-
1
-
-
0034013435
-
Validation of protein crystal structures
-
Kleywegt GJ (2000) Validation of protein crystal structures. Acta Crystallogr D 56: 249-265.
-
(2000)
Acta Crystallogr D
, vol.56
, pp. 249-265
-
-
Kleywegt, G.J.1
-
2
-
-
2342525085
-
Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography
-
Camb
-
DePristo MA, de Bakker PI, Blundell TL (2004) Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. Structure (Camb) 12: 831-838.
-
(2004)
Structure
, vol.12
, pp. 831-838
-
-
DePristo, Ma.1
De Bakker, P.I.2
Blundell, T.L.3
-
3
-
-
0001644632
-
Between objectivity and subjectivity
-
Branden CI, Jones TA (1990) Between objectivity and subjectivity. Nature 343: 687-689.
-
(1990)
Nature
, vol.343
, pp. 687-689
-
-
Branden, C.I.1
Jones, T.A.2
-
5
-
-
0032493714
-
Quality assessment of NMR structures: A statistical survey
-
Doreleijers JF, Rullmann JA, Kaptein R (1998) Quality assessment of NMR structures: A statistical survey. J Mol Biol 281: 149-164.
-
(1998)
J Mol Biol
, vol.281
, pp. 149-164
-
-
Doreleijers, J.F.1
Rullmann, J.A.2
Kaptein, R.3
-
6
-
-
0036219167
-
Improving the quality of protein structures derived by NMR spectroscopy
-
Spronk CA, Linge JP, Hilbers CW, Vuister GW (2002) Improving the quality of protein structures derived by NMR spectroscopy. J Biomol NMR 22: 281-289.
-
(2002)
J Biomol NMR
, vol.22
, pp. 281-289
-
-
Spronk, C.A.1
Linge, J.P.2
Hilbers, C.W.3
Vuister, G.W.4
-
7
-
-
0037441524
-
Refinement of protein structures in explicit solvent
-
Linge JP, Williams MA, Spronk CA, Bonvin AM, Nilges M (2003) Refinement of protein structures in explicit solvent. Proteins 50: 496-506.
-
(2003)
Proteins
, vol.50
, pp. 496-506
-
-
Linge, J.P.1
Williams, M.A.2
Spronk, C.A.3
Bonvin, A.M.4
Nilges, M.5
-
8
-
-
2442610955
-
DRESS: A Database of REfined Solution nmr Structures
-
Nabuurs SB, Nederveen AJ, Vranken W, Doreleijers JF, Bonvin AM, et al. (2004) DRESS: A Database of REfined Solution nmr Structures. Proteins 55: 483-486.
-
(2004)
Proteins
, vol.55
, pp. 483-486
-
-
Nabuurs, S.B.1
Nederveen, A.J.2
Vranken, W.3
Doreleijers, J.F.4
Bonvin, A.M.5
-
9
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
-
10
-
-
0024727887
-
Crystallographic structure of a photoreceptor protein at 2.4 A resolution
-
U S A
-
McRee DE, Tainer JA, Meyer TE, Van Beeumen J, Cusanovich MA, et al. (1989) Crystallographic structure of a photoreceptor protein at 2.4 A resolution. Proc Natl Acad Sci U S A 86: 6533-6537.
-
(1989)
Proc Natl Acad Sci
, vol.86
, pp. 6533-6537
-
-
McRee, D.E.1
Tainer, J.A.2
Meyer, T.E.3
Van Beeumen, J.4
Cusanovich, M.A.5
-
11
-
-
0029110488
-
1.4-A Structure of photoactive yellow protein, a cytosolic photoreceptor: Unusual fold, active site, and chromophore
-
Borgstahl GE, Williams DR, Getzoff ED (1995) 1.4-A Structure of photoactive yellow protein, a cytosolic photoreceptor: Unusual fold, active site, and chromophore. Biochemistry 34: 6278-6287.
