-
2
-
-
33750075732
-
Specificity of molecular interactions in transient protein-protein interaction interfaces
-
Cho K, Lee K, Lee KH, Kim D, Lee D (2006) Specificity of molecular interactions in transient protein-protein interaction interfaces. Proteins 65:593-606.
-
(2006)
Proteins
, vol.65
, pp. 593-606
-
-
Cho, K.1
Lee, K.2
Lee, K.H.3
Kim, D.4
Lee, D.5
-
3
-
-
2942615530
-
Protein-protein interfaces are special
-
Vakser IA (2004) Protein-protein interfaces are special. Structure 12:910-912.
-
(2004)
Structure
, vol.12
, pp. 910-912
-
-
Vakser, I.A.1
-
4
-
-
43149092276
-
Principles of protein-protein interactions: What are the preferred ways for proteins to interact?
-
Keskin O, Gursoy A, Ma B, Nussinov R (2008) Principles of protein-protein interactions: what are the preferred ways for proteins to interact?Chem Rev 108: 1225-1244.
-
(2008)
Chem Rev
, vol.108
, pp. 1225-1244
-
-
Keskin, O.1
Gursoy, A.2
Ma, B.3
Nussinov, R.4
-
5
-
-
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
-
6
-
-
39749113783
-
Dynamic property is a key determinant for protein-protein interactions
-
Bai H, Ma W, Liu S, Lai L (2008) Dynamic property is a key determinant for protein-protein interactions. Proteins 70:1323-1331.
-
(2008)
Proteins
, vol.70
, pp. 1323-1331
-
-
Bai, H.1
Ma, W.2
Liu, S.3
Lai, L.4
-
7
-
-
37249032102
-
Dynamic personalities of proteins
-
Henzler-Wildman K, Kern D (2007) Dynamic personalities of proteins. Nature 450:964-972.
-
(2007)
Nature
, vol.450
, pp. 964-972
-
-
Henzler-Wildman, K.1
Kern, D.2
-
8
-
-
0033548074
-
Enzyme specificity under dynamic control: A normal mode analysis of alpha-lytic protease
-
Miller DW, Agard DA (1999) Enzyme specificity under dynamic control: a normal mode analysis of alpha-lytic protease. J Mol Biol 286:267-278.
-
(1999)
J Mol Biol
, vol.286
, pp. 267-278
-
-
Miller, D.W.1
Agard, D.A.2
-
9
-
-
37249004920
-
Reaching for highhanging fruit in drug discovery at protein-protein interfaces
-
Wells JA, McClendon CL (2007) Reaching for highhanging fruit in drug discovery at protein-protein interfaces. Nature 450:1001-1009.
-
(2007)
Nature
, vol.450
, pp. 1001-1009
-
-
Wells, J.A.1
McClendon, C.L.2
-
10
-
-
79551681222
-
Protein binding specificity versus promiscuity
-
Schreiber G, Keating AE (2011) Protein binding specificity versus promiscuity. Curr Opin Struct Biol 21:50-61.
-
(2011)
Curr Opin Struct Biol
, vol.21
, pp. 50-61
-
-
Schreiber, G.1
Keating, A.E.2
-
12
-
-
3042848952
-
Evidence for dynamically organized modularity in the yeast protein-protein interaction network
-
Han J-DJ, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJM, Cusick ME, Roth FP, Vidal M (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430:88-93.
-
(2004)
Nature
, vol.430
, pp. 88-93
-
-
Han, J.-D.J.1
Bertin, N.2
Hao, T.3
Goldberg, D.S.4
Berriz, G.F.5
Zhang, L.V.6
Dupuy, D.7
Walhout, A.J.M.8
Cusick, M.E.9
Roth, F.P.10
Vidal, M.11
-
13
-
-
33845875196
-
Relating three-dimensional structures to protein networks provides evolutionary insights
-
Kim PM, Lu LJ, Xia Y, Gerstein MB (2006) Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314:1938-1941.
-
(2006)
Science
, vol.314
, pp. 1938-1941
-
-
Kim, P.M.1
Lu, L.J.2
Xia, Y.3
Gerstein, M.B.4
-
14
-
-
41149119083
-
The role of disorder in interaction networks: A structural analysis
-
Kim PM, Sboner A, Xia Y, Gerstein M (2008) The role of disorder in interaction networks: a structural analysis. Mol Syst Biol 4:179.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 179
-
-
Kim, P.M.1
Sboner, A.2
Xia, Y.3
Gerstein, M.4
-
16
-
-
79960903496
-
Distinct roles of overlapping and non-overlapping regions of hub protein interfaces in recognition of multiple partners
-
Dasgupta B, Nakamura H, Kinjo AR (2011) Distinct roles of overlapping and non-overlapping regions of hub protein interfaces in recognition of multiple partners. J Mol Biol 411:713-727.
