-
1
-
-
0029937635
-
Motions in hemoglobin studied by normal mode analysis and energy minimization: Evidence for the existence of tertiary T-like, quaternary R-like intermediate structures
-
DOI 10.1006/jmbi.1996.0257
-
L. Mouawad, and D. Perahia Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary T-like, quaternary R-like intermediate structures J. Mol. Biol. 258 1996 393 410 (Pubitemid 26131739)
-
(1996)
Journal of Molecular Biology
, vol.258
, Issue.2
, pp. 393-410
-
-
Mouawad, L.1
Perahia, D.2
-
2
-
-
0035044995
-
Conformational change of proteins arising from normal mode calculations
-
F. Tama, and Y.H. Sanejouand Conformational change of proteins arising from normal mode calculations Protein Eng. 14 2001 1 6 (Pubitemid 32318932)
-
(2001)
Protein Engineering
, vol.14
, Issue.1
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.-H.2
-
3
-
-
0036721233
-
Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic
-
DOI 10.1002/prot.10168
-
W.G. Krebs, and V. Alexandrov M. Gerstein Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic Proteins 48 2002 682 695 (Pubitemid 34925457)
-
(2002)
Proteins: Structure, Function and Genetics
, vol.48
, Issue.4
, pp. 682-695
-
-
Krebs, W.G.1
Alexandrov, V.2
Wilson, C.A.3
Echols, N.4
Yu, H.5
Gerstein, M.6
-
4
-
-
0141792364
-
Allosteric changes in protein structure computed by a simple mechanical model: Hemoglobin T R2 transition
-
DOI 10.1016/j.jmb.2003.08.027
-
C. Xu, D. Tobi, and I. Bahar Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T< - >R2 transition J. Mol. Biol. 333 2003 153 168 (Pubitemid 37153272)
-
(2003)
Journal of Molecular Biology
, vol.333
, Issue.1
, pp. 153-168
-
-
Xu, C.1
Tobi, D.2
Bahar, I.3
-
5
-
-
34547666968
-
How well can we understand large-scale protein motions using normal modes of elastic network models?
-
DOI 10.1529/biophysj.106.095927
-
L. Yang, G. Song, and R.L. Jernigan How well can we understand large-scale protein motions using normal modes of elastic network models? Biophys. J. 93 2007 920 929 (Pubitemid 47219784)
-
(2007)
Biophysical Journal
, vol.93
, Issue.3
, pp. 920-929
-
-
Yang, L.1
Song, G.2
Jernigan, R.L.3
-
6
-
-
70149090164
-
The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
-
A. Bakan, and I. Bahar The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding Proc. Natl. Acad. Sci. USA 106 2009 14349 14354
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 14349-14354
-
-
Bakan, A.1
Bahar, I.2
-
7
-
-
25844431698
-
Coarse-grained normal mode analysis in structural biology
-
DOI 10.1016/j.sbi.2005.08.007, PII S0959440X05001557, Carbohydrates and Glycoconjugates/Biophysical Methods
-
I. Bahar, and A.J. Rader Coarse-grained normal mode analysis in structural biology Curr. Opin. Struct. Biol. 15 2005 586 592 (Pubitemid 41393491)
-
(2005)
Current Opinion in Structural Biology
, vol.15
, Issue.5
, pp. 586-592
-
-
Bahar, I.1
Rader, A.J.2
-
8
-
-
14844286108
-
Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes
-
DOI 10.1016/j.str.2005.02.002
-
J. Ma Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes Structure 13 2005 373 380 (Pubitemid 40342876)
-
(2005)
Structure
, vol.13
, Issue.3
, pp. 373-380
-
-
Ma, J.1
-
9
-
-
33745024278
-
Symmetry, form, and shape: Guiding principles for robustness in macromolecular machines
-
DOI 10.1146/annurev.biophys.35.040405.102010
-
F. Tama, and C.L. Brooks Symmetry, form, and shape: guiding principles for robustness in macromolecular machines Annu. Rev. Biophys. Biomol. Struct. 35 2006 115 133 (Pubitemid 43877372)
-
(2006)
Annual Review of Biophysics and Biomolecular Structure
, vol.35
, pp. 115-133
-
-
Tama, F.1
Brooks III, C.L.2
-
10
-
-
80053142382
-
Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins
-
L. Meireles, and M. Gur I. Bahar Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins Protein Sci. 20 2011 1645 1658
-
(2011)
Protein Sci.
