-
1
-
-
0032489015
-
The cell as a collection of protein machines: Preparing the next generation of molecular biologists
-
Alberts B (1998) The cell as a collection of protein machines: Preparing the next generation of molecular biologists. Cell 92: 291-294.
-
(1998)
Cell
, vol.92
, pp. 291-294
-
-
Alberts, B.1
-
2
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636.
-
(2006)
Nature
, vol.440
, pp. 631-636
-
-
Gavin, A.C.1
Aloy, P.2
Grandi, P.3
Krause, R.4
Boesche, M.5
-
3
-
-
0036616218
-
The Protein Data Bank
-
Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, et al. (2002) The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 58: 899-907.
-
(2002)
Acta Crystallogr D Biol Crystallogr
, vol.58
, pp. 899-907
-
-
Berman, H.M.1
Battistuz, T.2
Bhat, T.N.3
Bluhm, W.F.4
Bourne, P.E.5
-
4
-
-
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
-
5
-
-
0030777303
-
CATH: A hierarchic classification of protein domain structures
-
Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, et al. (1997) CATH: A hierarchic classification of protein domain structures. Structure 5: 1093-1108.
-
(1997)
Structure
, vol.5
, pp. 1093-1108
-
-
Orengo, C.A.1
Michie, A.D.2
Jones, S.3
Jones, D.T.4
Swindells, M.B.5
-
7
-
-
13444257903
-
3did: Interacting protein domains of known three-dimensional structure
-
Stein A, Russell RB, Aloy P (2005) 3did: Interacting protein domains of known three-dimensional structure. Nucleic Acids Res 33: D413-D417.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Stein, A.1
Russell, R.B.2
Aloy, P.3
-
8
-
-
13844264506
-
iPfam: Visualization of protein-protein interactions in PDB at domain and amino acid resolutions
-
Finn RD, Marshall M, Bateman A (2005) iPfam: Visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics 21: 410-412.
-
(2005)
Bioinformatics
, vol.21
, pp. 410-412
-
-
Finn, R.D.1
Marshall, M.2
Bateman, A.3
-
9
-
-
21144432882
-
PSIbase: A database of Protein Structural Interactome map (PSIMAP)
-
Gong S, Yoon G, Jang I, Bolser D, Dafas P, et al. (2005) PSIbase: A database of Protein Structural Interactome map (PSIMAP). Bioinformatics 21: 2541-2543.
-
(2005)
Bioinformatics
, vol.21
, pp. 2541-2543
-
-
Gong, S.1
Yoon, G.2
Jang, I.3
Bolser, D.4
Dafas, P.5
-
10
-
-
18744382508
-
PIBASE: A comprehensive database of structurally defined protein interfaces
-
Davis FP, Sali A (2005) PIBASE: A comprehensive database of structurally defined protein interfaces. Bioinformatics 21: 1901-1907.
-
(2005)
Bioinformatics
, vol.21
, pp. 1901-1907
-
-
Davis, F.P.1
Sali, A.2
-
11
-
-
29244487908
-
Oligomeric protein structure networks: Insights into protein-protein interactions
-
Brinda KV, Vishveshwara S (2005) Oligomeric protein structure networks: Insights into protein-protein interactions. BMC Bioinformatics 6: 296.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 296
-
-
Brinda, K.V.1
Vishveshwara, S.2
-
14
-
-
13444301037
-
A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes
-
Levy Y, Cho SS, Onuchic JN, Wolynes PG (2005) A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. J Mol Biol 346: 1121-1145.
-
(2005)
J Mol Biol
, vol.346
, pp. 1121-1145
-
-
Levy, Y.1
Cho, S.S.2
Onuchic, J.N.3
Wolynes, P.G.4
-
15
-
-
0018417204
-
Probes of subunit assembly and reconstitution pathways in multisubunit proteins
-
Friedman FK, Beychok S (1979) Probes of subunit assembly and reconstitution pathways in multisubunit proteins. Annu Rev Biochem 48: 217-250.