-
(2011)
J Mol Biol
, vol.411
, pp. 713-727
-
-
Dasgupta, B.1
Nakamura, H.2
Kinjo, A.R.3
-
17
-
-
77955578700
-
Ubiquitin-molecular mechanisms for recognition of different structures
-
Perica T, Chothia C (2010) Ubiquitin-molecular mechanisms for recognition of different structures. Curr Opin Struct Biol 20:367-376.
-
(2010)
Curr Opin Struct Biol
, vol.20
, pp. 367-376
-
-
Perica, T.1
Chothia, C.2
-
18
-
-
79955562619
-
In silico elucidation of the recognition dynamics of ubiquitin
-
Long D, Bru schweiler R (2011) In silico elucidation of the recognition dynamics of ubiquitin. PLoS Comput Biol 7:9.
-
(2011)
PLoS Comput Biol
, vol.7
, pp. 9
-
-
Long, D.1
Bru Schweiler, R.2
-
19
-
-
0029791008
-
Normal-mode analysis suggests important flexibility between the two N-terminal domains of CD4 and supports the hypothesis of a conformational change in CD4 upon HIV binding
-
Sanejouand YH (1996) Normal-mode analysis suggests important flexibility between the two N-terminal domains of CD4 and supports the hypothesis of a conformational change in CD4 upon HIV binding. Protein Eng Des Sel 9:671-677.
-
(1996)
Protein Eng des Sel
, vol.9
, pp. 671-677
-
-
Sanejouand, Y.H.1
-
20
-
-
0035044995
-
Conformational change of proteins arising from normal mode calculations
-
Tama F, Sanejouand YH (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng Des Sel 14:1-6.
-
(2001)
Protein Eng des Sel
, vol.14
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.H.2
-
21
-
-
78349254189
-
Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses
-
Ahmed A, Villinger S, Gohlke H (2010) Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses. Proteins 78:3341-3352.
-
(2010)
Proteins
, vol.78
, pp. 3341-3352
-
-
Ahmed, A.1
Villinger, S.2
Gohlke, H.3
-
22
-
-
0033117937
-
Investigating protein dynamics in collective coordinate space
-
Kitao A, Go N (1999) Investigating protein dynamics in collective coordinate space. Curr Opin Struct Biol 9: 164-169.
-
(1999)
Curr Opin Struct Biol
, vol.9
, pp. 164-169
-
-
Kitao, A.1
Go, N.2
-
23
-
-
33646742004
-
Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations
-
Zheng W, Brooks BR, Thirumalai D (2006) Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proc Natl Acad Sci USA 103: 7664-7669.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 7664-7669
-
-
Zheng, W.1
Brooks, B.R.2
Thirumalai, D.3
-
24
-
-
80053446329
-
Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members
-
Marcos E, Crehuet R, Bahar I (2011) Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members. PLoS Comput Biol 7:e1002201.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Marcos, E.1
Crehuet, R.2
Bahar, I.3
-
25
-
-
80053142382
-
Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins
-
Meireles L, Gur M, Bakan A, Bahar I (2011) Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins. Protein Sci 20:1645-1658.
-
(2011)
Protein Sci
, vol.20
, pp. 1645-1658
-
-
Meireles, L.1
Gur, M.2
Bakan, A.3
Bahar, I.4
-
26
-
-
80053348799
-
Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis
-
Wako H, Endo S (2011) Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis. Biophys Chem 159:257-266.
-
(2011)
Biophys Chem
, vol.159
, pp. 257-266
-
-
Wako, H.1
Endo, S.2
-
27
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
-
Tirion M (1996) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 77:1905-1908.
-
(1996)
Phys Rev Lett
, vol.77
, pp. 1905-1908
-
-
Tirion, M.1
-
29
-
-
23244442698
-
Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: Myosin versus kinesin
-
Zheng W, Brooks BR (2005) Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin. Biophys J 89:167-178.
