-
2
-
-
33947278347
-
Towards fully automated structure-based function prediction in structural genomics: A case study
-
Watson JD, Sanderson S, Ezersky A, Savchenko A, Edwards A, et al. (2007) Towards fully automated structure-based function prediction in structural genomics: a case study. J Mol Biol 367: 1511-22.
-
(2007)
J Mol Biol
, vol.367
, pp. 1511-1522
-
-
Watson, J.D.1
Sanderson, S.2
Ezersky, A.3
Savchenko, A.4
Edwards, A.5
-
3
-
-
0033824470
-
DaliLite workbench for protein structure comparison
-
Holm L, Park J (2000) DaliLite workbench for protein structure comparison. Bioinformatics 16: 566-567.
-
(2000)
Bioinformatics
, vol.16
, pp. 566-567
-
-
Holm, L.1
Park, J.2
-
4
-
-
0028838717
-
Threading a database of protein cores
-
Madej T, Gibrat JF, Bryant SH (1995) Threading a database of protein cores. Proteins 23: 356-369.
-
(1995)
Proteins
, vol.23
, pp. 356-369
-
-
Madej, T.1
Gibrat, J.F.2
Bryant, S.H.3
-
5
-
-
13444307044
-
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
-
Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60: 2256-68.
-
(2004)
Acta Crystallogr D Biol Crystallogr
, vol.60
, pp. 2256-2268
-
-
Krissinel, E.1
Henrick, K.2
-
6
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov IN, Bourne PE (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 11: 739-47.
-
(1998)
Protein Eng
, vol.11
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
7
-
-
0033613813
-
Recognition of spatial motifs in protein structures
-
Kleywegt GJ (1999) Recognition of spatial motifs in protein structures. J Mol Biol 285: 1887-97.
-
(1999)
J Mol Biol
, vol.285
, pp. 1887-1897
-
-
Kleywegt, G.J.1
-
8
-
-
33947201695
-
Query3d: A new method for highthroughput analysis of functional residues in protein structures
-
Ausiello G, Via A, Helmer-Citterich M (2005) Query3d: a new method for highthroughput analysis of functional residues in protein structures. BMC Bioinformatics 6 Suppl 4: S5.
-
(2005)
BMC Bioinformatics
, vol.6 SUPPL. 4
-
-
Ausiello, G.1
Via, A.2
Helmer-Citterich, M.3
-
9
-
-
0041620372
-
Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures
-
Stark A, Russell RB (2003) Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res 31: 3341-4.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3341-3344
-
-
Stark, A.1
Russell, R.B.2
-
11
-
-
0036406643
-
A new method to detect related function among proteins independent of sequence and fold homology
-
Schmitt S, Kuhn D, Klebe G (2002) A new method to detect related function among proteins independent of sequence and fold homology. J Mol Biol 323: 387-406.
-
(2002)
J Mol Biol
, vol.323
, pp. 387-406
-
-
Schmitt, S.1
Kuhn, D.2
Klebe, G.3
-
12
-
-
0041842509
-
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site
-
Kinoshita K, Nakamura H (2003) Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci 12: 1589-1595.
-
(2003)
Protein Sci
, vol.12
, pp. 1589-1595
-
-
Kinoshita, K.1
Nakamura, H.2
-
13
-
-
0026345280
-
An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins
-
Fischer D, Bachar O, Nussinov R, Wolfson H (1992) An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins. J Biomol Struct Dyn 9: 769-89.
-
(1992)
J Biomol Struct Dyn
, vol.9
, pp. 769-789
-
-
Fischer, D.1
Bachar, O.2
Nussinov, R.3
Wolfson, H.4
-
14
-
-
0031697713
-
A geometric algorithm to find small but highly similar 3D substructures in proteins
-
Pennec X, Ayache N (1998) A geometric algorithm to find small but highly similar 3D substructures in proteins. Bioinformatics 14: 516-22.
-
(1998)
Bioinformatics
, vol.14
, pp. 516-522
-
-
Pennec, X.1
Ayache, N.2
-
15
-
-
2442614144
-
Recognition of functional sites in protein structures
-
Shulman-Peleg A, Nussinov R, Wolfson HJ (2004) Recognition of functional sites in protein structures. J Mol Biol 339: 607-633.
