-
1
-
-
0017309766
-
Structural patterns in globular proteins
-
Levitt M, Chothia C (1976) Structural patterns in globular proteins. Nature 261(5561): 552-558
-
(1976)
Nature
, vol.261
, Issue.5561
, pp. 552-558
-
-
Levitt, M.1
Chothia, C.2
-
3
-
-
34347383961
-
Evolutionary transitions in protein fold space
-
Taylor WR (2007) Evolutionary transitions in protein fold space. Curr Opin Struct Biol 17(3):354-361
-
(2007)
Curr Opin Struct Biol
, vol.17
, Issue.3
, pp. 354-361
-
-
Taylor, W.R.1
-
4
-
-
0033954256
-
The protein data bank
-
Berman HM, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28(1):235-242
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
-
5
-
-
33744805069
-
Protein structure comparison: Implications for the nature of ?fold space', and structure and function prediction
-
Kolodny R, PetreyD,Honig B (2006) Protein structure comparison: Implications for the nature of ?fold space', and structure and function prediction. Curr Opin Struct Biol 16(3):393-398
-
(2006)
Curr Opin Struct Biol
, vol.16
, Issue.3
, pp. 393-398
-
-
Kolodny, R.1
Petrey, D.2
Honig, B.3
-
6
-
-
63549151459
-
Cross-over between discrete and continuous protein structure space: Insights into automatic classification and networks of protein structures
-
Pascual-García A, Abia D, Ortiz ÁR, Bastolla U (2009) Cross-over between discrete and continuous protein structure space: Insights into automatic classification and networks of protein structures. PLOS Comput Biol 5(3):e1000331
-
(2009)
PLOS Comput Biol
, vol.5
, Issue.3
-
-
Pascual-García, A.1
Abia, D.2
Ortiz, Á.R.3
Bastolla, U.4
-
8
-
-
77958194276
-
On the evolutionary origins of "fold Space Continuity" A study of topological convergence and divergence in mixed alpha-beta domains
-
Sadowski MI, Taylor WR (2010) On the evolutionary origins of "Fold Space Continuity": A study of topological convergence and divergence in mixed alpha-beta domains. J Struct Biol 172(3):244-252
-
(2010)
J Struct Biol
, vol.172
, Issue.3
, pp. 244-252
-
-
Sadowski, M.I.1
Taylor, W.R.2
-
9
-
-
0036428739
-
Quantifying the similarities within fold space
-
Harrison A, Pearl F, Mott R, Thornton J, Orengo C (2002) Quantifying the similarities within fold space. J Mol Biol 323(5):909-926
-
(2002)
J Mol Biol
, vol.323
, Issue.5
, pp. 909-926
-
-
Harrison, A.1
Pearl, F.2
Mott, R.3
Thornton, J.4
Orengo, C.5
-
10
-
-
66549127972
-
Nothing about protein structure classification makes sense except in the light of evolution
-
Valas RE, Yang S, Bourne PE (2009) Nothing about protein structure classification makes sense except in the light of evolution. Curr Opin Struct Biol 19(3):329-334
-
(2009)
Curr Opin Struct Biol
, vol.19
, Issue.3
, pp. 329-334
-
-
Valas, R.E.1
Yang, S.2
Bourne, P.E.3
-
11
-
-
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(4):536-540
-
(1995)
J Mol Biol
, vol.247
, Issue.4
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
12
-
-
0030777303
-
CATH-A hierarchic classification of protein domain structures
-
Orengo CA, et al. (1997) CATH-A hierarchic classification of protein domain structures. Structure 5(8):1093-1108
-
(1997)
Structure
, vol.5
, Issue.8
, pp. 1093-1108
-
-
Orengo, C.A.1
-
13
-
-
33846074754
-
SISYPHUS-structural alignments for proteins with non-trivial relationships
-
Database issue
-
Andreeva A, Prli-c A, Hubbard TJP, Murzin AG (2007) SISYPHUS-structural alignments for proteins with non-trivial relationships. Nucleic Acids Res 35(Database issue, suppl 1): D253-D259
-
(2007)
Nucleic Acids Res
, vol.35
, Issue.SUPPL. 1
-
-
Andreeva, A.1
Prli-C, A.2
Hubbard, T.J.P.3
Murzin, A.G.4
-
14
-
-
0034651866
-
An alternative view of protein fold space
-
Shindyalov IN, Bourne PE (2000) An alternative view of protein fold space. Proteins 38(3):247-260
-
(2000)
Proteins