, vol.20
, pp. 1645-1658
-
-
Meireles, L.1
Gur, M.2
Bahar, I.3
-
11
-
-
0036708474
-
Efficient generation of feasible pathways for protein conformational transitions
-
M.K. Kim, R.L. Jernigan, and G.S. Chirikjian Efficient generation of feasible pathways for protein conformational transitions Biophys. J. 83 2002 1620 1630 (Pubitemid 34977733)
-
(2002)
Biophysical Journal
, vol.83
, Issue.3
, pp. 1620-1630
-
-
Kim, M.K.1
Jernigan, R.L.2
Chirikjian, G.S.3
-
12
-
-
23244465157
-
Rigid-cluster models of conformational transitions in macromolecular machines and assemblies
-
DOI 10.1529/biophysj.104.044347
-
M.K. Kim, R.L. Jernigan, and G.S. Chirikjian Rigid-cluster models of conformational transitions in macromolecular machines and assemblies Biophys. J. 89 2005 43 55 (Pubitemid 41098261)
-
(2005)
Biophysical Journal
, vol.89
, Issue.1
, pp. 43-55
-
-
Kim, M.K.1
Jernigan, R.L.2
Chirikjian, G.S.3
-
13
-
-
24644483073
-
Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
-
DOI 10.1016/j.jmb.2005.07.031, PII S0022283605008193
-
P. Maragakis, and M. Karplus Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase J. Mol. Biol. 352 2005 807 822 (Pubitemid 41267070)
-
(2005)
Journal of Molecular Biology
, vol.352
, Issue.4
, pp. 807-822
-
-
Maragakis, P.1
Karplus, M.2
-
14
-
-
34548304871
-
Protein conformational transitions explored by mixed elastic network models
-
DOI 10.1002/prot.21465
-
W. Zheng, B.R. Brooks, and G. Hummer Protein conformational transitions explored by mixed elastic network models Proteins 69 2007 43 57 (Pubitemid 47339138)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.69
, Issue.1
, pp. 43-57
-
-
Zheng, W.1
Brooks, B.R.2
Hummer, G.3
-
15
-
-
58749093927
-
Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes
-
N. Kantarci-Carsibasi, T. Haliloglu, and P. Doruker Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes Biophys. J. 95 2008 5862 5873
-
(2008)
Biophys. J.
, vol.95
, pp. 5862-5873
-
-
Kantarci-Carsibasi, N.1
Haliloglu, T.2
Doruker, P.3
-
16
-
-
37349101940
-
An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins
-
DOI 10.1002/prot.21570
-
S. Kirillova, and J. Cortés T. Siméon An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins Proteins 70 2008 131 143 (Pubitemid 350293455)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.70
, Issue.1
, pp. 131-143
-
-
Kirillova, S.1
Cortes, J.2
Stefaniu, A.3
Simeon, T.4
-
17
-
-
66249135330
-
Allosteric transitions of supramolecular systems explored by network models: Application to chaperonin GroEL
-
Z. Yang, P. Májek, and I. Bahar Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL PLOS Comput. Biol. 5 2009 e1000360
-
(2009)
PLOS Comput. Biol.
, vol.5
, pp. 1000360
-
-
Yang, Z.1
Májek, P.2
Bahar, I.3
-
18
-
-
70349336348
-
The energy profiles of atomic conformational transition intermediates of adenylate kinase
-
Y. Feng, and L. Yang R.L. Jernigan The energy profiles of atomic conformational transition intermediates of adenylate kinase Proteins 77 2009 551 558
-
(2009)
Proteins
, vol.77
, pp. 551-558
-
-
Feng, Y.1
Yang, L.2
Jernigan, R.L.3
-
19
-
-
84885111575
-
Global transitions of proteins explored by a multiscale hybrid methodology: Application to adenylate kinase
-
M. Gur, J.D. Madura, and I. Bahar Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase Biophys. J. 105 2013 1643 1652
-
(2013)
Biophys. J.
, vol.105
, pp. 1643-1652
-
-
Gur, M.1
Madura, J.D.2
Bahar, I.3
-
20
-
-
33744811942
-
Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes
-
DOI 10.1529/biophysj.105.076836
-
W. Zheng, and B.R. Brooks Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes Biophys. J. 90 2006 4327 4336 (Pubitemid 43830881)
-
(2006)
Biophysical Journal
, vol.90
, Issue.12
, pp. 4327-4336
-
-
Zheng, W.1
Brooks, B.R.2
-
21
-
-
79960718392
-
A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins
-
A. Ahmed, and F. Rippmann H. Gohlke A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins J. Chem. Inf. Model. 51 2011 1604 1622
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 1604-1622
-
-
Ahmed, A.1
Rippmann, F.2
Gohlke, H.3
-
23
-
-
35748982413
-
Geometry-Based Sampling of Conformational Transitions in Proteins
-
DOI 10.1016/j.str.2007.09.017, PII S0969212607003681
-
D. Seeliger, J. Haas, and B.L. de Groot Geometry-based sampling of conformational transitions in proteins Structure 15 2007 1482 1492 (Pubitemid 350051928)
-
(2007)
Structure
, vol.15
, Issue.11
, pp. 1482-1492
-
-
Seeliger, D.1
Haas, J.2
De Groot, B.L.3
-
24
-
-
76749123486
-
Conformational transitions upon ligand binding: Holo-structure prediction from apo conformations
-
D. Seeliger, and B.L. de Groot Conformational transitions upon ligand binding: holo-structure prediction from apo conformations PLOS Comput. Biol. 6 2010 e1000634
-
(2010)
PLOS Comput. Biol.
