-
1
-
-
0344083733
-
Enzymes
-
Anderson, S., Fox, J Eds.; Worth Publishers, Inc.: New York
-
Lehninger, A. L. Enzymes. In Principles of Biochemistry; Anderson, S., Fox, J., Eds.; Worth Publishers, Inc.: New York, 1982.
-
(1982)
Principles of Biochemistry
-
-
Lehninger, A.L.1
Anderson, S.2
Fox, J.3
-
2
-
-
0031776823
-
Molecular shape comparisons in searches for active sites and functional similarity
-
Rosen, M.; Lin, S. L.; Wolfson, H.; Nussinov, R. Molecular shape comparisons in searches for active sites and functional similarity Protein Eng. 1998, 11, 263-277
-
(1998)
Protein Eng.
, vol.11
, pp. 263-277
-
-
Rosen, M.1
Lin, S.L.2
Wolfson, H.3
Nussinov, R.4
-
3
-
-
0030691197
-
Structure of Haemophilus influenzae Fe(+3)-binding protein reveals convergent evolution within a superfamily
-
Bruns, C. M.; Nowalk, A. J.; Arvai, A. S.; McTigue, M. A.; Vaughan, K. G.; Mietzner, T. A.; McRee, D. E. Structure of Haemophilus influenzae Fe(+3)-binding protein reveals convergent evolution within a superfamily Nat. Struct. Biol. 1997, 4, 919-924
-
(1997)
Nat. Struct. Biol.
, vol.4
, pp. 919-924
-
-
Bruns, C.M.1
Nowalk, A.J.2
Arvai, A.S.3
McTigue, M.A.4
Vaughan, K.G.5
Mietzner, T.A.6
McRee, D.E.7
-
4
-
-
0036890333
-
Protein reconstitution and 3D domain swapping
-
Hakansson, M.; Linse, S. Protein reconstitution and 3D domain swapping Curr. Protein Pept. Sci. 2002, 3, 629-642
-
(2002)
Curr. Protein Pept. Sci.
, vol.3
, pp. 629-642
-
-
Hakansson, M.1
Linse, S.2
-
5
-
-
0028865843
-
3D domain swapping: A mechanism for oligomer assembly
-
Bennett, M. J.; Schlunegger, M. P.; Eisenberg, D. 3D domain swapping: a mechanism for oligomer assembly Protein Sci. 1995, 4, 2455-2468
-
(1995)
Protein Sci.
, vol.4
, pp. 2455-2468
-
-
Bennett, M.J.1
Schlunegger, M.P.2
Eisenberg, D.3
-
6
-
-
0033514409
-
Trimeric domain-swapped barnase
-
Zegers, I.; Deswarte, J.; Wyns, L. Trimeric domain-swapped barnase Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 818-822
-
(1999)
Proc. Natl. Acad. Sci. U.S.A.
, vol.96
, pp. 818-822
-
-
Zegers, I.1
Deswarte, J.2
Wyns, L.3
-
7
-
-
65249117514
-
Identifying and characterizing binding sites and assessing druggability
-
Halgren, T. A. Identifying and characterizing binding sites and assessing druggability J. Chem. Inf. Model. 2009, 49, 377-389
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 377-389
-
-
Halgren, T.A.1
-
8
-
-
33846155913
-
Structure-based maximal affinity model predicts small-molecule druggability
-
Cheng, A. C.; Coleman, R. G.; Smyth, K. T.; Cao, Q.; Soulard, P.; Caffrey, D. R.; Salzberg, A. C.; Huang, E. S. Structure-based maximal affinity model predicts small-molecule druggability Nat. Biotechnol. 2007, 25, 71-75
-
(2007)
Nat. Biotechnol.
