-
1
-
-
0028335096
-
Structural mechanisms for domain movements in proteins
-
8204609
-
Structural mechanisms for domain movements in proteins. M Gerstein AM Lesk C Chothia, Biochemistry 1994 33 6739 6749 8204609
-
(1994)
Biochemistry
, vol.33
, pp. 6739-6749
-
-
Gerstein, M.1
Lesk, A.M.2
Chothia, C.3
-
2
-
-
23444454552
-
The Amber biomolecular simulation programs
-
16200636
-
The Amber biomolecular simulation programs. DA Case T Cheatham T Darden H Gohlke R Luo KM Merz Jr A Onufriev C Simmerling B Wang R Woods, J Comput Chem 2005 26 1668 1688 16200636
-
(2005)
J Comput Chem
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham, T.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr, K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.10
-
4
-
-
0037398844
-
Minimalist models for protein folding and design
-
DOI 10.1016/S0959-440X(03)00030-7
-
Minimalist models for protein folding and design. T Head-Gordon S Brown, Curr. Opin. Struct. Biol. 2003 13 2 160 167 12727508 (Pubitemid 36515143)
-
(2003)
Current Opinion in Structural Biology
, vol.13
, Issue.2
, pp. 160-167
-
-
Head-Gordon, T.1
Brown, S.2
-
6
-
-
13444305369
-
Simple energy landscape model for the kinetics of functional transitions in proteins
-
16851180
-
Simple Energy Landscape Model for the Kinetics of Functional Transitions in Proteins. O Miyashita PG Wolynes JN Onucic, J Phys Chem B 2005 109 5 1959 1969 16851180
-
(2005)
J Phys Chem B
, vol.109
, Issue.5
, pp. 1959-1969
-
-
Miyashita, O.1
Wolynes, P.G.2
Onucic, J.N.3
-
7
-
-
36749078686
-
Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution
-
18073112
-
Combining Efficient Conformational Sampling with a Deformable Elastic Network Model Facilitates Structure Refinement at Low Resolution. G Schroeder AT Brunger M Levitt, Structure 2007 15 1630 1641 18073112
-
(2007)
Structure
, vol.15
, pp. 1630-1641
-
-
Schroeder, G.1
Brunger, A.T.2
Levitt, M.3
-
8
-
-
59849093621
-
Iterative cluster-NMA: A tool for generating conformational transitions in proteins
-
18712827
-
Iterative cluster-NMA: A tool for generating conformational transitions in proteins. A Schuyler R Jernigan P Qasba B Ramakrishnan G Chirikjian, Proteins 2009 74 760 776 18712827
-
(2009)
Proteins
, vol.74
, pp. 760-776
-
-
Schuyler, A.1
Jernigan, R.2
Qasba, P.3
Ramakrishnan, B.4
Chirikjian, G.5
-
9
-
-
13844276692
-
Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model
-
15713460
-
Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model. W Zheng B Brooks, J. Mol. Biol. 2005 346 3 745 759 15713460
-
(2005)
J. Mol. Biol.
, vol.346
, Issue.3
, pp. 745-759
-
-
Zheng, W.1
Brooks, B.2
-
11
-
-
4344685227
-
Global ribosome motions revealed with elastic network model
-
15450299
-
Global ribosome motions revealed with elastic network model. Y Wang A Rader I Bahar R Jernigan, J. Struct. Biol. 2004 147 3 302 314 15450299
-
(2004)