-
(2005)
Biophys J
, vol.89
, pp. 167-178
-
-
Zheng, W.1
Brooks, B.R.2
-
30
-
-
0032529585
-
Dynamic structure of subtilisin-eglin c complex studied by normal mode analysis
-
Ishida H, Jochi Y, Kidera A (1998) Dynamic structure of subtilisin-eglin c complex studied by normal mode analysis. Proteins 32:324-333.
-
(1998)
Proteins
, vol.32
, pp. 324-333
-
-
Ishida, H.1
Jochi, Y.2
Kidera, A.3
-
31
-
-
45949088702
-
Protein structure databases with new web services for structural biology and biomedical research
-
Standley DM, Kinjo AR, Kinoshita K, Nakamura H (2008) Protein structure databases with new web services for structural biology and biomedical research. Briefings Bioinf 9:276-285.
-
(2008)
Briefings Bioinf
, vol.9
, pp. 276-285
-
-
Standley, D.M.1
Kinjo, A.R.2
Kinoshita, K.3
Nakamura, H.4
-
32
-
-
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
-
33
-
-
84858077472
-
The Pfam protein families database
-
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer ELL, Eddy SR, Bateman A (2011) The Pfam protein families database. Nucleic Acids Res 40:290-301.
-
(2011)
Nucleic Acids Res
, vol.40
, pp. 290-301
-
-
Punta, M.1
Coggill, P.C.2
Eberhardt, R.Y.3
Mistry, J.4
Tate, J.5
Boursnell, C.6
Pang, N.7
Forslund, K.8
Ceric, G.9
Clements, J.10
Heger, A.11
Holm, L.12
Sonnhammer, E.L.L.13
Eddy, S.R.14
Bateman, A.15
-
35
-
-
77954759220
-
Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: An exhaustive structural classification study
-
Kinjo AR, Nakamura H (2010) Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: an exhaustive structural classification study. J Mol Biol 399: 526-540.
-
(2010)
J Mol Biol
, vol.399
, pp. 526-540
-
-
Kinjo, A.R.1
Nakamura, H.2
-
36
-
-
84866623373
-
Dynamic features of homodimer interfaces calculated by normal-mode analysis
-
Tsuchiya Y, Kinoshita K, Endo S, Wako H (2012) Dynamic features of homodimer interfaces calculated by normal-mode analysis. Protein Sci 21:1503-1513.
-
(2012)
Protein Sci
, vol.21
, pp. 1503-1513
-
-
Tsuchiya, Y.1
Kinoshita, K.2
Endo, S.3
Wako, H.4
-
37
-
-
80054983080
-
Independent interactions of ubiquitin-binding domains in a ubiquitin-mediated ternary complex
-
Garner TP, Strachan J, Shedden EC, Long JE, Cavey JR, Shaw B, Layfield R, Searle MS (2011) Independent interactions of ubiquitin-binding domains in a ubiquitin-mediated ternary complex. Biochemistry 50: 9076-9087.
-
(2011)
Biochemistry
, vol.50
, pp. 9076-9087
-
-
Garner, T.P.1
Strachan, J.2
Shedden, E.C.3
Long, J.E.4
Cavey, J.R.5
Shaw, B.6
Layfield, R.7
Searle, M.S.8
-
38
-
-
14844286108
-
Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes
-
Ma J (2005) Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure 13:373-380.
-
(2005)
Structure
, vol.13
, pp. 373-380
-
-
Ma, J.1
-
39
-
-
18144418170
-
Protein structural change upon ligand binding: Linear response theory
-
Ikeguchi M, Ueno J, Sato M, Kidera A (2005) Protein structural change upon ligand binding: linear response theory. Phys Rev Lett 94:078102.
-
(2005)
Phys Rev Lett
, vol.94
, pp. 078102
-
-
Ikeguchi, M.1
Ueno, J.2
Sato, M.3
Kidera, A.4
-
40
-
-
0345687171
-
A comparative study of motor-protein motions by using a simple elastic-network model
-
Zheng W, Doniach S (2003) A comparative study of motor-protein motions by using a simple elastic-network model. Proc Natl Acad Sci USA 100:13253-13258.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 13253-13258
-
-
Zheng, W.1
Doniach, S.2
-
41
-
-
33645770731
-
Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase
-
Koga N, Takada S (2006) Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase. Proc Natl Acad Sci USA 103:5367-5372.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 5367-5372
-
-
Koga, N.1
Takada, S.2
-
42
-
-
48749126860
-
Insights into protein flexibility: The relationship between normal modes and conformational change upon proteinprotein docking
-
Dobbins SE, Lesk VI, Sternberg MJE (2008) Insights into protein flexibility: The relationship between normal modes and conformational change upon proteinprotein docking. Proc Natl Acad Sci USA 105: 10390-10395.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 10390-10395
-
-
Dobbins, S.E.1
Lesk, V.I.2
Sternberg, M.J.E.3
-
43
-
-
0025066772
-
Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion
-
Gibrat JF, Go N (1990) Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion. Proteins 8:258-279.