-
(1979)
Annu Rev Biochem
, vol.48
, pp. 217-250
-
-
Friedman, F.K.1
Beychok, S.2
-
16
-
-
0348129526
-
The ASTRAL Compendium in 2004
-
Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, et al. (2004) The ASTRAL Compendium in 2004. Nucleic Acids Res 32: D189-D192.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Chandonia, J.M.1
Hon, G.2
Walker, N.S.3
Lo Conte, L.4
Koehl, P.5
-
17
-
-
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: 1116-1122.
-
(2003)
J Appl Cryst
, vol.36
, pp. 1116-1122
-
-
Ponstingl, H.1
Kabir, T.2
Thornton, J.M.3
-
18
-
-
0032169688
-
PQS: A protein quaternary structure file server
-
Henrick K, Thornton JM (1998) PQS: A protein quaternary structure file server. Trends Biochem Sci 23: 358-361.
-
(1998)
Trends Biochem Sci
, vol.23
, pp. 358-361
-
-
Henrick, K.1
Thornton, J.M.2
-
19
-
-
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
-
20
-
-
1042275583
-
A dissection of specific and non-specific protein-protein interfaces
-
Bahadur RP, Chakrabarti P, Rodier F, Janin J (2004) A dissection of specific and non-specific protein-protein interfaces. J Mol Biol 336: 943-955.
-
(2004)
J Mol Biol
, vol.336
, pp. 943-955
-
-
Bahadur, R.P.1
Chakrabarti, P.2
Rodier, F.3
Janin, J.4
-
22
-
-
2442676733
-
Disease-associated mutations in human mannose-binding lectin compromise oligomerization and activity of the final protein
-
Larsen F, Madsen HO, Sim RB, Koch C, Garred P (2004) Disease-associated mutations in human mannose-binding lectin compromise oligomerization and activity of the final protein. J Biol Chem 279: 21302-21311.
-
(2004)
J Biol Chem
, vol.279
, pp. 21302-21311
-
-
Larsen, F.1
Madsen, H.O.2
Sim, R.B.3
Koch, C.4
Garred, P.5
-
23
-
-
8644290067
-
Folding of human superoxide dismutase: Disulfide reduction prevents dimerization and produces marginally stable monomers
-
Lindberg MJ, Normark J, Holmgren A, Oliveberg M (2004) Folding of human superoxide dismutase: Disulfide reduction prevents dimerization and produces marginally stable monomers. Proc Natl Acad Sci U S A 101: 15893-15898.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 15893-15898
-
-
Lindberg, M.J.1
Normark, J.2
Holmgren, A.3
Oliveberg, M.4
-
24
-
-
0033516705
-
The packing density in proteins: Standard radii and volumes
-
Tsai J, Taylor R, Chothia C, Gerstein M (1999) The packing density in proteins: Standard radii and volumes. J Mol Biol 290: 253-266.
-
(1999)
J Mol Biol
, vol.290
, pp. 253-266
-
-
Tsai, J.1
Taylor, R.2
Chothia, C.3
Gerstein, M.4
-
26
-
-
1842405464
-
Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect
-
Tsai CJ, Lin SL, Wolfson HJ, Nussinov R (1997) Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect. Protein Sci 6: 53-64.
-
(1997)
Protein Sci
, vol.6
, pp. 53-64
-
-
Tsai, C.J.1
Lin, S.L.2
Wolfson, H.J.3
Nussinov, R.4
-
27
-
-
0016708122
-
Principles of protein-protein recognition
-
Chothia C, Janin J (1975) Principles of protein-protein recognition. Nature 256: 705-708.
-
(1975)
Nature
, vol.256
, pp. 705-708
-
-
Chothia, C.1
Janin, J.2
-
28
-
-
0037435031
-
From words to literature in structural proteomics
-
Sali A, Glaeser R, Earnest T, Baumeister W (2003) From words to literature in structural proteomics. Nature 422: 216-225.