J. Struct. Biol.
, vol.147
, Issue.3
, pp. 302-314
-
-
Wang, Y.1
Rader, A.2
Bahar, I.3
Jernigan, R.4
-
12
-
-
6344231648
-
Escherichia coli adenylate kinase dynamics: Comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data
-
15382240
-
Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data. N Temiz E Meirovitch I Bahar, Proteins 2004 57 468 480 15382240
-
(2004)
Proteins
, vol.57
, pp. 468-480
-
-
Temiz, N.1
Meirovitch, E.2
Bahar, I.3
-
13
-
-
33748448490
-
A natural coarse graining for simulating large biomolecular motion
-
A Natural Coarse Graining for Simulating Large Biomolecular Motion. H Gohlke M Thorpe, Biophysical J 2006 91 2115 2120
-
(2006)
Biophysical J
, vol.91
, pp. 2115-2120
-
-
Gohlke, H.1
Thorpe, M.2
-
14
-
-
34147166490
-
Comment on elastic network models and proteins
-
17406086
-
Comment on Elastic Network Models and Proteins. M Thorpe, Phys. Biol. 2007 4 60 63 17406086
-
(2007)
Phys. Biol.
, vol.4
, pp. 60-63
-
-
Thorpe, M.1
-
15
-
-
0000220710
-
Nudged elastic band method for finding minimum energy paths of transitions
-
World Scientific Edited by Berne BJ, Ciccoti G, Coker DF, Singapore
-
Nudged elastic band method for finding minimum energy paths of transitions. H Jánsson G Mills KW Jacobsen, Classical and Quantum Dynamics in Condensed Phase Simulations World Scientific, Edited by Berne BJ, Ciccoti G, Coker DF, Singapore, 1998 385 404
-
(1998)
Classical and Quantum Dynamics in Condensed Phase Simulations
, pp. 385-404
-
-
Jánsson, H.1
Mills, G.2
Jacobsen, K.W.3
-
16
-
-
58149089145
-
Can morphing methods predict intermediate structures?
-
18996395
-
Can morphing methods predict intermediate structures? D Weiss M Levitt, J. Mol. Biol. 2009 385 665 674 18996395
-
(2009)
J. Mol. Biol.
, vol.385
, pp. 665-674
-
-
Weiss, D.1
Levitt, M.2
-
17
-
-
33644893440
-
-
MIT Press
-
Principles of Robot Motion: Theory, Algorithms, and Implementations. H Choset KM Lynch S Hutchinson G Kantor W Burgard LE Kavraki S Thrun, MIT Press 2005
-
(2005)
Principles of Robot Motion: Theory, Algorithms, and Implementations
-
-
Choset, H.1
Lynch, K.M.2
Hutchinson, S.3
Kantor, G.4
Burgard, W.5
Kavraki, L.E.6
Thrun, S.7
-
20
-
-
33847776838
-
On the characterization of protein native state ensembles
-
17158570
-
On the Characterization of Protein Native State Ensembles. A Shehu L Kavraki C Clementi, Biophysical Journal 2007 92 5 1503 1511 17158570
-
(2007)
Biophysical Journal
, vol.92
, Issue.5
, pp. 1503-1511
-
-
Shehu, A.1
Kavraki, L.2
Clementi, C.3
-
22
-
-
37349101940
-
An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins
-
17640073
-
An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins. S Kirillova J Cortes A Stefaniu T Siméon, Proteins 2008 70 131 143 17640073
-
(2008)
Proteins
, vol.70
, pp. 131-143
-
-
Kirillova, S.1
Cortes, J.2
Stefaniu, A.3
Siméon, T.4
-
23
-
-
34547699008
-
Simulating protein motions with rigidity analysis
-
17691897
-
Simulating Protein Motions with Rigidity Analysis. S Thomas X Tang L Tapia NM Amato, J Comput Biol 2007 14 6 839 855 17691897
-
(2007)
J Comput Biol
, vol.14
, Issue.6
, pp. 839-855
-
-
Thomas, S.1
Tang, X.2
Tapia, L.3
Amato, N.M.4
-
24
-
-
27744446287
-
Protein folding by motion planning
-
16280620
-
Protein folding by motion planning. S Thomas G Song NM Amato, Phys. Biol. 2005 2 148 S155 16280620
-
(2005)
Phys. Biol.