-
(1990)
Proteins
, vol.8
, pp. 258-279
-
-
Gibrat, J.F.1
Go, N.2
-
44
-
-
78651338019
-
Extending CATH: Increasing coverage of the protein structure universe and linking structure with function
-
Cuff AL, Sillitoe I, Lewis T, Clegg AB, Rentzsch R, Furnham N, Pellegrini-Calace M, Jones D, Thornton J, Orengo CA (2011) Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic Acids Res 39:D420-D426.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Cuff, A.L.1
Sillitoe, I.2
Lewis, T.3
Clegg, A.B.4
Rentzsch, R.5
Furnham, N.6
Pellegrini-Calace, M.7
Jones, D.8
Thornton, J.9
Orengo, C.A.10
-
45
-
-
0030777303
-
CATH-A hierarchic classification of protein domain structures
-
Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM (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
Thornton, J.M.6
-
46
-
-
77955214740
-
Comparing interfacial dynamics in protein-protein complexes: An elastic network approach
-
Zen A, Micheletti C, Keskin O, Nussinov R (2010) Comparing interfacial dynamics in protein-protein complexes: an elastic network approach. BMC Struct Biol 10:26.
-
(2010)
BMC Struct Biol
, vol.10
, pp. 26
-
-
Zen, A.1
Micheletti, C.2
Keskin, O.3
Nussinov, R.4
-
47
-
-
44949215646
-
Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model
-
Haliloglu T, Seyrek E, Erman B (2008) Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model. Phys Rev Lett 100:228102.
-
(2008)
Phys Rev Lett
, vol.100
, pp. 228102
-
-
Haliloglu, T.1
Seyrek, E.2
Erman, B.3
-
48
-
-
45849131354
-
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution
-
Lange OF, Lakomek N-A, Fares C, Schroder GF, Walter KFA, Becker S, Meiler J, Grubmu ller H, Griesinger C, De Groot BL (2008) Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 320:1471-1475.
-
(2008)
Science
, vol.320
, pp. 1471-1475
-
-
Lange, O.F.1
Lakomek, N.-A.2
Fares, C.3
Schroder, G.F.4
Walter, K.F.A.5
Becker, S.6
Meiler, J.7
Grubmu Ller, H.8
Griesinger, C.9
De Groot, B.L.10
-
49
-
-
73349117207
-
Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin
-
Wlodarski T, Zagrovic B (2009) Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin. Proc Natl Acad Sci USA 106:19346-19351.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 19346-19351
-
-
Wlodarski, T.1
Zagrovic, B.2
-
50
-
-
14644424521
-
NMR snapshots of a fluctuating protein structure: Ubiquitin at 30 bar-3 kbar
-
Kitahara R, Yokoyama S, Akasaka K (2005) NMR snapshots of a fluctuating protein structure: ubiquitin at 30 bar-3 kbar. J Mol Biol 347:277-285.
-
(2005)
J Mol Biol
, vol.347
, pp. 277-285
-
-
Kitahara, R.1
Yokoyama, S.2
Akasaka, K.3
-
51
-
-
0035856546
-
Two folded conformers of ubiquitin revealed by high-pressure NMR
-
Kitahara R, Yamada H, Akasaka K (2001) Two folded conformers of ubiquitin revealed by high-pressure NMR. Biochemistry 40:13556-13563.
-
(2001)
Biochemistry
, vol.40
, pp. 13556-13563
-
-
Kitahara, R.1
Yamada, H.2
Akasaka, K.3
-
52
-
-
36448991500
-
ClustalW and ClustalX version
-
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) ClustalW and ClustalX version Bioinformatics 23:2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
Thompson, J.D.11
Gibson, T.J.12
Higgins, D.G.13
-
53
-
-
0001382861
-
A note on the rotational superposition problem
-
Diamond R (1988) A note on the rotational superposition problem. Acta Cryst. 44:211-216.
-
(1988)
Acta Cryst
, vol.44
, pp. 211-216
-
-
Diamond, R.1
-
55
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
|