-
1
-
-
35448929112
-
A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing
-
Andrec M, Snyder DA, Zhou Z, et al. 2007. A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing. Proteins, 69:449-65.
-
(2007)
Proteins
, vol.69
, pp. 449-465
-
-
Andrec, M.1
Snyder, D.A.2
Zhou, Z.3
-
2
-
-
0242299201
-
Dissecting subunit interfaces in homodimeric proteins
-
Bahadur RP, Chakrabarti P, Rodier F, et al. 2003. Dissecting subunit interfaces in homodimeric proteins. Proteins, 53:708-19.
-
(2003)
Proteins
, vol.53
, pp. 708-719
-
-
Bahadur, R.P.1
Chakrabarti, P.2
Rodier, F.3
-
3
-
-
1042275583
-
A dissection of specific and non-specific protein-protein interfaces
-
Bahadur RP, Chakrabarti P, Rodier F, et al. 2004. A dissection of specific and non-specific protein-protein interfaces. J Mol Biol, 336:943-55.
-
(2004)
J Mol Biol
, vol.336
, pp. 943-955
-
-
Bahadur, R.P.1
Chakrabarti, P.2
Rodier, F.3
-
5
-
-
40049091293
-
DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions
-
Bernauer J, Bahadur RP, Rodier F, et al. 2008. DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions. Bioinformatics, 24:652-8.
-
(2008)
Bioinformatics
, vol.24
, pp. 652-658
-
-
Bernauer, J.1
Bahadur, R.P.2
Rodier, F.3
-
6
-
-
0027062751
-
Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals
-
Billeter M. 1992. Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals. Q Rev Biophys, 25:325-77.
-
(1992)
Q Rev Biophys
, vol.25
, pp. 325-377
-
-
Billeter, M.1
-
7
-
-
0030850230
-
Protein-protein crystal-packing contacts
-
Carugo O, Argos P. 1997. Protein-protein crystal-packing contacts. Protein Sci, 6:2261-3.
-
(1997)
Protein Sci
, vol.6
, pp. 2261-2263
-
-
Carugo, O.1
Argos, P.2
-
8
-
-
0021107965
-
Solvent-accessible surfaces of proteins and nucleic acids
-
Connolly ML. 1983. Solvent-accessible surfaces of proteins and nucleic acids. Science, 221:709-13.
-
(1983)
Science
, vol.221
, pp. 709-713
-
-
Connolly, M.L.1
-
9
-
-
0030877077
-
Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers
-
Dasgupta S, Iyer GH, Bryant SH, et al. 1997. Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers. Proteins, 28:494-514.
-
(1997)
Proteins
, vol.28
, pp. 494-514
-
-
Dasgupta, S.1
Iyer, G.H.2
Bryant, S.H.3
-
10
-
-
0035956544
-
Toward the de novo design of a catalytically active helix bundle: a substrate-accessible carboxylate-bridged dinuclear metal center
-
Di Costanzo L, Wade H, Geremia S, et al. 2001. Toward the de novo design of a catalytically active helix bundle: a substrate-accessible carboxylate-bridged dinuclear metal center. J Am Chem Soc, 123:12749-57.
-
(2001)
J Am Chem Soc
, vol.123
, pp. 12749-12757
-
-
Di Costanzo, L.1
Wade, H.2
Geremia, S.3
-
11
-
-
0035853028
-
Identification of protein oligomerization states by analysis of interface conservation
-
Elcock AH, McCammon JA. 2001. Identification of protein oligomerization states by analysis of interface conservation. Proc Natl Acad Sci U S A, 98:2990-4.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 2990-2994
-
-
Elcock, A.H.1
McCammon, J.A.2
-
12
-
-
0032481344
-
Synapsin I is structurally similar to ATP-utilizing enzymes
-
Esser L, Wang CR, Hosaka M, et al. 1998. Synapsin I is structurally similar to ATP-utilizing enzymes. Embo J, 17:977-84.
-
(1998)
Embo J
, vol.17
, pp. 977-984
-
-
Esser, L.1
Wang, C.R.2
Hosaka, M.3
-
13
-
-
0034847376
-
Structure of the TRFH dimerization domain of the human telomeric proteins TRF1 and TRF2
-
Fairall L, Chapman L, Moss H, et al. 2001. Structure of the TRFH dimerization domain of the human telomeric proteins TRF1 and TRF2. Mol Cell, 8:351-61.