-
(2003)
Nature
, vol.422
, pp. 216-225
-
-
Sali, A.1
Glaeser, R.2
Earnest, T.3
Baumeister, W.4
-
29
-
-
0043122944
-
ExPASy: The proteomics server for in-depth protein knowledge and analysis
-
Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, et al. (2003) ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31: 3784-3788.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3784-3788
-
-
Gasteiger, E.1
Gattiker, A.2
Hoogland, C.3
Ivanyi, I.4
Appel, R.D.5
-
30
-
-
17844390103
-
Novel specificities emerge by stepwise duplication of functional modules
-
Pereira-Leal JB, Teichmann SA (2005) Novel specificities emerge by stepwise duplication of functional modules. Genome Res 15: 552-559.
-
(2005)
Genome Res
, vol.15
, pp. 552-559
-
-
Pereira-Leal, J.B.1
Teichmann, S.A.2
-
31
-
-
33744783371
-
Evolution of protein fold in the presence of functional constraints
-
Andreeva A, Murzin AG (2006) Evolution of protein fold in the presence of functional constraints. Curr Opin Struct Biol 16: 399-408.
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 399-408
-
-
Andreeva, A.1
Murzin, A.G.2
-
32
-
-
21244464335
-
Binding properties and evolution of homodimers in protein-protein interaction networks
-
Ispolatov I, Yuryev A, Mazo I, Maslov S (2005) Binding properties and evolution of homodimers in protein-protein interaction networks. Nucleic Acids Res 33: 3629-3635.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 3629-3635
-
-
Ispolatov, I.1
Yuryev, A.2
Mazo, I.3
Maslov, S.4
-
34
-
-
0033120809
-
Variability in quaternary association of proteins with the same tertiary fold: A case study and rationalization involving legume lectins
-
Prabu MM, Suguna K, Vijayan M (1999) Variability in quaternary association of proteins with the same tertiary fold: A case study and rationalization involving legume lectins. Proteins 35: 58-69.
-
(1999)
Proteins
, vol.35
, pp. 58-69
-
-
Prabu, M.M.1
Suguna, K.2
Vijayan, M.3
-
35
-
-
0042386609
-
The relationship between sequence and interaction divergence in proteins
-
Aloy P, Ceulemans H, Stark A, Russell RB (2003) The relationship between sequence and interaction divergence in proteins. J Mol Biol 332: 989-998.
-
(2003)
J Mol Biol
, vol.332
, pp. 989-998
-
-
Aloy, P.1
Ceulemans, H.2
Stark, A.3
Russell, R.B.4
-
36
-
-
0037559627
-
Structure of the Rho transcription terminator: Mechanism of mRNA recognition and helicase loading
-
Skordalakes E, Berger JM (2003) Structure of the Rho transcription terminator: Mechanism of mRNA recognition and helicase loading. Cell 114: 135-146.
-
(2003)
Cell
, vol.114
, pp. 135-146
-
-
Skordalakes, E.1
Berger, J.M.2
-
37
-
-
0032979147
-
The two types of 3-dehydroquinase have distinct structures but catalyze the same overall reaction
-
Gourley DG, Shrive AK, Polikarpov I, Krell T, Coggins JR, et al. (1999) The two types of 3-dehydroquinase have distinct structures but catalyze the same overall reaction. Nat Struct Biol 6: 521-525.
-
(1999)
Nat Struct Biol
, vol.6
, pp. 521-525
-
-
Gourley, D.G.1
Shrive, A.K.2
Polikarpov, I.3
Krell, T.4
Coggins, J.R.5
-
38
-
-
0142242176
-
Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in vitamin K2 biosynthesis
-
Truglio JJ, Theis K, Feng Y, Gajda R, Machutta C, et al. (2003) Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in vitamin K2 biosynthesis. J Biol Chem 278: 42352-42360.
-
(2003)
J Biol Chem
, vol.278
, pp. 42352-42360
-
-
Truglio, J.J.1
Theis, K.2
Feng, Y.3
Gajda, R.4
Machutta, C.5
-
39
-
-
55449107518
-
Functional coverage of the human genome by existing structures, structural genomics targets, and homology models
-
Available: Accessed 22 October 2006
-
Xie L, Bourne PE (2005) Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput Biol 1(3): e31. Available: http://compbiol.plosjournals.org/perlserv/? request=get-document&doi=10.1371/journal.pcbi.0010031. Accessed 22 October 2006.