-
(1995)
Biochemistry
, vol.34
, pp. 6278-6287
-
-
Borgstahl, G.E.1
Williams, D.R.2
Getzoff, E.D.3
-
12
-
-
0021892867
-
2.8-A Structure of penicillin-sensitive D-alanyl carboxypeptidase- transpeptidase from Streptomyces R61 and complexes with beta-lactams
-
Kelly JA, Knox JR, Moews PC, Hite GJ, Bartolone JB, et al. (1985) 2.8-A Structure of penicillin-sensitive D-alanyl carboxypeptidase-transpeptidase from Streptomyces R61 and complexes with beta-lactams. J Biol Chem 260: 6449-6458.
-
(1985)
J Biol Chem
, vol.260
, pp. 6449-6458
-
-
Kelly, J.A.1
Knox, J.R.2
Moews, P.C.3
Hite, G.J.4
Bartolone, J.B.5
-
13
-
-
0028806595
-
The refined crystallographic structure of a DD-peptidase penicillin-target enzyme at 1.6 A resolution
-
Kelly JA, Kuzin AP (1995) The refined crystallographic structure of a DD-peptidase penicillin-target enzyme at 1.6 A resolution. J Mol Biol 254: 223-236.
-
(1995)
J Mol Biol
, vol.254
, pp. 223-236
-
-
Kelly, J.A.1
Kuzin, A.P.2
-
14
-
-
0028124665
-
High-resolution structure of the oligomerization domain of p53 by multidimensional NMR
-
Clore GM, Omichinski JG, Sakaguchi K, Zambrano N, Sakamoto H, et al. (1994) High-resolution structure of the oligomerization domain of p53 by multidimensional NMR. Science 265: 386-391.
-
(1994)
Science
, vol.265
, pp. 386-391
-
-
Clore, G.M.1
Omichinski, J.G.2
Sakaguchi, K.3
Zambrano, N.4
Sakamoto, H.5
-
15
-
-
0028952841
-
Crystal structure of the tetramerization domain of the p53 tumor suppressor at 1.7 angstroms
-
Jeffrey PD, Gorina S, Pavletich NP (1995) Crystal structure of the tetramerization domain of the p53 tumor suppressor at 1.7 angstroms. Science 267: 1498-1502.
-
(1995)
Science
, vol.267
, pp. 1498-1502
-
-
Jeffrey, P.D.1
Gorina, S.2
Pavletich, N.P.3
-
16
-
-
0028939079
-
Interhelical angles in the solution structure of the oligomerization domain of p53: Correction
-
Clore GM, Omichinski JG, Sakaguchi K, Zambrano N, Sakamoto H, et al. (1995) Interhelical angles in the solution structure of the oligomerization domain of p53: Correction. Science 267: 1515-1516.
-
(1995)
Science
, vol.267
, pp. 1515-1516
-
-
Clore, G.M.1
Omichinski, J.G.2
Sakaguchi, K.3
Zambrano, N.4
Sakamoto, H.5
-
17
-
-
0037126593
-
Flipping a genetic switch by subunit exchange
-
Lambert LJ, Schirf V, Demeler B, Cadene M, Werner MH (2001) Flipping a genetic switch by subunit exchange. EMBO J 20: 7149-7159.
-
(2001)
EMBO J
, vol.20
, pp. 7149-7159
-
-
Lambert, L.J.1
Schirf, V.2
Demeler, B.3
Cadene, M.4
Werner, M.H.5
-
18
-
-
0037133152
-
Solution structure and stability of the anti-sigma factor AsiA: Implications for novel functions
-
U S A
-
Urbauer JL, Simeonov MF, Urbauer RJ, Adelman K, Gilmore JM, et al. (2002) Solution structure and stability of the anti-sigma factor AsiA: Implications for novel functions. Proc Natl Acad Sci U S A 99: 1831-1835.
-
(2002)
Proc Natl Acad Sci
, vol.99
, pp. 1831-1835
-
-
Urbauer, J.L.1
Simeonov, M.F.2
Urbauer, R.J.3
Adelman, K.4
Gilmore, J.M.5
-
19
-
-
4143092787
-
Flipping a genetic switch by subunit exchange
-
Lambert LJ, Schirf V, Demeler B, Cadene M, Werner MH (2004) Flipping a genetic switch by subunit exchange. EMBO J 23: 3186.
-
(2004)
EMBO J
, vol.23
, pp. 3186
-
-
Lambert, L.J.1
Schirf, V.2
Demeler, B.3
Cadene, M.4
Werner, M.H.5
-
20
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
-
21
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5: 823-826.
