-
1
-
-
69449095861
-
REACH coarse-grained normal mode analysis of protein dimer interaction dynamics
-
Moritsugu K, Kurkal-Siebert V, Smith JC (2009) REACH coarse-grained normal mode analysis of protein dimer interaction dynamics. Biophys J 97:1158-1167.
-
(2009)
Biophys J
, vol.97
, pp. 1158-1167
-
-
Moritsugu, K.1
Kurkal-Siebert, V.2
Smith, J.C.3
-
2
-
-
84857706228
-
ProMode-Oligomer: Database of normal mode analysis in dihedral angle space for a full-atom system of oligomeric proteins
-
Wako H, Endo S (2012) ProMode-Oligomer: database of normal mode analysis in dihedral angle space for a full-atom system of oligomeric proteins. Open Bioinformatics J 6:9-19.
-
(2012)
Open Bioinformatics J
, vol.6
, pp. 9-19
-
-
Wako, H.1
Endo, S.2
-
3
-
-
56749176808
-
Dynameomics: Largescale assessment of native protein flexibility
-
Benson NC, Daggett V (2008) Dynameomics: largescale assessment of native protein flexibility. Protein Sci 17:2038-2050.
-
(2008)
Protein Sci
, vol.17
, pp. 2038-2050
-
-
Benson, N.C.1
Daggett, V.2
-
4
-
-
67650065004
-
Computational methods for predicting sites of functionally important dynamics
-
Schuyler AD, Carlson HA, Feldman EL (2009) Computational methods for predicting sites of functionally important dynamics. J Phys Chem B 113:6613-6622.
-
(2009)
J Phys Chem B
, vol.113
, pp. 6613-6622
-
-
Schuyler, A.D.1
Carlson, H.A.2
Feldman, E.L.3
-
5
-
-
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
-
6
-
-
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
-
8
-
-
0020771265
-
Dynamics of a small globular protein in terms of low-frequency vibrational modes
-
Go N, Noguti T, Nishikawa T (1983) Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc Natl Acad Sci USA 80:3696-3700.
-
(1983)
Proc Natl Acad Sci USA
, vol.80
, pp. 3696-3700
-
-
Go, N.1
Noguti, T.2
Nishikawa, T.3
-
9
-
-
0022419152
-
Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
-
Levitt M, Sander C, Stern PS (1985) Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J Mol Biol 181:423-447.
-
(1985)
J Mol Biol
, vol.181
, pp. 423-447
-
-
Levitt, M.1
Sander, C.2
Stern, P.S.3
-
10
-
-
0025753631
-
Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: Human lysozyme
-
Horiuchi T, Go N (1991) Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme. Proteins 10:106-116.
-
(1991)
Proteins
, vol.10
, pp. 106-116
-
-
Horiuchi, T.1
Go, N.2
-
11
-
-
0000081668
-
Collective variable description of native protein dynamics
-
Hayward S, Go N (1995) Collective variable description of native protein dynamics. Annu Rev Phys Chem 46:223-250.
-
(1995)
Annu Rev Phys Chem
, vol.46
, pp. 223-250
-
-
Hayward, S.1
Go, N.2
-
12
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
Hinsen K (1998) Analysis of domain motions by approximate normal mode calculations. Proteins 33:417-429.
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
13
-
-
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
-
14
-
-
70149090164
-
The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
-
Bakan A, Bahar I (2009) The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc Natl Acad Sci USA 106:14349-14354.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 14349-14354
-
-
Bakan, A.1
Bahar, I.2
-
15
-
-
39149108868
-
Structural flexibility in proteins: Impact of the crystal environment
-
Hinsen K (2008) Structural flexibility in proteins: impact of the crystal environment. Bioinformatics 24:521-528.
-
(2008)
Bioinformatics
, vol.24
, pp. 521-528
-
-
Hinsen, K.1
-
16
-
-
34248182936
-
vGNM: A Better Model for Understanding the Dynamics of Proteins in Crystals
-
DOI 10.1016/j.jmb.2007.03.059, PII S002228360700424X
-
Song G, Jernigan RL (2007) vGNM: a better model for understanding the dynamics of proteins in crystals. J Mol Biol 369:880-893. (Pubitemid 46709923)
-
(2007)
Journal of Molecular Biology
, vol.369
, Issue.3
, pp. 880-893
-
-
Song, G.1
Jernigan, R.L.2
-
17
-
-
30044434744
-
Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
-
DOI 10.1073/pnas.0507603102
-
Tobi D, Bahar I (2005) Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc Natl Acad Sci USA 102:18908-18913. (Pubitemid 43049540)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.52
, pp. 18908-18913
-
-
Tobi, D.1
Bahar, I.2
-
18
-
-
48749126860
-
Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking
-
Dobbins SE, Lesk VI, Sternberg MJ (2008) Insights into protein flexibility: the relationship between normal modes and conformational change upon protein-protein 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.3
-
19
-
-
33645961330
-
Flexible protein-protein docking
-
Bonvin AM (2006) Flexible protein-protein docking. Curr Opin Struct Biol 16:194-200.