-
(2005)
PLoS Comput Biol
, vol.1
, Issue.3
-
-
Xie, L.1
Bourne, P.E.2
-
40
-
-
0036322695
-
Target space for structural genomics revisited
-
Liu J, Rost B (2002) Target space for structural genomics revisited. Bioinformatics 18: 922-933.
-
(2002)
Bioinformatics
, vol.18
, pp. 922-933
-
-
Liu, J.1
Rost, B.2
-
41
-
-
33751418828
-
Sur certaines implications de l'hypothèse d'équivalence stricte entre les protomères des protéines oligomériques
-
Claverie P, Hofnung M, Monod J (1968) Sur certaines implications de l'hypothèse d'équivalence stricte entre les protomères des protéines oligomériques. Comptes rendus des séances de l'académie des sciences: 1616-1618.
-
(1968)
Comptes Rendus des Séances de L'académie des Sciences
, pp. 1616-1618
-
-
Claverie, P.1
Hofnung, M.2
Monod, J.3
-
42
-
-
0035807966
-
Dimer formation drives the activation of the cell death protease caspase 9
-
Renatus M, Stennicke HR, Scott FL, Liddington RC, Salvesen GS (2001) Dimer formation drives the activation of the cell death protease caspase 9. Proc Natl Acad Sci U S A 98: 14250-14255.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 14250-14255
-
-
Renatus, M.1
Stennicke, H.R.2
Scott, F.L.3
Liddington, R.C.4
Salvesen, G.S.5
-
43
-
-
73649152457
-
Allosteric proteins and cellular control systems
-
Monod J, Changeux JP, Jacob F (1963) Allosteric proteins and cellular control systems. J Mol Biol 6: 306-329.
-
(1963)
J Mol Biol
, vol.6
, pp. 306-329
-
-
Monod, J.1
Changeux, J.P.2
Jacob, F.3
-
44
-
-
0037204948
-
TNF-R1 signaling: A beautiful pathway
-
Chen G, Goeddel DV (2002) TNF-R1 signaling: A beautiful pathway. Science 296: 1634-1635.
-
(2002)
Science
, vol.296
, pp. 1634-1635
-
-
Chen, G.1
Goeddel, D.V.2
-
45
-
-
0035836765
-
A comprehensive two-hybrid analysis to explore the yeast protein interactome
-
Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98: 4569-4574.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 4569-4574
-
-
Ito, T.1
Chiba, T.2
Ozawa, R.3
Yoshida, M.4
Hattori, M.5
-
46
-
-
0029042511
-
Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 Å resolution
-
Lowe J, Stock D, Jap B, Zwickl P, Baumeister W, et al. (1995) Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 Å resolution. Science 268: 533-539.
-
(1995)
Science
, vol.268
, pp. 533-539
-
-
Lowe, J.1
Stock, D.2
Jap, B.3
Zwickl, P.4
Baumeister, W.5
-
47
-
-
0141524060
-
A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary
-
Day R, Beck DA, Armen RS, Daggett V (2003) A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary. Protein Sci 12: 2150-2160.
-
(2003)
Protein Sci
, vol.12
, pp. 2150-2160
-
-
Day, R.1
Beck, D.A.2
Armen, R.S.3
Daggett, V.4
-
49
-
-
84867453337
-
Graphviz: Open source graph drawing tools
-
Ellson J, Gansner E, Koutsofios L, North SC, Woodhull G (2002) Graphviz: Open source graph drawing tools. Lecture Notes Comput Sci 2265: 483.
-
(2002)
Lecture Notes Comput Sci
, vol.2265
, pp. 483
-
-
Ellson, J.1
Gansner, E.2
Koutsofios, L.3
North, S.C.4
Woodhull, G.5
-
50
-
-
0025272240
-
Rapid and sensitive sequence comparison with FASTP and FASTA
-
Pearson WR (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 183: 63-98.
-
(1990)
Methods Enzymol
, vol.183
, pp. 63-98
-
-
Pearson, W.R.1
|