-
(2001)
Mol Cell
, vol.8
, pp. 351-361
-
-
Fairall, L.1
Chapman, L.2
Moss, H.3
-
15
-
-
0028823713
-
Structures of protein complexes by multidimensional heteronuclear magnetic resonance spectroscopy
-
Gronenborn AM, Clore GM. 1995. Structures of protein complexes by multidimensional heteronuclear magnetic resonance spectroscopy. Crit Rev Biochem Mol Biol, 30:351-85.
-
(1995)
Crit Rev Biochem Mol Biol
, vol.30
, pp. 351-385
-
-
Gronenborn, A.M.1
Clore, G.M.2
-
16
-
-
0032169688
-
PQS: a protein quaternary structure file server
-
Henrick K, Thornton JM. 1998. PQS: a protein quaternary structure file server. Trends Biochem Sci, 23:358-61.
-
(1998)
Trends Biochem Sci
, vol.23
, pp. 358-361
-
-
Henrick, K.1
Thornton, J.M.2
-
17
-
-
0029586759
-
Protein-protein interaction at crystal contacts
-
Janin J, Rodier F. 1995. Protein-protein interaction at crystal contacts. Proteins, 23:580-7.
-
(1995)
Proteins
, vol.23
, pp. 580-587
-
-
Janin, J.1
Rodier, F.2
-
18
-
-
0031297461
-
Specific versus non-specific contacts in protein crystals
-
Janin J. 1997. Specific versus non-specific contacts in protein crystals. Nat Struct Biol, 4:973-4.
-
(1997)
Nat Struct Biol
, vol.4
, pp. 973-974
-
-
Janin, J.1
-
19
-
-
0038359614
-
CAPRI: a Critical Assessment of PRedicted Interactions
-
Janin J, Henrick K, Moult J, et al. 2003. CAPRI: a Critical Assessment of PRedicted Interactions. Proteins, 52:2-9.
-
(2003)
Proteins
, vol.52
, pp. 2-9
-
-
Janin, J.1
Henrick, K.2
Moult, J.3
-
20
-
-
33751088850
-
Biological units and their effect upon the properties and prediction of protein-protein interactions
-
Jefferson ER, Walsh TP, Barton GJ. 2006. Biological units and their effect upon the properties and prediction of protein-protein interactions. J Mol Biol, 364:1118-29.
-
(2006)
J Mol Biol
, vol.364
, pp. 1118-1129
-
-
Jefferson, E.R.1
Walsh, T.P.2
Barton, G.J.3
-
22
-
-
9144241174
-
Structure-and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum
-
Kim Y, Yakunin AF, Kuznetsova E, et al. 2004. Structure-and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum. J Biol Chem, 279:517-26.
-
(2004)
J Biol Chem
, vol.279
, pp. 517-526
-
-
Kim, Y.1
Yakunin, A.F.2
Kuznetsova, E.3
-
23
-
-
3042683893
-
eF-site and PDBjViewer: database and viewer for protein functional sites
-
Kinoshita K, Nakamura H. 2004. eF-site and PDBjViewer: database and viewer for protein functional sites. Bioinformatics, 20:1329-30.
-
(2004)
Bioinformatics
, vol.20
, pp. 1329-1330
-
-
Kinoshita, K.1
Nakamura, H.2
-
24
-
-
34548232365
-
Inference of macromolecular assemblies from crystalline state
-
Krissinel E, Henrick K. 2007. Inference of macromolecular assemblies from crystalline state. J Mol Biol, 372:774-97.
-
(2007)
J Mol Biol
, vol.372
, pp. 774-797
-
-
Krissinel, E.1
Henrick, K.2
-
25
-
-
0037137184
-
Ligand-induced structural changes in adenosine 5'-phosphosulfate kinase from Penicillium chrysogenum
-
Lansdon EB, Segel IH, Fisher AJ. 2002. Ligand-induced structural changes in adenosine 5'-phosphosulfate kinase from Penicillium chrysogenum. Biochemistry, 41:13672-80.
-
(2002)
Biochemistry
, vol.41
, pp. 13672-13680
-
-
Lansdon, E.B.1
Segel, I.H.2
Fisher, A.J.3
-
27
-
-
46249083761
-
Assembly refl ects evolution of protein complexes
-
Levy ED, Boeri Erba E, Robinson CV, et al. 2008. Assembly refl ects evolution of protein complexes. Nature, 453:1262-5.
-
(2008)
Nature
, vol.453
, pp. 1262-1265
-
-
Levy, E.D.1
Boeri Erba, E.2
Robinson, C.V.3
-
28
-
-
0033571103
-
Crystal structure of colicin E3 immunity protein: an inhibitor of a ribosome-inactivating RNase
-
Li C, Zhao D, Djebli A, et al. 1999. Crystal structure of colicin E3 immunity protein: an inhibitor of a ribosome-inactivating RNase. Structure, 7:1365-72.