, vol.6
, pp. 1000634
-
-
Seeliger, D.1
De Groot, B.L.2
-
25
-
-
0028203492
-
Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme
-
A. Kolinski, and J. Skolnick Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme Proteins 18 1994 338 352 (Pubitemid 24111533)
-
(1994)
Proteins: Structure, Function and Genetics
, vol.18
, Issue.4
, pp. 338-352
-
-
Kolinski, A.1
Skolnick, J.2
-
26
-
-
0034663710
-
Dynamics of proteins predicted by molecular simulations and analytical approaches: Application to α-amylase inhibitor
-
DOI 10.1002/ 1097-0134 (20000815) 40:3<512::AID-PROT180>3.0.CO;2-M
-
P. Doruker, A.R. Atilgan, and I. Bahar Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor Proteins 40 2000 512 524 (Pubitemid 30624460)
-
(2000)
Proteins: Structure, Function and Genetics
, vol.40
, Issue.3
, pp. 512-524
-
-
Doruker, P.1
Atilgan, A.R.2
Bahar, I.3
-
27
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
A.R. Atilgan, and S.R. Durell I. Bahar Anisotropy of fluctuation dynamics of proteins with an elastic network model Biophys. J. 80 2001 505 515
-
(2001)
Biophys. J.
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
Durell, S.R.2
Bahar, I.3
-
28
-
-
0032525271
-
Coarse-grained simulations of conformational dynamics of proteins: Application to apomyoglobin
-
DOI 10.1002 /(SICI) 1097-0134 (19980515) 31:3<271::AID-PROT4>3.0. CO;2-M
-
T. Haliloglu, and I. Bahar Coarse-grained simulations of conformational dynamics of proteins: application to apomyoglobin Proteins 31 1998 271 281 (Pubitemid 28217815)
-
(1998)
Proteins: Structure, Function and Genetics
, vol.31
, Issue.3
, pp. 271-281
-
-
Haliloglu, T.1
Bahar, I.2
-
29
-
-
0032852778
-
Coarse-grained simulations of the conformational dynamics of proteins
-
DOI 10.1016/S1089-3156(99)00012-4, PII S1089315699000124
-
T. Haliloglu Coarse-grained simulations of the conformational dynamics of proteins Comput. Theor. Polym. Sci. 9 1999 255 260 (Pubitemid 29453973)
-
(1999)
Computational and Theoretical Polymer Science
, vol.9
, Issue.3-4
, pp. 255-260
-
-
Haliloglu, T.1
-
30
-
-
0345281586
-
Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations
-
DOI 10.1002 /(SICI) 1097-0134 (19991115) 37:3<454::AID-PROT12>3.0. CO;2-V
-
N. Kurt, and T. Haliloǧlu Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations Proteins 37 1999 454 464 (Pubitemid 29519734)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.37
, Issue.3
, pp. 454-464
-
-
Kurt, N.1
Haliloglu, T.2
-
32
-
-
0031566950
-
Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
-
DOI 10.1006/jmbi.1996.0758
-
I. Bahar, and R.L. Jernigan Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation J. Mol. Biol. 266 1997 195 214 (Pubitemid 27170528)
-
(1997)
Journal of Molecular Biology
, vol.266
, Issue.1
, pp. 195-214
-
-
Bahar, I.1
Jernigan, R.L.2
-
33
-
-
0030832809
-
Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches
-
DOI 10.1002 /(SICI) 1097-0134 (199711) 29:3<292::AID-PROT4>3.0. CO;2-D
-
I. Bahar, M. Kaplan, and R.L. Jernigan Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches Proteins 29 1997 292 308 (Pubitemid 27484221)
-
(1997)
Proteins: Structure, Function and Genetics
, vol.29
, Issue.3
, pp. 292-308
-
-
Bahar, I.1
Kaplan, M.2
Jernigan, R.L.3
-
34
-
-
0001976163
-
A shifted block Lanczos-algorithm for solving sparse symmetrical generalized eigenproblems
-
R.G. Grimes, J.G. Lewis, and H.D. Simon A shifted block Lanczos-algorithm for solving sparse symmetrical generalized eigenproblems SIAM J. Matrix Anal. Appl. 15 1994 228 272
-
(1994)
SIAM J. Matrix Anal. Appl.