, vol.2
-
-
Thomas, S.1
Song, G.2
Amato, N.M.3
-
25
-
-
34447281773
-
Using stochastic roadmap simulation to predict experimental quantities in protein folding kinetics
-
17683262
-
Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics. TH Chiang MS Apaydin DL Brutlag D Hsu JC Latombe, J Comput Biol 2007 14 5 578 593 17683262
-
(2007)
J Comput Biol
, vol.14
, Issue.5
, pp. 578-593
-
-
Chiang, T.H.1
Apaydin, M.S.2
Brutlag, D.L.3
Hsu, D.4
Latombe, J.C.5
-
26
-
-
55949100432
-
Efficient algorithms to explore conformation spaces of flexible protein loops
-
18989041
-
Efficient algorithms to explore conformation spaces of flexible protein loops. P Yao A Dhanik N Marz R Propper C Kou G Liu H van den Bedem JC Latombe I Halperin-Landsberg RB Altman, IEEE/ACM Trans Comput Biol Bioinform 2008 5 4 534 545 18989041
-
(2008)
IEEE/ACM Trans Comput Biol Bioinform
, vol.5
, Issue.4
, pp. 534-545
-
-
Yao, P.1
Dhanik, A.2
Marz, N.3
Propper, R.4
Kou, C.5
Liu, G.6
Van Den Bedem, H.7
Latombe, J.C.8
Halperin-Landsberg, I.9
Altman, R.B.10
-
27
-
-
34547442884
-
Tools for simulating and analyzing RNA folding kinetics
-
San Francisco, CA, USA
-
Tools for Simulating and Analyzing RNA Folding Kinetics. X Tang S Thomas L Tapia NM Amato, Proc. Int. Conf. Comput. Molecular Biology (RECOMB) San Francisco, CA, USA 2007 268 282
-
(2007)
Proc. Int. Conf. Comput. Molecular Biology (RECOMB)
, pp. 268-282
-
-
Tang, X.1
Thomas, S.2
Tapia, L.3
Amato, N.M.4
-
28
-
-
61449189835
-
Rapid sampling of molecular motions with prior information constraints
-
19247429
-
Rapid sampling of molecular motions with prior information constraints. B Raveh A Enosh O Furman-Schueler D Halperin, PLoS Comput Biol 2009 5 2 1000295 19247429
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.2
, pp. 51000295
-
-
Raveh, B.1
Enosh, A.2
Furman-Schueler, O.3
Halperin, D.4
-
29
-
-
68149125150
-
Multiscale characterization of Protein Conformational Ensembles
-
19280604
-
Multiscale characterization of Protein Conformational Ensembles. A Shehu L Kavraki C Clementi, Proteins 2009 76 4 837 851 19280604
-
(2009)
Proteins
, vol.76
, Issue.4
, pp. 837-851
-
-
Shehu, A.1
Kavraki, L.2
Clementi, C.3
-
30
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
6667333
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. W Kabsch C Sander, Biopolymers 1983 22 2577 2637 6667333
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
31
-
-
34547260921
-
Ultrafast shape recognition to search compound databases for similar molecular shapes
-
17342716
-
Ultrafast shape recognition to search compound databases for similar molecular shapes. PJ Ballester WG Richards, J. Comput. Chem. 2007 28 10 1711 1723 17342716
-
(2007)
J. Comput. Chem.
, vol.28
, Issue.10
, pp. 1711-1723
-
-
Ballester, P.J.1
Richards, W.G.2
-
32
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
14531054
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Y Duan C Wu S Chowdhury M Lee G Xiong W Zhang R Yang P Cieplak R Luo T Lee, J. Comput. Chem. 2003 24 1999 2012 14531054
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
-
34
-
-
84880150050
-
Fast tree-based exploration of state space for robots with dynamics
-
Springer, STAR 17 Erdmann M, Hsu D, Overmars M, van der Stappen AF
-
Fast Tree-Based Exploration of State Space for Robots with Dynamics. AM Ladd LE Kavraki, Algorithmic Foundations of Robotics VI. Springer, STAR 17, Erdmann M, Hsu D, Overmars M, van der Stappen AF, 2005 297 312
-
(2005)
Algorithmic Foundations of Robotics VI.