-
(1999)
Structure
, vol.7
, pp. 1365-1372
-
-
Li, C.1
Zhao, D.2
Djebli, A.3
-
29
-
-
33744797911
-
A combinatorial score to distinguish biological and nonbiological protein-protein interfaces
-
Liu S, Li Q, Lai L. 2006. A combinatorial score to distinguish biological and nonbiological protein-protein interfaces. Proteins, 64:68-78.
-
(2006)
Proteins
, vol.64
, pp. 68-78
-
-
Liu, S.1
Li, Q.2
Lai, L.3
-
30
-
-
0027999315
-
Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy
-
MacArthur MW, Laskowski RA, Thornton JM. 1994. Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy. Curr Opinion Struct Biol, 4:731-7.
-
(1994)
Curr Opinion Struct Biol
, vol.4
, pp. 731-737
-
-
MacArthur, M.W.1
Laskowski, R.A.2
Thornton, J.M.3
-
31
-
-
0034701013
-
Crystal structure of adenosine 5'-phosphosulfate kinase from Penicillium chrysogenum
-
MacRae IJ, Segel IH, Fisher AJ. 2000. Crystal structure of adenosine 5'-phosphosulfate kinase from Penicillium chrysogenum. Biochemistry, 39:1613-21.
-
(2000)
Biochemistry
, vol.39
, pp. 1613-1621
-
-
MacRae, I.J.1
Segel, I.H.2
Fisher, A.J.3
-
32
-
-
0035834058
-
Crystal structure of the central region of bovine fibrinogen (E5 fragment) at 1. 4-A resolution
-
Madrazo J, Brown JH, Litvinovich S, et al. 2001. Crystal structure of the central region of bovine fibrinogen (E5 fragment) at 1.4-A resolution. Proc Natl Acad Sci U S A, 98:11967-72.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 11967-11972
-
-
Madrazo, J.1
Brown, J.H.2
Litvinovich, S.3
-
33
-
-
0016772212
-
Comparison of the predicted and observed secondary structure of T4 phage lysozyme
-
Matthews BW. 1975. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta, 405:442-51.
-
(1975)
Biochim Biophys Acta
, vol.405
, pp. 442-451
-
-
Matthews, B.W.1
-
34
-
-
0028304962
-
Satisfying hydrogen bonding potential in proteins
-
McDonald IK, Thornton JM. 1994. Satisfying hydrogen bonding potential in proteins. J Mol Biol, 238:777-93.
-
(1994)
J Mol Biol
, vol.238
, pp. 777-793
-
-
McDonald, I.K.1
Thornton, J.M.2
-
35
-
-
0034612280
-
Functional implications from crystal structures of the conserved Bacillus subtilis protein Maf with and without dUTP
-
Minasov G, Teplova M, Stewart GC, et al. 2000. Functional implications from crystal structures of the conserved Bacillus subtilis protein Maf with and without dUTP. Proc Natl Acad Sci U S A, 97:6328-33.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 6328-6333
-
-
Minasov, G.1
Teplova, M.2
Stewart, G.C.3
-
36
-
-
0242299207
-
Atomic contact vectors in protein-protein recognition
-
Mintseris J, Weng Z. 2003. Atomic contact vectors in protein-protein recognition. Proteins, 53:629-39.
-
(2003)
Proteins
, vol.53
, pp. 629-639
-
-
Mintseris, J.1
Weng, Z.2
-
37
-
-
0028961335
-
SCOP: a structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, et al. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol, 247:536-40.
-
(1995)
J Mol Biol
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
-
38
-
-
0000758624
-
Numerical calculations of electrostatic potentials of protein-solvent systems by the self consistent boundary method
-
Nakamura H, Nishida S. 1987. Numerical calculations of electrostatic potentials of protein-solvent systems by the self consistent boundary method. J Phys Soc Jpn, 56:1609-22.
-
(1987)
J Phys Soc Jpn
, vol.56
, pp. 1609-1622
-
-
Nakamura, H.1
Nishida, S.2
-
39
-
-
0037229456
-
Analysing six types of protein-protein interfaces
-
Ofran Y, Rost B. 2003. Analysing six types of protein-protein interfaces. J Mol Biol, 325:377-87.
-
(2003)
J Mol Biol
, vol.325
, pp. 377-387
-
-
Ofran, Y.1
Rost, B.2
-
40
-
-
0023338543
-
Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
-
Ooi T, Oobatake M, Nemethy G, et al. 1987. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc Natl Acad Sci U S A, 84:3086-90.
