-
1
-
-
14144256567
-
Normal modes for predicting protein motions: A comprehensive database assessment and associated web tool
-
Alexandrov,V. et al. (2005) Normal modes for predicting protein motions: a comprehensive database assessment and associated web tool. Protein Sci., 14, 633-643.
-
(2005)
Protein Sci.
, vol.14
, pp. 633-643
-
-
Alexandrov, V.1
-
2
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Atilgan,A.R. et al. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J., 80, 505-515.
-
(2001)
Biophys. J.
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
-
3
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
Bahar,I. et al. (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des., 2, 173-181.
-
(1997)
Fold. Des.
, vol.2
, pp. 173-181
-
-
Bahar, I.1
-
4
-
-
0033954256
-
The Protein Data Bank
-
Berman,H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
-
5
-
-
3242891875
-
MoViES: Molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids
-
Cao,Z.W. et al. (2004) MoViES: Molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids. Nucleic Acids Res., 32, W679-W685.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Cao, Z.W.1
-
6
-
-
25844440811
-
Elastic network models for understanding biomolecular machinary: From enzymes to supramolecular assemblies
-
Chennubhotla,C. et al. (2005) Elastic network models for understanding biomolecular machinary: From enzymes to supramolecular assemblies. Phys. Biol., 2, S173-S180.
-
(2005)
Phys. Biol.
, vol.2
-
-
Chennubhotla, C.1
-
7
-
-
0141792364
-
Computational prediction of allosteric structural changes by a simple mechanical model: Application to hemoglobin T to R transition
-
Chunyan,X. et al. (2003) Computational prediction of allosteric structural changes by a simple mechanical model: Application to hemoglobin T to R transition. J. Mol. Biol., 333, 153-168.
-
(2003)
J. Mol. Biol.
, vol.333
, pp. 153-168
-
-
Chunyan, X.1
-
10
-
-
0036077875
-
Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: The elastic network model
-
Delarue,M. and Sanejouand,Y.H. (2002) Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: The elastic network model. J. Mol. Biol., 320, 1011-1024.
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 1011-1024
-
-
Delarue, M.1
Sanejouand, Y.H.2
-
11
-
-
0034663710
-
Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to alpha-amylase inhibitor
-
Doruker,P. et al. (2000) Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to alpha-amylase inhibitor. Proteins, 40, 512-524.
-
(2000)
Proteins
, vol.40
, pp. 512-524
-
-
Doruker, P.1
-
12
-
-
0028454915
-
A new approach for determining low-frequency normal modes in macromolecules
-
Durand,P. et al. (1994) A new approach for determining low-frequency normal modes in macromolecules. Biopolymers, 34, 759-771.
-
(1994)
Biopolymers
, vol.34
, pp. 759-771
-
-
Durand, P.1
-
13
-
-
22444436454
-
The limit of accuracy of protein modeling: Influence of crystal packing on protein structure
-
Eyal,E. et al. (2005) The limit of accuracy of protein modeling: influence of crystal packing on protein structure. J. Mol. Biol., 351, 431-442.
-
(2005)
J. Mol. Biol.
, vol.351
, pp. 431-442
-
-
Eyal, E.1
-
14
-
-
0345973041
-
Gaussian dynamics of folded proteins
-
Haliloglu,T. et al. (1997) Gaussian dynamics of folded proteins. Phys. Rev. Lett., 79, 3090-3093.
-
(1997)
Phys. Rev. Lett.
, vol.79
, pp. 3090-3093
-
-
Haliloglu, T.1
-
15
-
-
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
-
16
-
-
0001962564
-
The molecular modeling toolkit: A new approach to molecular simulations
-
Hinsen,K. (2000) The molecular modeling toolkit: A new approach to molecular simulations. J. Comput. Chem., 21, 79-85.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 79-85
-
-
Hinsen, K.1
-
17
-
-
25444528449
-
WEBnm" A web application for normal mode analysis of proteins
-
Hollup,S.M. et al. (2005) WEBnm" a web application for normal mode analysis of proteins. BMC Bioinformatics, 11, 52.
-
(2005)
BMC Bioinformatics
, vol.11
, pp. 52
-
-
Hollup, S.M.1
-
18
-
-
0029878720
-
VMD: Visual molecular dynamics
-
Humphrey,W. et al. (1996) VMD: Visual molecular dynamics. J. Mol. Graph., 14, 27-38.
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 27-38
-
-
Humphrey, W.1
-
19
-
-
17844364634
-
Molecular dynamics simulation of the M2 helices within the nicotinic acetylcholine receptor transmembrane domain: Structure and collective motions
-
Hung,A. et al. (2005) Molecular dynamics simulation of the M2 helices within the nicotinic acetylcholine receptor transmembrane domain: structure and collective motions. Biophys. J., 88, 3321-3333.
-
(2005)
Biophys. J.
, vol.88
, pp. 3321-3333
-
-
Hung, A.1
-
20
-
-
0036154101
-
Functional motions of influenza virus hemagglutinin: A structure-based analytical approach
-
Isin,B. et al. (2002) Functional motions of influenza virus hemagglutinin: A structure-based analytical approach. Biophys. J., 82, 569-581.