-
(1986)
EMBO J
, vol.5
, pp. 823-826
-
-
Chothia, C.1
Lesk, A.M.2
-
22
-
-
0026030641
-
Database of homology-derived protein structures and the structural meaning of sequence alignment
-
Sander C, Schneider R (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9: 56-68.
-
(1991)
Proteins
, vol.9
, pp. 56-68
-
-
Sander, C.1
Schneider, R.2
-
23
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Rost B (1999) Twilight zone of protein sequence alignments. Prot Eng 12: 85-94.
-
(1999)
Prot Eng
, vol.12
, pp. 85-94
-
-
Rost, B.1
-
24
-
-
0033768267
-
Protein NMR spectroscopy in structural genomics
-
Montelione GT, Zheng D, Huang YJ, Gunsalus KC, Szyperski T (2000) Protein NMR spectroscopy in structural genomics. Nat Struct Biol 7 (Suppl): 982-985.
-
(2000)
Nat Struct Biol
, vol.7
, Issue.SUPPL.
, pp. 982-985
-
-
Montelione, G.T.1
Zheng, D.2
Huang, Y.J.3
Gunsalus, K.C.4
Szyperski, T.5
-
25
-
-
0000195671
-
Natural abundance N-15 NMR by enhanced heteronuclear spectroscopy
-
Bodenhausen G, Ruben DJ (1980) Natural abundance N-15 NMR by enhanced heteronuclear spectroscopy. Chem Phys Lett 69: 185-189.
-
(1980)
Chem Phys Lett
, vol.69
, pp. 185-189
-
-
Bodenhausen, G.1
Ruben, D.J.2
-
26
-
-
0027350599
-
Isotope-edited multidimensional NMR of calcineurin B in the presence of the nondeuterated detergent CHAPS
-
Anglister J, Grzesiek S, Ren H, Klee CB, Bax A (1993) Isotope-edited multidimensional NMR of calcineurin B in the presence of the nondeuterated detergent CHAPS. J Biomol NMR 3: 121-126.
-
(1993)
J Biomol NMR
, vol.3
, pp. 121-126
-
-
Anglister, J.1
Grzesiek, S.2
Ren, H.3
Klee, C.B.4
Bax, A.5
-
27
-
-
0027222060
-
Observation of inter-subunit nuclear Overhauser effects in a dimeric protein. Application to the Arc repressor
-
Burgering MJ, Boelens R, Caffrey M, Breg JN, Kaptein R (1993) Observation of inter-subunit nuclear Overhauser effects in a dimeric protein. Application to the Arc repressor. FEBS Lett 330: 105-109.
-
(1993)
FEBS Lett
, vol.330
, pp. 105-109
-
-
Burgering, M.J.1
Boelens, R.2
Caffrey, M.3
Breg, J.N.4
Kaptein, R.5
-
28
-
-
23944489900
-
Structure and dynamics of the homodimeric dynein light chain km23
-
Ilangovan U, Ding W, Zhong Y, Wilson CL, Groppe JC, et al. (2005) Structure and dynamics of the homodimeric dynein light chain km23. J Mol Biol 352: 338-354.
-
(2005)
J Mol Biol
, vol.352
, pp. 338-354
-
-
Ilangovan, U.1
Ding, W.2
Zhong, Y.3
Wilson, C.L.4
Groppe, J.C.5
-
29
-
-
0000243829
-
PROCHECK: A program to check the stereochemical quality of protein structures
-
Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Cryst 26: 283-291.
-
(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
-
30
-
-
0025398721
-
Vriend G (1990) WHAT IF: A molecular modeling and drug design program
-
Vriend G (1990) . Vriend G (1990) WHAT IF: A molecular modeling and drug design program. J Mol Graph 8: 52-56, 29.
-
(1990)
J Mol Graph
, vol.8
, pp. 52-56
-
-
Vriend, G.1
-
31
-
-
0030870075
-
Objectively judging the quality of a protein structure from a Ramachandran plot
-
Hooft RW, Sander C, Vriend G (1997) Objectively judging the quality of a protein structure from a Ramachandran plot. Comp Appl Biosci 13: 425-430.