-
(2004)
J Mol Biol
, vol.339
, pp. 607-633
-
-
Shulman-Peleg, A.1
Nussinov, R.2
Wolfson, H.J.3
-
16
-
-
3242889058
-
ProteMiner-SSM: A web server for efficient analysis of similar protein tertiary substructures
-
Chang DT, Chen C, Chung W, Oyang Y, Juan H, et al. (2004) ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures. Nucleic Acids Res 32: W76-82.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Chang, D.T.1
Chen, C.2
Chung, W.3
Oyang, Y.4
Juan, H.5
-
18
-
-
0348129526
-
The ASTRAL Compendium in 2004
-
Chandonia J, Hon G, Walker NS, Lo Conte L, Koehl P, et al. (2004) The ASTRAL Compendium in 2004. Nucleic Acids Res 32: D189-192.
-
(2004)
Nucleic Acids Res
, vol.32 D
, pp. 189-192
-
-
Chandonia, J.1
Hon, G.2
Walker, N.S.3
Lo Conte, L.4
Koehl, P.5
-
19
-
-
0032510685
-
Snapshot of a phosphorylated substrate intermediate by kinetic crystallography
-
Käck H, Gibson KJ, Lindqvist Y, Schneider G (1998) Snapshot of a phosphorylated substrate intermediate by kinetic crystallography. Proc Natl Acad Sci U S A 95: 5495-500.
-
(1998)
Proc Natl Acad Sci U S A
, vol.95
, pp. 5495-5500
-
-
Käck, H.1
Gibson, K.J.2
Lindqvist, Y.3
Schneider, G.4
-
20
-
-
18744385215
-
Yeast Damino acid oxidase: Structural basis of its catalytic properties
-
Pollegioni L, Diederichs K, Molla G, Umhau S, Welte W, et al. (2002) Yeast Damino acid oxidase: structural basis of its catalytic properties. J Mol Biol 324: 535-46.
-
(2002)
J Mol Biol
, vol.324
, pp. 535-546
-
-
Pollegioni, L.1
Diederichs, K.2
Molla, G.3
Umhau, S.4
Welte, W.5
-
21
-
-
0036293842
-
A novel main-chain anion-binding site in proteins: The nest. A particular combination of phi,psi values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions
-
Watson JD, Milner-White EJ (2002) A novel main-chain anion-binding site in proteins: the nest. A particular combination of phi,psi values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions. J Mol Biol 315: 171-182.
-
(2002)
J Mol Biol
, vol.315
, pp. 171-182
-
-
Watson, J.D.1
Milner-White, E.J.2
-
22
-
-
36148955400
-
Structures of human monoamine oxidase B complexes with selective noncovalent inhibitors: Safinamide and coumarin analogs
-
Binda C, Wang J, Pisani L, Caccia C, Carotti A, et al. (2007) Structures of human monoamine oxidase B complexes with selective noncovalent inhibitors: safinamide and coumarin analogs. J Med Chem 50: 5848-52.
-
(2007)
J Med Chem
, vol.50
, pp. 5848-5852
-
-
Binda, C.1
Wang, J.2
Pisani, L.3
Caccia, C.4
Carotti, A.5
-
24
-
-
12944300317
-
Binding of nucleotides by proteins
-
Schulz G (1992) Binding of nucleotides by proteins. Curr Opin Struct Biol 2: 61-67.
-
(1992)
Curr Opin Struct Biol
, vol.2
, pp. 61-67
-
-
Schulz, G.1
-
25
-
-
0142154391
-
''Acceptor-donor-acceptor'' motifs recognize the Watson-Crick, Hoogsteen and Sugar ''donor-acceptor-donor'' edges of adenine and adenosine-containing ligands
-
Denessiouk KA, Johnson MS (2003) ''Acceptor-donor-acceptor'' motifs recognize the Watson-Crick, Hoogsteen and Sugar ''donor-acceptor-donor'' edges of adenine and adenosine-containing ligands. J Mol Biol 333: 1025-1043.
-
(2003)
J Mol Biol
, vol.333
, pp. 1025-1043
-
-
Denessiouk, K.A.1
Johnson, M.S.2
-
26
-
-
7744244599
-
Recent Advances in Zinc Enzymology
-
Lipscomb WN, Sträter N (1996) Recent Advances in Zinc Enzymology. Chem Rev 96: 2375-2434.
-
(1996)
Chem Rev
, vol.96
, pp. 2375-2434
-
-
Lipscomb, W.N.1
Sträter, N.2
-
28
-
-
22444442099
-
Insights into pneumococcal pathogenesis from the crystal structure of the modular teichoic acid phosphorylcholine esterase Pce
-
Hermoso JA, Lagartera L, González A, Stelter M, Garciá P, et al. (2005) Insights into pneumococcal pathogenesis from the crystal structure of the modular teichoic acid phosphorylcholine esterase Pce. Nat Struct Mol Biol 12: 533-8.
