-
1
-
-
25144498379
-
A human protein-protein interaction network: A resource for annotating the proteome
-
Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122: 957-68.
-
(2005)
Cell
, vol.122
, pp. 957-968
-
-
Stelzl, U.1
Worm, U.2
Lalowski, M.3
Haenig, C.4
Brembeck, F.H.5
-
2
-
-
33745161050
-
Structural biology and drug discovery
-
Scapin G (2006) Structural biology and drug discovery. Curr Pharm Des 12: 2087-97.
-
(2006)
Curr Pharm Des
, vol.12
, pp. 2087-2097
-
-
Scapin, G.1
-
4
-
-
44849127103
-
Alignment of Non-Covalent Interactions at Protein-Protein Interfaces
-
Zhu H, Sommer I, Lengauer T, Domingues FS (2008) Alignment of Non-Covalent Interactions at Protein-Protein Interfaces. PLoS ONE 3(4): e1926.
-
(2008)
PLoS ONE
, vol.3
, Issue.4
-
-
Zhu, H.1
Sommer, I.2
Lengauer, T.3
Domingues, F.S.4
-
5
-
-
0035393302
-
Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
-
Luscombe NM, Laskowski RA, Thornton JM (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res 29: 2860-74.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2860-2874
-
-
Luscombe, N.M.1
Laskowski, R.A.2
Thornton, J.M.3
-
6
-
-
33847042739
-
Protein-RNA interactions: Structural analysis and functional classes
-
Ellis JJ, Broom M, Jones S (2007) Protein-RNA interactions: structural analysis and functional classes. Proteins 66: 903-11.
-
(2007)
Proteins
, vol.66
, pp. 903-911
-
-
Ellis, J.J.1
Broom, M.2
Jones, S.3
-
8
-
-
0037609791
-
Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces
-
Ma B, Elkayam T, Wolfson H, Nussinov R (2003) Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci U S A 100: 5772-7.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 5772-5777
-
-
Ma, B.1
Elkayam, T.2
Wolfson, H.3
Nussinov, R.4
-
9
-
-
0037366128
-
Principles governing Mg, Ca, and Zn binding and selectivity in proteins
-
Dudev T, Lim C (2008) Principles governing Mg, Ca, and Zn binding and selectivity in proteins. Chem Rev 103: 773-88.
-
(2008)
Chem Rev
, vol.103
, pp. 773-788
-
-
Dudev, T.1
Lim, C.2
-
10
-
-
48249153490
-
Metal binding affinity and selectivity in metalloproteins: Insights from computational studies
-
Dudev T, Lim C (2008) Metal binding affinity and selectivity in metalloproteins: insights from computational studies. Annu Rev Biophys 37: 97-116.
-
(2008)
Annu Rev Biophys
, vol.37
, pp. 97-116
-
-
Dudev, T.1
Lim, C.2
-
11
-
-
34447130835
-
Structures and metal-ion-binding properties of the Ca2+-binding helix-loop-helix EF-hand motifs
-
Gifford JL, Walsh MP, Vogel HJ (2007) Structures and metal-ion-binding properties of the Ca2+-binding helix-loop-helix EF-hand motifs. Biochem J 405: 199-221.
-
(2007)
Biochem J
, vol.405
, pp. 199-221
-
-
Gifford, J.L.1
Walsh, M.P.2
Vogel, H.J.3
-
12
-
-
24344445329
-
Zinc coordination environments in proteins determine zinc functions
-
Maret W (2005) Zinc coordination environments in proteins determine zinc functions. J Trace Elem Med Biol 19: 7-12.
-
(2005)
J Trace Elem Med Biol
, vol.19
, pp. 7-12
-
-
Maret, W.1
-
13
-
-
33745597909
-
Predicting protein interaction sites: Binding hot-spots in protein-protein and protein-ligand interfaces
-
Burgoyne NJ, Jackson RM (2006) Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces. Bioinformatics 22: 1335-42.
-
(2006)
Bioinformatics
, vol.22
, pp. 1335-1342
-
-
Burgoyne, N.J.1
Jackson, R.M.2
-
14
-
-
33646839120
-
Characterization of protein-ligand interaction sites using experimental and computational methods
-
Vajda S, Guarnieri F (2006) Characterization of protein-ligand interaction sites using experimental and computational methods. Curr Opin Drug Discov Devel 9: 354-62.