-
(1997)
Comp Appl Biosci
, vol.13
, pp. 425-430
-
-
Hooft, R.W.1
Sander, C.2
Vriend, G.3
-
32
-
-
9944221417
-
Validation of protein structures derived by NMR spectroscopy
-
Spronk CA, Nabuurs SB, Krieger E, Vriend G, Vuister GW (2004) Validation of protein structures derived by NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 45: 315-337.
-
(2004)
Prog Nucl Magn Reson Spectrosc
, vol.45
, pp. 315-337
-
-
Spronk, C.A.1
Nabuurs, S.B.2
Krieger, E.3
Vriend, G.4
Vuister, G.W.5
-
33
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292: 195-202.
-
(1999)
J Mol Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
34
-
-
0027542118
-
Quality control of protein models: Directional atomic contact analysis
-
Vriend G, Sander C (1993) Quality control of protein models: Directional atomic contact analysis. J Appl Cryst 26: 47-60.
-
(1993)
J Appl Cryst
, vol.26
, pp. 47-60
-
-
Vriend, G.1
Sander, C.2
-
35
-
-
2542554197
-
Verification of protein structures: Side-chain planarity
-
Hooft RWW, Sander C, Vriend G (1996) Verification of protein structures: Side-chain planarity. J Appl Cryst 29: 714-716.
-
(1996)
J Appl Cryst
, vol.29
, pp. 714-716
-
-
Hooft, R.W.W.1
Sander, C.2
Vriend, G.3
-
36
-
-
0141508959
-
Quantitative evaluation of experimental NMR restraints
-
Nabuurs SB, Spronk CA, Krieger E, Maassen H, Vriend G, et al. (2003) Quantitative evaluation of experimental NMR restraints. J Am Chem Soc 125: 12026-12034.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 12026-12034
-
-
Nabuurs, S.B.1
Spronk, C.A.2
Krieger, E.3
Maassen, H.4
Vriend, G.5
-
37
-
-
1642493671
-
A closed binding pocket and global destabilization modify the binding properties of an alternatively spliced form of the second PDZ domain of PTP-BL
-
Camb
-
Walma T, Aelen J, Nabuurs SB, Oostendorp M, van den Berk L, et al. (2004) A closed binding pocket and global destabilization modify the binding properties of an alternatively spliced form of the second PDZ domain of PTP-BL. Structure (Camb) 12: 11-20.
-
(2004)
Structure
, vol.12
, pp. 11-20
-
-
Walma, T.1
Aelen, J.2
Nabuurs, S.B.3
Oostendorp, M.4
Van Den Berk, L.5
-
38
-
-
18844433630
-
Assessing precision and accuracy of protein structures derived from NMR data
-
Snyder DA, Bhattacharya A, Huang YJ, Montelione GT (2005) Assessing precision and accuracy of protein structures derived from NMR data. Proteins 59: 655-661.
-
(2005)
Proteins
, vol.59
, pp. 655-661
-
-
Snyder, D.A.1
Bhattacharya, A.2
Huang, Y.J.3
Montelione, G.T.4
-
39
-
-
0142226863
-
Structure determination and ligand interactions of the PDZ2b domain of PTP-Bas (hPTP1E): Splicing-induced modulation of ligand specificity
-
Kachel N, Erdmann KS, Kremer W, Wolff P, Gronwald W, et al. (2003) Structure determination and ligand interactions of the PDZ2b domain of PTP-Bas (hPTP1E): splicing-induced modulation of ligand specificity. J Mol Biol 334: 143-155.
-
(2003)
J Mol Biol
, vol.334
, pp. 143-155
-
-
Kachel, N.1
Erdmann, K.S.2
Kremer, W.3
Wolff, P.4
Gronwald, W.5
-
40
-
-
0030722243
-
Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium
-
Tjandra N, Bax A (1997) Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278: 1111-1114.
-
(1997)
Science
, vol.278
, pp. 1111-1114
-
-
Tjandra, N.1
Bax, A.2
-
41
-
-
0032879507
-
R-factor, free R, and complete cross-validation for dipolar coupling refinement of NMR structures
-
Clore GM, Garrett DS (1999) R-factor, free R, and complete cross-validation for dipolar coupling refinement of NMR structures. J Am Chem Soc 121: 9008-9012.