, vol.15
, pp. 228-272
-
-
Grimes, R.G.1
Lewis, J.G.2
Simon, H.D.3
-
36
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
A.G. Murzin, and S.E. Brenner C. Chothia SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247 1995 536 540
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Chothia, C.3
-
37
-
-
0029644168
-
Adenylate kinase motions during catalysis: An energetic counterweight balancing substrate binding
-
C.W. Müller, and G.J. Schlauderer G.E. Schulz Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding Structure 4 1996 147 156 (Pubitemid 126658978)
-
(1996)
Structure
, vol.4
, Issue.2
, pp. 147-156
-
-
Muller, C.W.1
Schlauderer, G.J.2
Reinstein, J.3
Schulz, G.E.4
-
38
-
-
0026544877
-
Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state
-
C.W. Müller, and G.E. Schulz Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state J. Mol. Biol. 224 1992 159 177
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 159-177
-
-
Müller, C.W.1
Schulz, G.E.2
-
39
-
-
33846847773
-
Conformational Transitions of Adenylate Kinase: Switching by Cracking
-
DOI 10.1016/j.jmb.2006.11.085, PII S0022283606016445
-
P.C. Whitford, and O. Miyashita J.N. Onuchic Conformational transitions of adenylate kinase: switching by cracking J. Mol. Biol. 366 2007 1661 1671 (Pubitemid 46215597)
-
(2007)
Journal of Molecular Biology
, vol.366
, Issue.5
, pp. 1661-1671
-
-
Whitford, P.C.1
Miyashita, O.2
Levy, Y.3
Onuchic, J.N.4
-
40
-
-
33746565283
-
Molecular dynamics of apo-adenylate kinase: A principal component analysis
-
DOI 10.1021/jp061976m
-
H. Lou, and R.I. Cukier Molecular dynamics of apo-adenylate kinase: a principal component analysis J. Phys. Chem. B 110 2006 12796 12808 (Pubitemid 44139472)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.25
, pp. 12796-12808
-
-
Lou, H.1
Cukier, R.I.2
-
41
-
-
78149441109
-
Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase
-
D. Bhatt, and D.M. Zuckerman Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase J. Chem. Theory Comput. 6 2010 3527 3539
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 3527-3539
-
-
Bhatt, D.1
Zuckerman, D.M.2
-
42
-
-
70350146298
-
Zipping and unzipping of adenylate kinase: Atomistic insights into the ensemble of open< - >closed transitions
-
O. Beckstein, and E.J. Denning T.B. Woolf Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open< - >closed transitions J. Mol. Biol. 394 2009 160 176
-
(2009)
J. Mol. Biol.
, vol.394
, pp. 160-176
-
-
Beckstein, O.1
Denning, E.J.2
Woolf, T.B.3
-
43
-
-
0030939896
-
A new method for modeling large-scale rearrangements of protein domains
-
DOI 10.1002 /(SICI) 1097-0134 (199703) 27:3<410::AID-PROT9>3.0. CO;2-G
-
V. Maiorov, and R. Abagyan A new method for modeling large-scale rearrangements of protein domains Proteins 27 1997 410 424 (Pubitemid 27149293)
-
(1997)
Proteins: Structure, Function and Genetics
, vol.27
, Issue.3
, pp. 410-424
-
-
Maiorov, V.1
Abagyan, R.2
-
44
-
-
0035966323
-
ATP-bound states of GroEL captured by cryo-electron microscopy
-
DOI 10.1016/S0092-8674(01)00617-1
-
N.A. Ranson, and G.W. Farr H.R. Saibil ATP-bound states of GroEL captured by cryo-electron microscopy Cell 107 2001 869 879 (Pubitemid 34084978)
-
(2001)
Cell
, vol.107
, Issue.7
, pp. 869-879
-
-
Ranson, N.A.1
Farr, G.W.2
Roseman, A.M.3
Gowen, B.4
Fenton, W.A.5
Horwich, A.L.6
Saibil, H.R.7
-
45
-
-
0037418665
-
14 at 2.0 resolution
-
DOI 10.1016/S0022-2836(03)00184-0
-
J. Wang, and D.C. Boisvert Structural basis for GroEL-assisted protein folding from the crystal structure of (GroEL-KMgATP)14 at 2.0A resolution J. Mol. Biol. 327 2003 843 855 (Pubitemid 36315923)
-
(2003)
Journal of Molecular Biology
, vol.327
, Issue.4
, pp. 843-855
-
-
Wang, J.1
Boisvert, D.C.2
-
46
-
-
33750407288
-
Anisotropic network model: Systematic evaluation and a new web interface
-
DOI 10.1093/bioinformatics/btl448
-
E. Eyal, L.W. Yang, and I. Bahar Anisotropic network model: systematic evaluation and a new web interface Bioinformatics 22 2006 2619 2627 (Pubitemid 44642600)
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2619-2627
-
-
Eyal, E.1
Yang, L.-W.2
Bahar, I.3
|