-
(2006)
Curr Opin Drug Discov Devel
, vol.9
, pp. 354-362
-
-
Vajda, S.1
Guarnieri, F.2
-
15
-
-
0345735309
-
Shape signatures: A new approach to computer-aided ligand- and receptor-based drug design
-
Zauhar RJ, Moyna G, Tian L, Li Z, Welsh WJ (2003) Shape signatures: a new approach to computer-aided ligand- and receptor-based drug design. J Med Chem 46: 5674-90.
-
(2003)
J Med Chem
, vol.46
, pp. 5674-5690
-
-
Zauhar, R.J.1
Moyna, G.2
Tian, L.3
Li, Z.4
Welsh, W.J.5
-
16
-
-
17044372385
-
Absolute and relative entropies from computer simulation with applications to ligand binding
-
Carlsson J, Aqvist J (2005) Absolute and relative entropies from computer simulation with applications to ligand binding. J Phys Chem B 109: 6448-56.
-
(2005)
J Phys Chem B
, vol.109
, pp. 6448-6456
-
-
Carlsson, J.1
Aqvist, J.2
-
18
-
-
0038336897
-
Application and limitations of X-ray crystallographic data in structure-based ligand and drug design
-
Davis AM, Teague SJ, Kleywegt GJ (2003) Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angew Chem Int Ed Engl 42: 2718-36.
-
(2003)
Angew Chem Int Ed Engl
, vol.42
, pp. 2718-2736
-
-
Davis, A.M.1
Teague, S.J.2
Kleywegt, G.J.3
-
19
-
-
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
-
20
-
-
0033614004
-
Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
-
Word JM, Lovell SC, Richardson JS, Richardson DC (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285: 1735-47.
-
(1999)
J Mol Biol
, vol.285
, pp. 1735-1747
-
-
Word, J.M.1
Lovell, S.C.2
Richardson, J.S.3
Richardson, D.C.4
-
21
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2003) The Protein Data Bank. Nucleic Acids Res 28: 235-42.
-
(2003)
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
-
22
-
-
0043180474
-
PISCES: A protein sequence culling server
-
Wang G, Dunbrack RL Jr (2003) PISCES: a protein sequence culling server. Bioinformatics 19: 1589-91.
-
(2003)
Bioinformatics
, vol.19
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack Jr, R.L.2
-
23
-
-
38549153238
-
Data growth and its impact on the SCOP database: New developments
-
Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TP, et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 36: D419-D425.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Andreeva, A.1
Howorth, D.2
Chandonia, J.M.3
Brenner, S.E.4
Hubbard, T.P.5
-
24
-
-
33745011804
-
The Mycobacterium tuberculosis LipB enzyme functions as a cysteine/lysine dyad acyltransferase
-
Ma Q, Zhao X, Nasser Eddine A, Geerlof A, Li X, et al. (2006) The Mycobacterium tuberculosis LipB enzyme functions as a cysteine/lysine dyad acyltransferase. Proc Natl Acad Sci U S A 103: 8662-7.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 8662-8667
-
-
Ma, Q.1
Zhao, X.2
Nasser Eddine, A.3
Geerlof, A.4
Li, X.5
-
25
-
-
34249080375
-
Conformational switching in the fungal light sensor Vivid
-
Zoltowski BD, Schwerdtfeger C, Widom J, Loros JJ, Bilwes AM, et al. (2007) Conformational switching in the fungal light sensor Vivid. Science 316: 1054-7.
-
(2007)
Science
, vol.316
, pp. 1054-1057
-
-
Zoltowski, B.D.1
Schwerdtfeger, C.2
Widom, J.3
Loros, J.J.4
Bilwes, A.M.5
-
26
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132.
-
(1982)
J Mol Biol
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
27
-
-
0035083950
-
Analysis of inhibitor binding in influenza virus neuraminidase
-
Smith BJ, Colman PM, Von Itzstein M, Danylec B, Varghese JN (2001) Analysis of inhibitor binding in influenza virus neuraminidase. Protein Sci 10: 689-96.