-
(1999)
J Am Chem Soc
, vol.121
, pp. 9008-9012
-
-
Clore, G.M.1
Garrett, D.S.2
-
42
-
-
15244349863
-
A copper(I) protein possibly involved in the assembly of CuA center of bacterial cytochrome c oxidase
-
U S A
-
Banci L, Bertini I, Ciofi-Baffoni S, Katsari E, Katsaros N, et al. (2005) A copper(I) protein possibly involved in the assembly of CuA center of bacterial cytochrome c oxidase. Proc Natl Acad Sci U S A 102: 3994-3999.
-
(2005)
Proc Natl Acad Sci
, vol.102
, pp. 3994-3999
-
-
Banci, L.1
Bertini, I.2
Ciofi-Baffoni, S.3
Katsari, E.4
Katsaros, N.5
-
43
-
-
0343081069
-
RFAC, a program for automated NMR R-factor estimation
-
Gronwald W, Kirchhofer R, Gorler A, Kremer W, Ganslmeier B, et al. (2000) RFAC, a program for automated NMR R-factor estimation. J Biomol NMR 17: 137-151.
-
(2000)
J Biomol NMR
, vol.17
, pp. 137-151
-
-
Gronwald, W.1
Kirchhofer, R.2
Gorler, A.3
Kremer, W.4
Ganslmeier, B.5
-
44
-
-
0038725124
-
A use of Ramachandran potentials in protein solution structure determinations
-
Bertini I, Cavallaro G, Luchinat C, Poli I (2003) A use of Ramachandran potentials in protein solution structure determinations. J Biomol NMR 26: 355-366.
-
(2003)
J Biomol NMR
, vol.26
, pp. 355-366
-
-
Bertini, I.1
Cavallaro, G.2
Luchinat, C.3
Poli, I.4
-
45
-
-
16244377434
-
An integrated platform for automated analysis of protein NMR structures
-
Huang YJ, Moseley HN, Baran MC, Arrowsmith C, Powers R, et al. (2005) An integrated platform for automated analysis of protein NMR structures. Methods Enzymol 394: 111-141.
-
(2005)
Methods Enzymol
, vol.394
, pp. 111-141
-
-
Huang, Y.J.1
Moseley, H.N.2
Baran, M.C.3
Arrowsmith, C.4
Powers, R.5
-
46
-
-
13644252170
-
Protein NMR recall, precision, and F-measure scores (RPF scores): Structure quality assessment measures based on information retrieval statistics
-
Huang YJ, Powers R, Montelione GT (2005) Protein NMR recall, precision, and F-measure scores (RPF scores): Structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 127: 1665-1674.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 1665-1674
-
-
Huang, Y.J.1
Powers, R.2
Montelione, G.T.3
-
47
-
-
23044509110
-
NMR data collection and analysis protocol for high-throughput protein structure determination
-
U S A
-
Liu G, Shen Y, Atreya HS, Parish D, Shao Y, et al. (2005) NMR data collection and analysis protocol for high-throughput protein structure determination. Proc Natl Acad Sci U S A 102: 10487-10492.
-
(2005)
Proc Natl Acad Sci
, vol.102
, pp. 10487-10492
-
-
Liu, G.1
Shen, Y.2
Atreya, H.S.3
Parish, D.4
Shao, Y.5
-
48
-
-
3543012707
-
Crystallography and NMR system (CNS): A new software system for macromolecular structure determination
-
Brünger AT, Adams PD, Clore GM, Delano WL, Gros P, et al. (1998) Crystallography and NMR system (CNS): A new software system for macromolecular structure determination. Acta Cryst D54: 905-921.
-
(1998)
Acta Cryst
, vol.D54
, pp. 905-921
-
-
Brünger, A.T.1
Adams, P.D.2
Clore, G.M.3
Delano, W.L.4
Gros, P.5
-
50
-
-
0034044314
-
The PSIPRED protein structure prediction server
-
McGuffin LJ, Bryson K, Jones DT (2000) The PSIPRED protein structure prediction server. Bioinformatics 16: 404-405.
-
(2000)
Bioinformatics
, vol.16
, pp. 404-405
-
-
McGuffin, L.J.1
Bryson, K.2
Jones, D.T.3
|