn 1988 Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations FEBS Lett 229 317 324 10.1016/0014-5793(88)81148-7
-
(1988)
FEBS Lett
, vol.229
, pp. 317-324
-
-
Nilges, M.1
Clore, G.M.2
Gronenborn, A.M.3
-
22
-
-
84984768921
-
Protein Data Bank
-
Protein Data Bank
-
Protein Data Bank 1971 Protein Data Bank Nature New Biol 233 223
-
(1971)
Nature New Biol
, vol.233
, pp. 223
-
-
-
23
-
-
69549138143
-
CASD-NMR: A rolling experiment for the critical assessment of automated structure determination from NMR data
-
Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, Giachetti A, Guerry P, Güntert P, Herrmann T, Huang YJ, Jonker H, Mao B, Malliavin TE, Montelione GT, Nilges M, Raman S, van der Schot G, Vranken WF, Vuister GW, Bonvin AM (2009) CASD-NMR: a rolling experiment for the critical assessment of automated structure determination from NMR data. Nat Meth 6(9):625-626
-
(2009)
Nat Meth
, vol.6
, Issue.9
, pp. 625-626
-
-
Rosato, A.1
Bagaria, A.2
Baker, D.3
Bardiaux, B.4
Cavalli, A.5
Doreleijers, J.F.6
Giachetti, A.7
Guerry, P.8
Güntert, P.9
Herrmann, T.10
Huang, Y.J.11
Jonker, H.12
Mao, B.13
Malliavin, T.E.14
Montelione, G.T.15
Nilges, M.16
Raman, S.17
Van Der Schot, G.18
Vranken, W.F.19
Vuister, G.W.20
Bonvin, A.M.21
more..
-
24
-
-
52049100956
-
The war of tools: How can NMR spectroscopists detect errors in their structures?
-
10.1007/s10858-008-9228-4
-
E Saccenti A Rosato 2008 The war of tools: how can NMR spectroscopists detect errors in their structures? J Biomol NMR 40 251 261 10.1007/s10858-008- 9228-4
-
(2008)
J Biomol NMR
, vol.40
, pp. 251-261
-
-
Saccenti, E.1
Rosato, A.2
-
25
-
-
67649566969
-
New protein structures replace the old
-
10.1038/4591038b
-
K Sanderson 2009 New protein structures replace the old Nature 459 1038 1039 10.1038/4591038b
-
(2009)
Nature
, vol.459
, pp. 1038-1039
-
-
Sanderson, K.1
-
26
-
-
0026223896
-
A relational database for sequence-specific protein NMR data
-
10.1007/BF01875516
-
BR Seavey EA Farr WM Westler JL Markley 1991 A relational database for sequence-specific protein NMR data J Biomol NMR 1 217 236 10.1007/BF01875516
-
(1991)
J Biomol NMR
, vol.1
, pp. 217-236
-
-
Seavey, B.R.1
Farr, E.A.2
Westler, W.M.3
Markley, J.L.4
-
27
-
-
0024572653
-
Creation of a nuclear magnetic resonance data repository and literature database
-
EL Ulrich JL Markley Y Kyogoku 1989 Creation of a nuclear magnetic resonance data repository and literature database Protein Seq Data Anal 2 23 37
-
(1989)
Protein Seq Data Anal
, vol.2
, pp. 23-37
-
-
Ulrich, E.L.1
Markley, J.L.2
Kyogoku, Y.3
-
28
-
-
38549138986
-
BioMagResBank
-
DOI 10.1093/nar/gkm957
-
EL Ulrich H Akutsu JF Doreleijers Y Harano YE Ioannidis J Lin M Livny S Mading D Maziuk Z Miller E Nakatani CF Schulte DE Tolmie R Kent Wenger H Yao JL Markley 2008 BioMagResBank Nucleic Acids Res 36 D402 D408 10.1093/nar/gkm957 (Pubitemid 351149757)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Ulrich, E.L.1
Akutsu, H.2
Doreleijers, J.F.3
Harano, Y.4
Ioannidis, Y.E.5
Lin, J.6
Livny, M.7
Mading, S.8
Maziuk, D.9
Miller, Z.10
Nakatani, E.11
Schulte, C.F.12
Tolmie, D.E.13
Kent Wenger, R.14
Yao, H.15
Markley, J.L.16
-
29
-
-
35848952931
-
A global analysis of NMR distance constraints from the PDB
-
DOI 10.1007/s10858-007-9199-x
-
WF Vranken 2007 A global analysis of NMR distance constraints from the PDB J Biomol NMR 39 303 314 10.1007/s10858-007-9199-x (Pubitemid 350055752)
-
(2007)
Journal of Biomolecular NMR
, vol.39
, Issue.4
, pp. 303-314
-
-
Vranken, W.1
-
30
-
-
19444382397
-
The CCPN data model for NMR spectroscopy: Development of a software pipeline
-
DOI 10.1002/prot.20449
-
WF Vranken W Boucher TJ Stevens RH Fogh A Pajon M Llinas EL Ulrich JL Markley J Ionides E Laue 2005 The CCPN Data Model for NMR Spectroscopy: Development of a Software Pipeline Proteins 59 687 696 10.1002/prot.20449 (Pubitemid 40695845)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.59
, Issue.4
, pp. 687-696
-
-
Vranken, W.F.1
Boucher, W.2
Stevens, T.J.3
Fogh, R.H.4
Pajon, A.5
Llinas, M.6
Ulrich, E.L.7
Markley, J.L.8
Ionides, J.9
Laue, E.D.10
-
31
-
-
0022429237
-
Solution conformation of proteinase inhibitor IIA from bull seminal plasma by 1 H nuclear magnetic resonance and distance geometry
-
10.1016/0022-2836(85)90347-X
-
MP Williamson TF Havel K Wüthrich 1985 Solution conformation of proteinase inhibitor IIA from bull seminal plasma by 1 H nuclear magnetic resonance and distance geometry J Mol Biol 182 295 315 10.1016/0022-2836(85) 90347-X
-
(1985)
J Mol Biol
, vol.182
, pp. 295-315
-
-
Williamson, M.P.1
Havel, T.F.2
Wüthrich, K.3
|