-
(2001)
Protein Sci
, vol.10
, pp. 689-696
-
-
Smith, B.J.1
Colman, P.M.2
Von Itzstein, M.3
Danylec, B.4
Varghese, J.N.5
-
28
-
-
0030037645
-
Structure of 4-chlorobenzoyl coenzyme A dehalogenase determined to 1.8 A resolution: An enzyme catalyst generated via adaptive mutation
-
Benning MM, Taylor KL, Liu RQ, Yang G, Xiang H, et al. (1996) Structure of 4-chlorobenzoyl coenzyme A dehalogenase determined to 1.8 A resolution: an enzyme catalyst generated via adaptive mutation. Biochemistry 35: 8103-9.
-
(1996)
Biochemistry
, vol.35
, pp. 8103-8109
-
-
Benning, M.M.1
Taylor, K.L.2
Liu, R.Q.3
Yang, G.4
Xiang, H.5
-
29
-
-
0034651691
-
Crystal structure of human sex hormone-binding globulin: Steroid transport by a laminin G-like domain
-
Grishkovskaya I, Avvakumov GV, Sklenar G, Dales D, Hammond GL, et al. (2000) Crystal structure of human sex hormone-binding globulin: steroid transport by a laminin G-like domain. EMBO J 19: 504-12.
-
(2000)
EMBO J
, vol.19
, pp. 504-512
-
-
Grishkovskaya, I.1
Avvakumov, G.V.2
Sklenar, G.3
Dales, D.4
Hammond, G.L.5
-
30
-
-
35348909085
-
Crystal structure of a family I.3 lipase from Pseudomonas sp. MIS38 in a closed conformation
-
Angkawidjaja C, You DJ, Matsumura H, Kuwahara K, Koga Y, et al. (2007) Crystal structure of a family I.3 lipase from Pseudomonas sp. MIS38 in a closed conformation. FEBS Lett 581: 5060-4.
-
(2007)
FEBS Lett
, vol.581
, pp. 5060-5064
-
-
Angkawidjaja, C.1
You, D.J.2
Matsumura, H.3
Kuwahara, K.4
Koga, Y.5
-
31
-
-
0032881610
-
Crystal structure of the EF-hand parvalbumin at atomic resolution (0.91 A) and at low temperature (100 K). Evidence for conformational multistates within the hydrophobic core
-
Declercq JP, Evrard C, Lamzin V, Parello J (1999) Crystal structure of the EF-hand parvalbumin at atomic resolution (0.91 A) and at low temperature (100 K). Evidence for conformational multistates within the hydrophobic core. Protein Sci 8: 2194-2204.
-
(1999)
Protein Sci
, vol.8
, pp. 2194-2204
-
-
Declercq, J.P.1
Evrard, C.2
Lamzin, V.3
Parello, J.4
-
32
-
-
34547793043
-
Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression
-
Lan F, Collins RE, De Cegli R, Alpatov R, Horton JR, et al. (2007) Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature 448: 718-22.
-
(2007)
Nature
, vol.448
, pp. 718-722
-
-
Lan, F.1
Collins, R.E.2
De Cegli, R.3
Alpatov, R.4
Horton, J.R.5
-
33
-
-
35448969842
-
Structure and specificity of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens
-
Liu D, Thomas PW, Momb J, Hoang QQ, Petsko GA, et al. (2007) Structure and specificity of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens. Biochemistry 46: 11789-99.
-
(2007)
Biochemistry
, vol.46
, pp. 11789-11799
-
-
Liu, D.1
Thomas, P.W.2
Momb, J.3
Hoang, Q.Q.4
Petsko, G.A.5
-
34
-
-
33747081033
-
Crystal structure of the apo-PerR-Zn protein from Bacillus subtilis
-
Traoré DA, El Ghazouani A, Ilango S, Dupuy J, Jacquamet L, et al. (2006) Crystal structure of the apo-PerR-Zn protein from Bacillus subtilis. Mol Microbiol 61: 1211-9.
-
(2006)
Mol Microbiol
, vol.61
, pp. 1211-1219
-
-
Traoré, D.A.1
El Ghazouani, A.2
Ilango, S.3
Dupuy, J.4
Jacquamet, L.5
-
35
-
-
0036045592
-
Crystal structure of the dinuclear zinc aminopeptidase PepV from Lactobacillus delbrueckii unravels its preference for dipeptides
-
Jozic D, Bourenkow G, Bartunik H, Scholze H, Dive V, et al. (2002) Crystal structure of the dinuclear zinc aminopeptidase PepV from Lactobacillus delbrueckii unravels its preference for dipeptides. Structure 10: 1097-106.