, vol.25
, pp. 71-75
-
-
Cheng, A.C.1
Coleman, R.G.2
Smyth, K.T.3
Cao, Q.4
Soulard, P.5
Caffrey, D.R.6
Salzberg, A.C.7
Huang, E.S.8
-
9
-
-
37249021821
-
Identification of the druggable concavity in homology models using the PLB index
-
Soga, S.; Shirai, H.; Kobori, M.; Hirayama, N. Identification of the druggable concavity in homology models using the PLB index J. Chem. Inf. Model. 2007, 47, 2287-2292
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 2287-2292
-
-
Soga, S.1
Shirai, H.2
Kobori, M.3
Hirayama, N.4
-
10
-
-
34247265436
-
Use of amino acid composition to predict ligand-binding sites
-
Soga, S.; Shirai, H.; Kobori, M.; Hirayama, N.?Use of amino acid composition to predict ligand-binding sites J. Chem. Inf. Model. 2007, 47, 400-406
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 400-406
-
-
Soga, S.1
Shirai, H.2
Kobori, M.3
Hirayama, N.4
-
11
-
-
0027967593
-
A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures
-
Artymiuk, P. J.; Poirrette, A. R.; Grindley, H. M.; Rice, D. W.; Willett, P. A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures J. Mol. Biol. 1994, 243, 327-344
-
(1994)
J. Mol. Biol.
, vol.243
, pp. 327-344
-
-
Artymiuk, P.J.1
Poirrette, A.R.2
Grindley, H.M.3
Rice, D.W.4
Willett, P.5
-
12
-
-
77952849162
-
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment
-
Konc, J.; JaneNi?, D. ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment Bioinformatics 2010, 26, 1160-1168
-
(2010)
Bioinformatics
, vol.26
, pp. 1160-1168
-
-
Konc, J.1
Janei, D.2
-
13
-
-
0032568859
-
Detection of protein three-dimensional side-chain patterns: New examples of convergent evolution
-
Russell, R. B. Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution J. Mol. Biol. 1998, 279, 1211-1227
-
(1998)
J. Mol. Biol.
, vol.279
, pp. 1211-1227
-
-
Russell, R.B.1
-
14
-
-
73349097886
-
Rapid comparison of protein binding site surfaces with property encoded shape distributions
-
Das, S.; Kokardekar, A.; Breneman, C. M. Rapid comparison of protein binding site surfaces with property encoded shape distributions J. Chem. Inf. Model. 2009, 49, 2863-2872
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 2863-2872
-
-
Das, S.1
Kokardekar, A.2
Breneman, C.M.3
-
15
-
-
75749155406
-
Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites
-
Weill, N.; Rognan, D. Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites J. Chem. Inf. Model. 2010, 50, 123-135
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 123-135
-
-
Weill, N.1
Rognan, D.2
-
16
-
-
33947420139
-
Shape variation in protein binding pockets and their ligands
-
Kahraman, A.; Morris, R. J.; Laskowski, R. A.; Thornton, J. M. Shape variation in protein binding pockets and their ligands J. Mol. Biol. 2007, 368, 283-301
-
(2007)
J. Mol. Biol.
, vol.368
, pp. 283-301
-
-
Kahraman, A.1
Morris, R.J.2
Laskowski, R.A.3
Thornton, J.M.4
-
17
-
-
77950423796
-
A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: Application to ligand prediction
-
Hoffmann, B.; Zaslavskiy, M.; Vert, J. P.; Stoven, V. A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction BMC Bioinf. 2010, 11, 99
-
(2010)
BMC Bioinf.
, vol.11
, pp. 99
-
-
Hoffmann, B.1
Zaslavskiy, M.2
Vert, J.P.3
Stoven, V.4
-
18
-
-
44349119204
-
A simple and fuzzy method to align and compare druggable ligand-binding sites
-
Schalon, C.; Surgand, J. S.; Kellenberger, E.; Rognan, D. A simple and fuzzy method to align and compare druggable ligand-binding sites Proteins 2008, 71, 1755-1778
-
(2008)
Proteins
, vol.71
, pp. 1755-1778
-
-
Schalon, C.1
Surgand, J.S.2
Kellenberger, E.3
Rognan, D.4
-
19
-
-
77951987753
-
Protein pockets: Inventory, shape, and comparison
-
Coleman, R. G.; Sharp, K. A. Protein pockets: inventory, shape, and comparison J. Chem. Inf. Model. 2010, 50, 589-603
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 589-603
-
-
Coleman, R.G.1
Sharp, K.A.2
-
20
-
-
0033557381
-
Finding local structural similarities among families of unrelated protein structures: A generic non-linear alignment algorithm
-
Lehtonen, J. V.; Denessiouk, K.; May, A. C.; Johnson, M. S. Finding local structural similarities among families of unrelated protein structures: a generic non-?inear alignment algorithm Proteins 1999, 34, 341-355
-
(1999)
Proteins
, vol.34
, pp. 341-355
-
-
Lehtonen, J.V.1
Denessiouk, K.2
May, A.C.3
Johnson, M.S.4
-
21
-
-
3543053391
-
Efficient similarity search in protein structure databases by k-clique hashing
-
Weskamp, N.; Kuhn, D.; Hullermeier, E.; Klebe, G. Efficient similarity search in protein structure databases by k-clique hashing Bioinformatics 2004, 20, 1522-1526
-
(2004)
Bioinformatics
, vol.20
, pp. 1522-1526
-
-
Weskamp, N.1
Kuhn, D.2
Hullermeier, E.3
Klebe, G.4
-
22
-
-
33646254603
-
A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships
-
Gold, N. D.; Jackson, R. M. A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships J. Chem. Inf. Model. 2006, 46, 736-742
-
(2006)