, vol.38
, Issue.3
, pp. 247-260
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
15
-
-
70349461173
-
The continuity of protein structure space is an intrinsic property of proteins
-
Skolnick J, Arakaki AK, Lee SY, Brylinski M (2009) The continuity of protein structure space is an intrinsic property of proteins. Proc Natl Acad Sci USA 106(37):15690-15695
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.37
, pp. 15690-15695
-
-
Skolnick, J.1
Arakaki, A.K.2
Lee, S.Y.3
Brylinski, M.4
-
16
-
-
66549120787
-
Is protein classification necessary? Toward alternative approaches to function annotation
-
Petrey D, Honig B (2009) Is protein classification necessary? Toward alternative approaches to function annotation. Curr Opin Struct Biol 19(3):363-368
-
(2009)
Curr Opin Struct Biol
, vol.19
, Issue.3
, pp. 363-368
-
-
Petrey, D.1
Honig, B.2
-
17
-
-
0035812694
-
Protein structure prediction and structural genomics
-
Baker D, Sali A (2001) Protein structure prediction and structural genomics. Science 294(5540):93-96
-
(2001)
Science
, vol.294
, Issue.5540
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
18
-
-
85040733640
-
Representation of the protein universe using classifications, maps, and networks
-
in press
-
Ben-Tal N, Kolodny R (2014) Representation of the protein universe using classifications, maps, and networks. Isr J Chem, in press
-
(2014)
Isr J Chem
-
-
Ben-Tal, N.1
Kolodny, R.2
-
19
-
-
33749014910
-
Evolution of protein structural classes and protein sequence families
-
Choi IG, Kim SH (2006) Evolution of protein structural classes and protein sequence families. Proc Natl Acad Sci USA 103(38):14056-14061
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.38
, pp. 14056-14061
-
-
Choi, I.G.1
Kim, S.H.2
-
20
-
-
79961038718
-
Maps of protein structure space reveal a fundamental relationship between protein structure and function
-
Osadchy M, Kolodny R (2011) Maps of protein structure space reveal a fundamental relationship between protein structure and function. Proc Natl Acad Sci USA 108(30): 12301-12306
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.30
, pp. 12301-12306
-
-
Osadchy, M.1
Kolodny, R.2
-
21
-
-
0029785147
-
Mapping the protein universe
-
Holm L, Sander C (1996) Mapping the protein universe. Science 273(5275):595-603
-
(1996)
Science
, vol.273
, Issue.5275
, pp. 595-603
-
-
Holm, L.1
Sander, C.2
-
22
-
-
0037195119
-
Expanding protein universe and its origin from the biological Big Bang
-
Dokholyan NV, Shakhnovich B, Shakhnovich EI (2002) Expanding protein universe and its origin from the biological Big Bang. Proc Natl Acad Sci USA 99(22): 14132-14136
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, Issue.22
, pp. 14132-14136
-
-
Dokholyan, N.V.1
Shakhnovich, B.2
Shakhnovich, E.I.3
-
23
-
-
75149131374
-
A galaxy of folds
-
Alva V, RemmertM, Biegert A, Lupas AN, Söding J (2010) A galaxy of folds. Protein Sci 19(1):124-130
-
(2010)
Protein Sci
, vol.19
, Issue.1
, pp. 124-130
-
-
Alva, V.1
Remmertm Biegert, A.2
Lupas, A.N.3
Söding, J.4
-
24
-
-
0035816218
-
Domain combinations in archaeal, eubacterial and eukaryotic proteomes
-
Apic G, Gough J, Teichmann SA (2001) Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol 310(2):311-325
-
(2001)
J Mol Biol
, vol.310
, Issue.2
, pp. 311-325
-
-
Apic, G.1
Gough, J.2
Teichmann, S.A.3
-
25
-
-
0034887573
-
Scale-free behavior in protein domain networks
-
Wuchty S (2001) Scale-free behavior in protein domain networks. Mol Biol Evol 18(9): 1694-1702
-
(2001)
Mol Biol Evol
, vol.18
, Issue.9
, pp. 1694-1702
-
-
Wuchty, S.1
-
26
-
-
84860138819
-
Evolution of protein domain architectures
-
Springer, Berlin
-
Forslund K, Sonnhammer EL (2012) Evolution of Protein Domain Architectures. Evolutionary Genomics (Springer, Berlin), pp 187-216