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 194-200
-
-
Bonvin, A.M.1
-
20
-
-
38549097715
-
Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking
-
DOI 10.1002/prot.21579
-
May A, Zacharias M (2008) Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking. Proteins 70:794-809. (Pubitemid 351161939)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.70
, Issue.3
, pp. 794-809
-
-
May, A.1
Zacharias, M.2
-
21
-
-
0036468385
-
Prediction of protein-protein interactions by docking methods
-
DOI 10.1016/S0959-440X(02)00285-3
-
Smith GR, Sternberg MJ (2002) Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 12:28-35. (Pubitemid 34142717)
-
(2002)
Current Opinion in Structural Biology
, vol.12
, Issue.1
, pp. 28-35
-
-
Smith, G.R.1
Sternberg, M.J.E.2
-
23
-
-
33748107163
-
Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity
-
DOI 10.1093/protein/gzl026
-
Tsuchiya Y, Kinoshita K, Nakamura H (2006) Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity. Protein Eng Des Sel 19:421-429. (Pubitemid 44306060)
-
(2006)
Protein Engineering, Design and Selection
, vol.19
, Issue.9
, pp. 421-429
-
-
Tsuchiya, Y.1
Kinoshita, K.2
Nakamura, H.3
-
24
-
-
80051558353
-
Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction
-
Tsuchiya Y, Kanamori E, Nakamura H, Kinoshita K (2009) Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction. Adv Appl Bioinform Chem 2:79-100.
-
(2009)
Adv Appl Bioinform Chem
, vol.2
, pp. 79-100
-
-
Tsuchiya, Y.1
Kanamori, E.2
Nakamura, H.3
Kinoshita, K.4
-
25
-
-
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
-
26
-
-
34548232365
-
Inference of Macromolecular Assemblies from Crystalline State
-
DOI 10.1016/j.jmb.2007.05.022, PII S0022283607006420
-
Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372:774-797. (Pubitemid 47321791)
-
(2007)
Journal of Molecular Biology
, vol.372
, Issue.3
, pp. 774-797
-
-
Krissinel, E.1
Henrick, K.2
-
27
-
-
84864937959
-
Discrimination between biological interfaces and crystal-packing contacts
-
Tsuchiya Y, Nakamura H, Kinoshita K (2008) Discrimination between biological interfaces and crystal-packing contacts. Adv Appl Bioinform Chem 1:99-113.
-
(2008)
Adv Appl Bioinform Chem
, vol.1
, pp. 99-113
-
-
Tsuchiya, Y.1
Nakamura, H.2
Kinoshita, K.3
-
28
-
-
0022137436
-
FORMULATION OF STATIC AND DYNAMIC CONFORMATIONAL ENERGY ANALYSIS OF BIOPOLYMER SYSTEMS CONSISTING OF TWO OR MORE MOLECULES - AVOIDING A SINGULARITY IN THE PREVIOUS METHOD.
-
Higo J, Seno Y, Go N (1985) Formulation of static and dynamic conformational energy analysis of biopolymer systems consisting of two or more molecules-avoiding a singularity in the previous method. J Phys Soc Jpn 54:4053-4058. (Pubitemid 16545855)
-
(1985)
Journal of the Physical Society of Japan
, vol.54
, Issue.10
, pp. 4053-4058
-
-
Higo, J.1
Seno, Y.2
Go, N.3
-
29
-
-
84988123096
-
Algorithm for rapid calculation of Hessian of conformational energy function of protein by supercomputer
-
Wako H, Go N (1987) Algorithm for rapid calculation of Hessian of conformational energy function of protein by supercomputer. J Comput Chem 8:625-635.
-
(1987)
J Comput Chem
, vol.8
, pp. 625-635
-
-
Wako, H.1
Go, N.2
-
30
-
-
0029633151
-
FEDER/2: Program for static and dynamic conformational energy analysis of macro-molecules in dihedral angle space
-
Wako H, Endo S, Nagayama K, Go N (1995) FEDER/2: program for static and dynamic conformational energy analysis of macro-molecules in dihedral angle space. Comput Phys Commun 91:233-251.
-
(1995)
Comput Phys Commun
, vol.91
, pp. 233-251
-
-
Wako, H.1
Endo, S.2
Nagayama, K.3
Go, N.4
-
31
-
-
0001731773
-
Energy parameters in polypeptides. X. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
-
Nemethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A, Rumsey S, Scheraga HA (1992) Energy parameters in polypeptides. X. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J Phys Chem 96:6472-6484.
-
(1992)
J Phys Chem
, vol.96
, pp. 6472-6484
-
-
Nemethy, G.1
Gibson, K.D.2
Palmer, K.A.3
Yoon, C.N.4
Paterlini, G.5
Zagari, A.6
Rumsey, S.7
Scheraga, H.A.8
-
32
-
-
0032529585
-
Dynamic structure of subtilisin-eglin c complex studied by normal mode analysis
-
DOI 10.1002/(SICI)1097-0134(19980815)32:3<324::AID-PROT8>3.0.CO;2-H
-
Ishida H, Jochi Y, Kidera A (1998) Dynamic structure of subtilisin-eglin c complex studied by normal mode analysis. Proteins 32:324-333. (Pubitemid 28360829)
-
(1998)
Proteins: Structure, Function and Genetics
, vol.32
, Issue.3
, pp. 324-333
-
-
Ishida, H.1
Jochi, Y.2
Kidera, A.3
-
33
-
-
5344244656
-
-
R Development Core Team R Foundation for Statistical Computing, Vienna, Austria. Available from: Accessed on Sep 18, 2011
-
R Development Core Team (2008) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available from: http://www.R-project.org (Accessed on Sep 18, 2011).
-
(2008)
R: A Language and Environment for Statistical Computing
-
-
|