-
(2005)
Nat Struct Mol Biol
, vol.12
, pp. 533-538
-
-
Hermoso, J.A.1
Lagartera, L.2
González, A.3
Stelter, M.4
Garciá, P.5
Et al.6
-
29
-
-
33846215584
-
Serendipitous discovery of novel bacterial methionine aminopeptidase inhibitors
-
Evdokimov AG, Pokross M, Walter RL, Mekel M, Barnett BL, et al. (2007) Serendipitous discovery of novel bacterial methionine aminopeptidase inhibitors. Proteins 66: 538-46.
-
(2007)
Proteins
, vol.66
, pp. 538-546
-
-
Evdokimov, A.G.1
Pokross, M.2
Walter, R.L.3
Mekel, M.4
Barnett, B.L.5
-
30
-
-
0033539594
-
Insights into the mechanism of Escherichia coli methionine aminopeptidase from the structural analysis of reaction products and phosphorus-based transition-state analogues
-
Lowther WT, Zhang Y, Sampson PB, Honek JF, Matthews BW (1999) Insights into the mechanism of Escherichia coli methionine aminopeptidase from the structural analysis of reaction products and phosphorus-based transition-state analogues. Biochemistry 38: 14810-9.
-
(1999)
Biochemistry
, vol.38
, pp. 14810-14819
-
-
Lowther, W.T.1
Zhang, Y.2
Sampson, P.B.3
Honek, J.F.4
Matthews, B.W.5
-
31
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247: 536-540.
-
(1995)
J Mol Biol
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
32
-
-
67649670256
-
Serine racemase with catalytically active lysinoalanyl residue
-
Yamauchi T, Goto M, Wu H, Uo T, Yoshimura T, et al. (2009) Serine racemase with catalytically active lysinoalanyl residue. J Biochem 145: 421-4.
-
(2009)
J Biochem
, vol.145
, pp. 421-424
-
-
Yamauchi, T.1
Goto, M.2
Wu, H.3
Uo, T.4
Yoshimura, T.5
-
33
-
-
0037013223
-
Crystal structure of argininosuccinate synthetase from Thermus thermophilus HB8. Structural basis for the catalytic action
-
Goto M, Nakajima Y, Hirotsu K (2002) Crystal structure of argininosuccinate synthetase from Thermus thermophilus HB8. Structural basis for the catalytic action. J Biol Chem 277: 15890-6.
-
(2002)
J Biol Chem
, vol.277
, pp. 15890-15896
-
-
Goto, M.1
Nakajima, Y.2
Hirotsu, K.3
-
34
-
-
75549090603
-
The Pfam protein families database
-
Finn RD, Mistry J, Tate J, Coggill P, Heger A, et al. (2010) The Pfam protein families database. Nucleic Acids Res 38: D211-222.
-
(2010)
Nucleic Acids Res
, vol.38 D
, pp. 211-222
-
-
Finn, R.D.1
Mistry, J.2
Tate, J.3
Coggill, P.4
Heger, A.5
-
35
-
-
0037424601
-
A model for statistical significance of local similarities in structure
-
Stark A, Sunyaev S, Russell RB (2003) A model for statistical significance of local similarities in structure. J Mol Biol 326: 1307-16.
-
(2003)
J Mol Biol
, vol.326
, pp. 1307-1316
-
-
Stark, A.1
Sunyaev, S.2
Russell, R.B.3
-
36
-
-
36448948641
-
The Poisson Index: A new probabilistic model for protein ligand binding site similarity
-
Davies JR, Jackson RM, Mardia KV, Taylor CC (2007) The Poisson Index: a new probabilistic model for protein ligand binding site similarity. Bioinformatics 23: 3001-8.
-
(2007)
Bioinformatics
, vol.23
, pp. 3001-3008
-
-
Davies, J.R.1
Jackson, R.M.2
Mardia, K.V.3
Taylor, C.C.4
-
37
-
-
0035888284
-
Universal similarity measure for comparing protein structures
-
Betancourt MR, Skolnick J (2001) Universal similarity measure for comparing protein structures. Biopolymers 59: 305-9.
-
(2001)
Biopolymers
, vol.59
, pp. 305-309
-
-
Betancourt, M.R.1
Skolnick, J.2
-
38
-
-
66349119013
-
A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery
-
Xie L, Xie L, Bourne PE (2009) A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. Bioinformatics 25: i305-12.
-
(2009)
Bioinformatics
, vol.25
-
-
Xie, L.1
Xie, L.2
Bourne, P.E.3
-
39
-
-
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
|