-
(2012)
Evolutionary Genomics
, pp. 187-216
-
-
Forslund, K.1
Sonnhammer, E.L.2
-
27
-
-
13444307044
-
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
-
Pt 1
-
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(Pt 12 Pt 1):2256-2268
-
(2004)
Acta Crystallogr D Biol Crystallogr
, vol.60
, Issue.PART 12
, pp. 2256-2268
-
-
Krissinel, E.1
Henrick, K.2
-
28
-
-
0041317258
-
More than the sum of their parts: On the evolution of proteins from peptides
-
Söding J, Lupas AN (2003) More than the sum of their parts: On the evolution of proteins from peptides. BioEssays 25(9):837-846
-
(2003)
Bio Essays
, vol.25
, Issue.9
, pp. 837-846
-
-
Söding, J.1
Lupas, A.N.2
-
29
-
-
84870665404
-
Touring protein space with Matt
-
Daniels NM, Kumar A, Cowen LJ, Menke M (2012) Touring protein space with Matt. IEEE/ACM Trans Comput Biol Bioinformatics 9(1):286-293
-
(2012)
IEEE/ACM Trans Comput Biol Bioinformatics
, vol.9
, Issue.1
, pp. 286-293
-
-
Daniels, N.M.1
Kumar, A.2
Cowen, L.J.3
Menke, M.4
-
30
-
-
13444279981
-
Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures
-
Kolodny R, Koehl P, Levitt M (2005) Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures. J Mol Biol 346(4):1173-1188
-
(2005)
J Mol Biol
, vol.346
, Issue.4
, pp. 1173-1188
-
-
Kolodny, R.1
Koehl, P.2
Levitt, M.3
-
31
-
-
0000840656
-
Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core
-
Subbiah S, Laurents DV, Levitt M (1993) Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core. Curr Biol 3(3):141-148
-
(1993)
Curr Biol
, vol.3
, Issue.3
, pp. 141-148
-
-
Subbiah, S.1
Laurents, D.V.2
Levitt, M.3
-
32
-
-
0036301445
-
Proteins with class α/β fold have high-level participation in fusion events
-
Hua S, Guo T, Gough J, Sun Z (2002) Proteins with class α/β fold have high-level participation in fusion events. J Mol Biol 320(4):713-719
-
(2002)
J Mol Biol
, vol.320
, Issue.4
, pp. 713-719
-
-
Hua, S.1
Guo, T.2
Gough, J.3
Sun, Z.4
-
33
-
-
40449095056
-
Evolution of protein domain promiscuity in eukaryotes
-
Basu MK, Carmel L, Rogozin IB, Koonin EV (2008) Evolution of protein domain promiscuity in eukaryotes. Genome Res 18(3):449-461
-
(2008)
Genome Res
, vol.18
, Issue.3
, pp. 449-461
-
-
Basu, M.K.1
Carmel, L.2
Rogozin, I.B.3
Koonin, E.V.4
-
34
-
-
0037841804
-
Evolution of the protein repertoire
-
Chothia C, Gough J, Vogel C, Teichmann SA (2003) Evolution of the protein repertoire. Science 300(5626):1701-1703
-
(2003)
Science
, vol.300
, Issue.5626
, pp. 1701-1703
-
-
Chothia, C.1
Gough, J.2
Vogel, C.3
Teichmann, S.A.4
-
35
-
-
0035783055
-
On the evolution of protein folds: Are similar motifs in different protein folds the result of convergence, insertion or relics of an ancient peptide world
-
Lupas AN, Ponting CP, Russell RB (2001) On the evolution of protein folds: Are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world? J Struct Biol 134(2-3):191-203
-
(2001)
J Struct Biol
, vol.134
, Issue.2-3
, pp. 191-203
-
-
Lupas, A.N.1
Ponting, C.P.2
Russell, R.B.3
-
36
-
-
37349020962
-
Probing protein fold space with a simplified model
-
Minary P, Levitt M (2008) Probing protein fold space with a simplified model. J Mol Biol 375(4):920-933
-
(2008)
J Mol Biol
, vol.375
, Issue.4
, pp. 920-933
-
-
Minary, P.1
Levitt, M.2
-
38
-
-
84869054051
-
A travel guide to Cytoscape plugins
-
Saito R, et al. (2012) A travel guide to Cytoscape plugins. Nat Methods 9(11): 1069-1076
-
(2012)
Nat Methods
, vol.9
, Issue.11
, pp. 1069-1076
-
-
Saito, R.1
-
40
-
-
0033977581
-
The ASTRAL compendium for protein structure and sequence analysis
-
Brenner SE, Koehl P, Levitt M (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res 28(1):254-256.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 254-256
-
-
Brenner, S.E.1
Koehl, P.2
Levitt, M.3
|