-
(1987)
Proc Natl Acad Sci U S A
, vol.84
, pp. 3086-3090
-
-
Ooi, T.1
Oobatake, M.2
Nemethy, G.3
-
41
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson WR, Lipman DJ. 1988. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A, 85:2444-8.
-
(1988)
Proc Natl Acad Sci U S A
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
42
-
-
0034308172
-
Discriminating between homodimeric and monomeric proteins in the crystalline state
-
Ponstingl H, Henrick K, Thornton JM. 2000. Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins, 41:47-57.
-
(2000)
Proteins
, vol.41
, pp. 47-57
-
-
Ponstingl, H.1
Henrick, K.2
Thornton, J.M.3
-
43
-
-
0141669302
-
Automatic inference of protein quaternary structure from crystals
-
Ponstingl H, Kabir T, Thornton JM. 2003. Automatic inference of protein quaternary structure from crystals. J Appl Cryst, 36:1116-22.
-
(2003)
J Appl Cryst
, vol.36
, pp. 1116-1122
-
-
Ponstingl, H.1
Kabir, T.2
Thornton, J.M.3
-
44
-
-
0032515101
-
A soft, mean-field potential derived from crystal contacts for predicting protein-protein interactions
-
Robert CH, Janin J. 1998. A soft, mean-field potential derived from crystal contacts for predicting protein-protein interactions. J Mol Biol, 283:1037-47.
-
(1998)
J Mol Biol
, vol.283
, pp. 1037-1047
-
-
Robert, C.H.1
Janin, J.2
-
45
-
-
0036903921
-
The X-ray crystal structure of pyrrolidone-carboxylate peptidase from hyperthermophilic archaea Pyrococcus horikoshii
-
Sokabe M, Kawamura T, Sakai N, et al. 2002. The X-ray crystal structure of pyrrolidone-carboxylate peptidase from hyperthermophilic archaea Pyrococcus horikoshii. J Struct Funct Genomics, 2:145-54.
-
(2002)
J Struct Funct Genomics
, vol.2
, pp. 145-154
-
-
Sokabe, M.1
Kawamura, T.2
Sakai, N.3
-
46
-
-
2542557409
-
Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces
-
Tsuchiya Y, Kinoshita K, Nakamura H. 2004. Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces. Proteins, 55:885-94.
-
(2004)
Proteins
, vol.55
, pp. 885-894
-
-
Tsuchiya, Y.1
Kinoshita, K.2
Nakamura, H.3
-
47
-
-
33747863302
-
PreBI: prediction of biological interfaces of proteins in crystals
-
Tsuchiya Y, Kinoshita K, Ito N, et al. 2006. PreBI: prediction of biological interfaces of proteins in crystals. Nucleic Acids Res, 34:W320-4.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Tsuchiya, Y.1
Kinoshita, K.2
Ito, N.3
-
48
-
-
33748107163
-
Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity
-
Tsuchiya Y, Kinoshita K, Nakamura H. 2006. Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity. Protein Eng Des Sel, 19:421-9.
-
(2006)
Protein Eng Des Sel
, vol.19
, pp. 421-429
-
-
Tsuchiya, Y.1
Kinoshita, K.2
Nakamura, H.3
-
49
-
-
0035914476
-
Conservation helps to identify biologically relevant crystal contacts
-
Valdar WS, Thornton JM. 2001. Conservation helps to identify biologically relevant crystal contacts. J Mol Biol, 313:399-416.
-
(2001)
J Mol Biol
, vol.313
, pp. 399-416
-
-
Valdar, W.S.1
Thornton, J.M.2
-
50
-
-
0026651557
-
NMR structure determination in solution: a critique and comparison with X-ray crystallography
-
Wagner G, Hyberts SG, Havel TF. 1992. NMR structure determination in solution: a critique and comparison with X-ray crystallography. Annu Rev Biophys Biomol Struct, 21:167-98.
-
(1992)
Annu Rev Biophys Biomol Struct
, vol.21
, pp. 167-198
-
-
Wagner, G.1
Hyberts, S.G.2
Havel, T.F.3
-
51
-
-
33751357065
-
ProtBuD: a database of biological unit structures of protein families and superfamilies
-
Xu Q, Canutescu A, Obradovic Z, et al. 2006. ProtBuD: a database of biological unit structures of protein families and superfamilies. Bioinformatics, 22:2876-82.
-
(2006)
Bioinformatics
, vol.22
, pp. 2876-2882
-
-
Xu, Q.1
Canutescu, A.2
Obradovic, Z.3
|