J. Chem. Inf. Model.
, vol.46
, pp. 736-742
-
-
Gold, N.D.1
Jackson, R.M.2
-
23
-
-
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. An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins J. Biomol. Struct. Dyn. 1992, 9, 769-789
-
(1992)
J. Biomol. Struct. Dyn.
, vol.9
, pp. 769-789
-
-
Fischer, D.1
Bachar, O.2
Nussinov, R.3
Wolfson, H.4
-
24
-
-
0037661398
-
A new bioinformatic approach to detect common 3D sites in protein structures
-
Jambon, M.; Imberty, A.; Deleage, G.; Geourjon, C. A new bioinformatic approach to detect common 3D sites in protein structures Proteins 2003, 52, 137-145
-
(2003)
Proteins
, vol.52
, pp. 137-145
-
-
Jambon, M.1
Imberty, A.2
Deleage, G.3
Geourjon, C.4
-
25
-
-
0041842509
-
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site
-
Kinoshita, K.; Nakamura, H. Identification of protein biochemical functions by similarity search using the molecular surface database eF-site Protein Sci. 2003, 12, 1589-1595
-
(2003)
Protein Sci.
, vol.12
, pp. 1589-1595
-
-
Kinoshita, K.1
Nakamura, H.2
-
26
-
-
33644873706
-
The RCSB PDB information portal for structural genomics
-
Kouranov, A.; Xie, L.; de la Cruz, J.; Chen, L.; Westbrook, J.; Bourne, P. E.; Berman, H. M. The RCSB PDB information portal for structural genomics Nucleic Acids Res. 2006, 34, D302-305
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 302-305
-
-
Kouranov, A.1
Xie, L.2
De La Cruz, J.3
Chen, L.4
Westbrook, J.5
Bourne, P.E.6
Berman, H.M.7
-
27
-
-
0027318317
-
An empirical energy function for threading protein sequence through the folding motif
-
Bryant, S. H.; Lawrence, C. E. An empirical energy function for threading protein sequence through the folding motif Proteins 1993, 16, 92-112
-
(1993)
Proteins
, vol.16
, pp. 92-112
-
-
Bryant, S.H.1
Lawrence, C.E.2
-
28
-
-
0027062943
-
Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds
-
Overington, J.; Donnelly, D.; Johnson, M. S.; Sali, A.; Blundell, T. L. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds Protein Sci. 1992, 1, 216-226
-
(1992)
Protein Sci.
, vol.1
, pp. 216-226
-
-
Overington, J.1
Donnelly, D.2
Johnson, M.S.3
Sali, A.4
Blundell, T.L.5
-
29
-
-
0032534026
-
Sequence and structure conservation in a protein core
-
Rodionov, M. A.; Blundell, T. L. Sequence and structure conservation in a protein core Proteins 1998, 33, 358-366
-
(1998)
Proteins
, vol.33
, pp. 358-366
-
-
Rodionov, M.A.1
Blundell, T.L.2
-
30
-
-
0036139188
-
Probabilistic sampling of protein conformations: New hope for brute force
-
Feldman, H. J.; Hogue, C. W. Probabilistic sampling of protein conformations: new hope for brute force Proteins 2002, 46, 8-23
-
(2002)
Proteins
, vol.46
, pp. 8-23
-
-
Feldman, H.J.1
Hogue, C.W.2
-
31
-
-
17844363992
-
A random polymer model of the statistical significance of structure alignment
-
Jia, Y.; Dewey, T. G. A random polymer model of the statistical significance of structure alignment J. Comput. Biol. 2005, 12, 298-313
-
(2005)