-
(2002)
Structure
, vol.10
, pp. 1097-1106
-
-
Jozic, D.1
Bourenkow, G.2
Bartunik, H.3
Scholze, H.4
Dive, V.5
-
37
-
-
0037402602
-
Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site
-
Teplyakov A, Obmolova G, Khil PP, Howard AJ, Camerini-Otero RD, et al. (2003) Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site. Proteins 51: 315-8.
-
(2003)
Proteins
, vol.51
, pp. 315-318
-
-
Teplyakov, A.1
Obmolova, G.2
Khil, P.P.3
Howard, A.J.4
Camerini-Otero, R.D.5
-
38
-
-
37549011426
-
A novel structural fold in polysaccharide lyases: Bacillus subtilis family 11 rhamnogalacturonan lyase YesW with an eight-bladed beta-propeller
-
Ochiai A, Itoh T, Maruyama Y, Kawamata A, Mikami B, et al. (2007) A novel structural fold in polysaccharide lyases: Bacillus subtilis family 11 rhamnogalacturonan lyase YesW with an eight-bladed beta-propeller. J Biol Chem 282: 37134-45.
-
(2007)
J Biol Chem
, vol.282
, pp. 37134-37145
-
-
Ochiai, A.1
Itoh, T.2
Maruyama, Y.3
Kawamata, A.4
Mikami, B.5
-
39
-
-
0034124849
-
Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase
-
Sankaranarayanan R, Dock-Bregeon AC, Rees B, Bovee M, Caillet J, et al. (2000) Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase. Nat Struct Biol 7: 461-5.
-
(2000)
Nat Struct Biol
, vol.7
, pp. 461-465
-
-
Sankaranarayanan, R.1
Dock-Bregeon, A.C.2
Rees, B.3
Bovee, M.4
Caillet, J.5
-
40
-
-
21444449107
-
Structure and function of carbonic anhydrases from Mycobacterium tuberculosis
-
Covarrubias S, Larsson AM, Högbom M, Lindberg J, Bergfors T, et al. (2005) Structure and function of carbonic anhydrases from Mycobacterium tuberculosis. J Biol Chem 280: 18782-9.
-
(2005)
J Biol Chem
, vol.280
, pp. 18782-18789
-
-
Covarrubias, S.1
Larsson, A.M.2
Högbom, M.3
Lindberg, J.4
Bergfors, T.5
-
41
-
-
0035342450
-
Residue frequencies and pairing preferences at protein-protein interfaces
-
Glaser F, Steinberg DM, Vakser IA, Ben-Tal N (2001) Residue frequencies and pairing preferences at protein-protein interfaces. Proteins 43: 89-102.
-
(2001)
Proteins
, vol.43
, pp. 89-102
-
-
Glaser, F.1
Steinberg, D.M.2
Vakser, I.A.3
Ben-Tal, N.4
-
42
-
-
26444568633
-
Statistical analysis of predominantly transient protein-protein interfaces
-
Ansari S, Helms V (2005) Statistical analysis of predominantly transient protein-protein interfaces. Proteins 61: 344-55.
-
(2005)
Proteins
, vol.61
, pp. 344-355
-
-
Ansari, S.1
Helms, V.2
-
43
-
-
38349100452
-
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
-
Brylinski M, Skolnick J (2008) A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci U S A 105: 129-34.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 129-134
-
-
Brylinski, M.1
Skolnick, J.2
-
44
-
-
33750029942
-
LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation
-
Huang B, Schroeder M (2006) LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol 24;6: 19.
-
(2006)
BMC Struct Biol
, vol.24
, Issue.6
, pp. 19
-
-
Huang, B.1
Schroeder, M.2
-
45
-
-
0031370977
-
LIGSITE: Automatic and efficient detection of potential small molecule-binding sites in proteins
-
Hendlich M, Rippmann F, Barnickel G (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graph Model 15(6): 359-363.
-
(1997)
J Mol Graph Model
, vol.15
, Issue.6
, pp. 359-363
-
-
Hendlich, M.1
Rippmann, F.2
Barnickel, G.3
|