-
(2002)
Biophys. J.
, vol.82
, pp. 569-581
-
-
Isin, B.1
-
21
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch,W. and 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
-
22
-
-
0035996975
-
Relating molecular flexibility to function: A case study of tubulin
-
Keskin,O. et al. (2002) Relating molecular flexibility to function: A case study of tubulin. Biophys. J., 83, 663-680.
-
(2002)
Biophys. J.
, vol.83
, pp. 663-680
-
-
Keskin, O.1
-
23
-
-
33749521415
-
Optimization and evaluation of a coarse-grained model of protein motion using X-ray crystal data
-
doi:10.1529/biophysj.106.85894
-
Kondrashov,D.A. et al. (2006) Optimization and evaluation of a coarse-grained model of protein motion using X-ray crystal data. Biophys. J., doi:10.1529/biophysj.106.85894.
-
(2006)
Biophys. J.
-
-
Kondrashov, D.A.1
-
24
-
-
0036721233
-
Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic
-
Krebs,W.G. et al. (2002) Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic. Proteins, 48, 682-695.
-
(2002)
Proteins
, vol.48
, pp. 682-695
-
-
Krebs, W.G.1
-
25
-
-
0035996990
-
Dynamics of proteins in crystals: Comparison of experiment with simple models
-
Kundu,S et al. (2002) Dynamics of proteins in crystals: Comparison of experiment with simple models. Biophys. J., 83, 723-732.
-
(2002)
Biophys. J.
, vol.83
, pp. 723-732
-
-
Kundu, S.1
-
26
-
-
0036840202
-
A coarse-grained normal mode approach for macromolecules: An efficient implementation and application to Ca2+-ATPase
-
Li,G. and Cui,Q. (2002) A coarse-grained normal mode approach for macromolecules: An efficient implementation and application to Ca2+-ATPase. Biophys. J., 83, 2457-2474.
-
(2002)
Biophys. J.
, vol.83
, pp. 2457-2474
-
-
Li, G.1
Cui, Q.2
-
27
-
-
33747858757
-
NOMAD-Ref: Visualization, deformation, and refinement of macromolecular structures based on all-atom normal mode analysis
-
Lindahl,E. et al. (2006) NOMAD-Ref: Visualization, deformation, and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res., 34, W52-W56.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Lindahl, E.1
-
28
-
-
0036773411
-
Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure
-
McConkey,B.J. et al. (2002) Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure. Bioinformatics, 18, 1365-1373.
-
(2002)
Bioinformatics
, vol.18
, pp. 1365-1373
-
-
McConkey, B.J.1
-
29
-
-
2442543557
-
Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models
-
Micheletti,C. et al. (2004) Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models. Proteins, 55, 635-645.
-
(2004)
Proteins
, vol.55
, pp. 635-645
-
-
Micheletti, C.1
-
30
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences structures
-
Murzin,A.G. et al. (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
-
31
-
-
33644517853
-
Functional modes of proteins are among the most robust
-
PMID: 16606146
-
Nicholay,S. and Sanejouand,Y.-H. (2006) Functional modes of proteins are among the most robust. Phys. Rev. Lett., 96, PMID: 16606146.
-
(2006)
Phys. Rev. Lett.
, vol.96
-
-
Nicholay, S.1
Sanejouand, Y.-H.2
-
32
-
-
0037250308
-
PDB-REPRDB: A database of representative protein chains from the Protein Data Bank (PDB) in 2003
-
Noguchi,T. and Akiyama,Y. (2003) PDB-REPRDB: A database of representative protein chains from the Protein Data Bank (PDB) in 2003. Nucleic Acids Res., 31, 492-493.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 492-493
-
-
Noguchi, T.1
Akiyama, Y.2
-
33
-
-
1842454635
-
HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: Possible contributions to drug resistance and a potential new target site for drugs
-
Perryman,A.L. et al. (2004) HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: Possible contributions to drug resistance and a potential new target site for drugs. Protein Sci., 13, 1108-1123.
-
(2004)
Protein Sci.
, vol.13
, pp. 1108-1123
-
-
Perryman, A.L.1
-
34
-
-
0036306459
-
Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease
-
Piana,S. et al. (2002) Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease. J. Mol. Biol., 319, 567-583.
-
(2002)
J. Mol. Biol.
, vol.319
, pp. 567-583
-
-
Piana, S.1
-
35
-
-
2442548750
-
Identification of core amino acids stabilizing rhodopsin
-
Rader,A.J. et al. (2004) Identification of core amino acids stabilizing rhodopsin. Proc. Natl Acad. Sci. USA, 101, 7246-7251.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 7246-7251
-
-
Rader, A.J.1
-
36
-
-
14844300852
-
Maturation dynamics of bacteriophage HK97 Capsid
-
Rader,A.J. et al. (2005) Maturation dynamics of bacteriophage HK97 Capsid. Structure, 13, 413-421.