J. Comput. Biol.
, vol.12
, pp. 298-313
-
-
Jia, Y.1
Dewey, T.G.2
-
32
-
-
58149203231
-
InterPro: The integrative protein signature database
-
Hunter, S.; Apweiler, R.; Attwood, T. K.; Bairoch, A.; Bateman, A.; Binns, D.; Bork, P.; Das, U.; Daugherty, L.; Duquenne, L.; Finn, R. D.; Gough, J.; Haft, D.; Hulo, N.; Kahn, D.; Kelly, E.; Laugraud, A.; Letunic, I.; Lonsdale, D.; Lopez, R.; Madera, M.; Maslen, J.; McAnulla, C.; McDowall, J.; Mistry, J.; Mitchell, A.; Mulder, N.; Natale, D.; Orengo, C.; Quinn, A. F.; Selengut, J. D.; Sigrist, C. J.; Thimma, M.; Thomas, P. D.; Valentin, F.; Wilson, D.; Wu, C. H.; Yeats, C. InterPro: the integrative protein signature database Nucleic Acids Res. 2009, 37, D211-215
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 211-215
-
-
Hunter, S.1
Apweiler, R.2
Attwood, T.K.3
Bairoch, A.4
Bateman, A.5
Binns, D.6
Bork, P.7
Das, U.8
Daugherty, L.9
Duquenne, L.10
Finn, R.D.11
Gough, J.12
Haft, D.13
Hulo, N.14
Kahn, D.15
Kelly, E.16
Laugraud, A.17
Letunic, I.18
Lonsdale, D.19
Lopez, R.20
Madera, M.21
Maslen, J.22
McAnulla, C.23
McDowall, J.24
Mistry, J.25
Mitchell, A.26
Mulder, N.27
Natale, D.28
Orengo, C.29
Quinn, A.F.30
Selengut, J.D.31
Sigrist, C.J.32
Thimma, M.33
Thomas, P.D.34
Valentin, F.35
Wilson, D.36
Wu, C.H.37
Yeats, C.38
more..
-
33
-
-
0034800374
-
InterProScan - An integration platform for the signature-recognition methods in InterPro
-
Zdobnov, E. M.; Apweiler, R. InterProScan - an integration platform for the signature-recognition methods in InterPro Bioinformatics.. 2001, 17, 847-848
-
(2001)
Bioinformatics.
, vol.17
, pp. 847-848
-
-
Zdobnov, E.M.1
Apweiler, R.2
-
34
-
-
0004313709
-
-
version 2009.10; Chemical Computing Group: Montreal, Canada.
-
Molecular Operating Environment, version 2009.10; Chemical Computing Group: Montreal, Canada, 2009.
-
(2009)
Molecular Operating Environment
-
-
-
35
-
-
77956046582
-
-
version 2010.02; Chemical Computing Group: Montreal, Canada.
-
PSILO, version 2010.02; Chemical Computing Group: Montreal, Canada, 2010.
-
PSILO
, pp. 2010
-
-
-
36
-
-
35949003882
-
Virus-encoded aminoacyl-tRNA synthetases: Structural and functional characterization of mimivirus TyrRS and MetRS
-
Abergel, C.; Rudinger-Thirion, J.; Giege, R.; Claverie, J. M. Virus-encoded aminoacyl-tRNA synthetases: structural and functional characterization of mimivirus TyrRS and MetRS J. Virol. 2007, 81, 12406-12417
-
(2007)
J. Virol.
, vol.81
, pp. 12406-12417
-
-
Abergel, C.1
Rudinger-Thirion, J.2
Giege, R.3
Claverie, J.M.4
-
37
-
-
0029643793
-
Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase
-
Doublie, S.; Bricogne, G.; Gilmore, C.; Carter, C. W., Jr. Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase Structure 1995, 3, 17-31
-
(1995)
Structure
, vol.3
, pp. 17-31
-
-
Doublie, S.1
Bricogne, G.2
Gilmore, C.3
Carter Jr., C.W.4
-
38
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner, M.; Ball, C. A.; Blake, J. A.; Botstein, D.; Butler, H.; Cherry, J. M.; Davis, A. P.; Dolinski, K.; Dwight, S. S.; Eppig, J. T.; Harris, M. A.; Hill, D. P.; Issel-Tarver, L.; Kasarskis, A.; Lewis, S.; Matese, J. C.; Richardson, J. E.; Ringwald, M.; Rubin, G. M.; Sherlock, G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium Nat. Genet. 2000, 25, 25-29
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
39
-
-
33845925764
-
Two crystal structures of the isochorismate pyruvate lyase from Pseudomonas aeruginosa
-
Zaitseva, J.; Lu, J.; O?echoski, K. L.; Lamb, A. L. Two crystal structures of the isochorismate pyruvate lyase from Pseudomonas aeruginosa J. Biol. Chem. 2006, 281, 33441-33449
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 33441-33449
-
-
Zaitseva, J.1
Lu, J.2
Olechoski, K.L.3
Lamb, A.L.4
-
40
-
-
43349106468
-
Using Dali for structural comparison of proteins
-
Chapter 5, Unit 5.5
-
Holm, L.; Kaariainen, S.; Wilton, C.; Plewczynski, D. Using Dali for structural comparison of proteins Curr. Protoc. Bioinformatics. 2006, Chapter 5, Unit 5.5
-
(2006)
Curr. Protoc. Bioinformatics.
-
-
Holm, L.1
Kaariainen, S.2
Wilton, C.3
Plewczynski, D.4
-
41
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A. G.; Brenner, S. E.; Hubbard, T.; Chothia, C. SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 1995, 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
-
42
-
-
33744935012
-
From the similarity analysis of protein cavities to the functional classification of protein families using cavbase
-
Kuhn, D.; Weskamp, N.; Schmitt, S.; Hullermeier, E.; Klebe, G. From the similarity analysis of protein cavities to the functional classification of protein families using cavbase J. Mol. Biol. 2006, 359, 1023-1044
-
(2006)
J. Mol. Biol.
, vol.359
, pp. 1023-1044
-
-
Kuhn, D.1
Weskamp, N.2
Schmitt, S.3
Hullermeier, E.4
Klebe, G.5
-
43
-
-
65249157397
-
Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures
-
Labute, P. Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures Proteins 2009, 75, 187-205
-
(2009)
Proteins
, vol.75
, pp. 187-205
-
-
Labute, P.1
-
44
-
-
84944178665
-
Hierarchical grouping to optimize an objective function
-
Ward, J. H. J. Hierarchical grouping to optimize an objective function J. Am. Stat. Assoc. 1963, 58, 236-244
-
(1963)
J. Am. Stat. Assoc.
, vol.58
, pp. 236-244
-
-
Ward, J.H.J.1
-
45
-
-
0032564339
-
Structural basis for efficient phosphorylation of 3?-azidothymidine monophosphate by Escherichia coli thymidylate kinase
-
Lavie, A.; Ostermann, N.; Brundiers, R.; Goody, R. S.; Reinstein, J.; Konrad, M.; Schlichting, I. Structural basis for efficient phosphorylation of 3?-azidothymidine monophosphate by Escherichia coli thymidylate kinase Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 14045-14050
-
(1998)
Proc. Natl. Acad. Sci. U.S.A.
, vol.95
, pp. 14045-14050
-
-
Lavie, A.1
Ostermann, N.2
Brundiers, R.3
Goody, R.S.4
Reinstein, J.5
Konrad, M.6
Schlichting, I.7
-
46
-
-
0030310298
-
On the definition and the construction of pockets in macromolecules
-
Edelsbrunner, H.; Facello, M.; Liang, J. On the definition and the construction of pockets in macromolecules Pac Symp Biocomput. 96 1996, 272-87
-
(1996)
Pac Symp Biocomput. 96
, pp. 272-287
-
-
Edelsbrunner, H.1
Facello, M.2
Liang, J.3
|