-
(2005)
Structure
, vol.13
, pp. 413-421
-
-
Rader, A.J.1
-
37
-
-
84893169025
-
General atomic and molecular electronic structure system
-
Schmidt,M.W. et al. (1993) General atomic and molecular electronic structure system. J. Comput. Chem., 14, 1347-1363.
-
(1993)
J. Comput. Chem.
, vol.14
, pp. 1347-1363
-
-
Schmidt, M.W.1
-
38
-
-
33744926664
-
Common mechanism of pore opening shared by five different potassium channels
-
Shrivastava,I.H. and Bahar,I. (2006) Common mechanism of pore opening shared by five different potassium channels. Biophys. J., 90, 3240-3929.
-
(2006)
Biophys. J.
, vol.90
, pp. 3240-3929
-
-
Shrivastava, I.H.1
Bahar, I.2
-
39
-
-
3242875210
-
ElNemo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement
-
Suhre,K. and Sanejouand,Y.-H. (2004) ElNemo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res., 32, W610-W614.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Suhre, K.1
Sanejouand, Y.-H.2
-
40
-
-
22244438519
-
Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism
-
Taly,A. et al. (2005) Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism. Biophys. J., 88, 3954-3965.
-
(2005)
Biophys. J.
, vol.88
, pp. 3954-3965
-
-
Taly, A.1
-
41
-
-
9644266693
-
Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis
-
Tama,F. and Brooks,C.L. (2005) Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. J. Mol. Biol., 345, 299-314.
-
(2005)
J. Mol. Biol.
, vol.345
, pp. 299-314
-
-
Tama, F.1
Brooks, C.L.2
-
42
-
-
0034308140
-
Building-block approach for determining low-frequency normal modes of macromolecules
-
Tama,F. et al. (2000) Building-block approach for determining low-frequency normal modes of macromolecules. Proteins, 41, 1-7.
-
(2000)
Proteins
, vol.41
, pp. 1-7
-
-
Tama, F.1
-
43
-
-
0042424707
-
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
-
Tama,F. et al. (2003) Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl Acad. Sci. USA, 100, 9319-9323.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 9319-9323
-
-
Tama, F.1
-
44
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
-
Tirion,M.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.M.1
-
45
-
-
0043238084
-
Dynamical properties of the MscL of Escherichia coli: A normal mode analysis
-
Valadie,H. et al. (2003) Dynamical properties of the MscL of Escherichia coli: A normal mode analysis. J. Mol. Biol., 332, 657-674.
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 657-674
-
-
Valadie, H.1
-
46
-
-
33746651090
-
Convergent dynamics in the protease enzymatic superfamily
-
Vincenzo,C. et al. (2006) Convergent dynamics in the protease enzymatic superfamily. J. Am. Chem. Soc., 128, 9766-9772.
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 9766-9772
-
-
Vincenzo, C.1
-
47
-
-
4544280144
-
ProMode: A database of normal mode analyses on protein molecules with a full-atom model
-
Wako,H. et al. (2004) ProMode: A database of normal mode analyses on protein molecules with a full-atom model. Bioinformatics, 20, 2035-2043.
-
(2004)
Bioinformatics
, vol.20
, pp. 2035-2043
-
-
Wako, H.1
-
48
-
-
4344685227
-
Global ribosome motions revealed with elastic network model
-
Wang,Y. et al. (2004) Global ribosome motions revealed with elastic network model. J. Struct. Biol., 147, 302-314.
-
(2004)
J. Struct. Biol.
, vol.147
, pp. 302-314
-
-
Wang, Y.1
-
49
-
-
20444409186
-
Coupling between catalytic site and collective dynamics: A requirement for mechanical activity of enzymes
-
Yang,L.-W. and Bahar,I. (2005) Coupling between catalytic site and collective dynamics: A requirement for mechanical activity of enzymes. Structure, 13, 893-904.
-
(2005)
Structure
, vol.13
, pp. 893-904
-
-
Yang, L.-W.1
Bahar, I.2
-
50
-
-
20444429274
-
iGNM: A database of protein functional motions based on Gaussian Network Model
-
Yang,L.-W. et al. (2005) iGNM: A database of protein functional motions based on Gaussian Network Model. Bioinformatics, 21, 2978-2987.
-
(2005)
Bioinformatics
, vol.21
, pp. 2978-2987
-
-
Yang, L.-W.1
-
51
-
-
33747829284
-
oGNM: Online computation of structural dynamics using the Gaussian network model
-
Yang,L.-W. et al. (2006) oGNM: Online computation of structural dynamics using the Gaussian network model. Nucleic Acids Res., 34, W24-W31.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Yang, L.-W.1
-
52
-
-
13844276692
-
Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model
-
Zheng,W. and Brooks,B.R. (2005a) Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model. J. Mol. Biol., 346, 745-759.
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 745-759
-
-
Zheng, W.1
Brooks, B.R.2
-
53
-
-
23244442698
-
Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: Myosin versus kinesin
-
Zheng,W. and Brooks,B.R. (2005b) 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
-
54
-
-
0345687171
-
A comparative study of motor-protein motions by using a simple elastic-network model
-
Zheng,W. and 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
|