, pp. 297-312
-
-
Ladd, A.M.1
Kavraki, L.E.2
-
35
-
-
38149048265
-
Motion planning for physical simulation
-
Dept. of Computer Science, Rice University, Houston, TX
-
Motion Planning for Physical Simulation. AM Ladd, PhD thesis Dept. of Computer Science, Rice University, Houston, TX 2006
-
(2006)
PhD Thesis
-
-
Ladd, A.M.1
-
39
-
-
0037072880
-
Structures of the complexes of a potent anti-HIV protein cyanovirin-N and high mannose oligosaccharides
-
12110688
-
Structures of the complexes of a potent anti-HIV protein cyanovirin-N and high mannose oligosaccharides. I Botos B O'Keefe S Shenoy L Cartner DM Ratner PH Seeberger MR Boyd A Wlodawer, J. Biol. Chem. 2002 277 34336 34342 12110688
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 34336-34342
-
-
Botos, I.1
O'Keefe, B.2
Shenoy, S.3
Cartner, L.4
Ratner, D.M.5
Seeberger, P.H.6
Boyd, M.R.7
Wlodawer, A.8
-
40
-
-
0036113691
-
The domain-swapped dimer of cyanovirin-N is in a metastable folded state: Reconciliation of X-ray and NMR structures
-
12015150
-
The domain-swapped dimer of cyanovirin-N is in a metastable folded state: reconciliation of X-ray and NMR structures. LG Barrientos JM Louis I Botos T Mori Z Han BR O'Keefe MR Boyd A Wlodawer AM Gronenborn, Structure 2002 10 673 686 12015150
-
(2002)
Structure
, vol.10
, pp. 673-686
-
-
Barrientos, L.G.1
Louis, J.M.2
Botos, I.3
Mori, T.4
Han, Z.5
O'Keefe, B.R.6
Boyd, M.R.7
Wlodawer, A.8
Gronenborn, A.M.9
-
42
-
-
34447515841
-
From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes
-
17523187
-
From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes. AP Heath LE Kavraki C Clementi, Proteins 2007 68 3 646 661 17523187
-
(2007)
Proteins
, vol.68
, Issue.3
, pp. 646-661
-
-
Heath, A.P.1
Kavraki, L.E.2
Clementi, C.3
-
43
-
-
36749008588
-
Large scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
-
18000050
-
Large scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. K Arora CL Brooks III, Proc Natl Acad Sci U S A 2007 104 47 18496 18501 18000050
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, Issue.47
, pp. 18496-18501
-
-
Arora, K.1
Brooks III, C.L.2
-
44
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. I. the method
-
The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. S Kumar JM Rosenberg D Bouzida RH Swendsen PA Kollman, J. Comput. Chem. 1992 13 8 1011 1021
-
(1992)
J. Comput. Chem.
, vol.13
, Issue.8
, pp. 1011-1021
-
-
Kumar, S.1
Rosenberg, J.M.2
Bouzida, D.3
Swendsen, R.H.4
Kollman, P.A.5
-
45
-
-
25144472137
-
Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein
-
16157349
-
Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein. KP Ravindranathan E Gallicchio R Levy, J. Mol. Biol. 2005 353 196 210 16157349
-
(2005)
J. Mol. Biol.
, vol.353
, pp. 196-210
-
-
Ravindranathan, K.P.1
Gallicchio, E.2
Levy, R.3
-
46
-
-
70349336348
-
The energy profiles of atomic conformational transition intermediates of adenylate kinase
-
19507242
-
The energy profiles of atomic conformational transition intermediates of adenylate kinase. Y Feng L Yang A Kloczkowski RL Jernigan, Proteins 2009 77 3 551 558 19507242
-
(2009)
Proteins
, vol.77
, Issue.3
, pp. 551-558
-
-
Feng, Y.1
Yang, L.2
Kloczkowski, A.3
Jernigan, R.L.4
-
47
-
-
36849048228
-
Intrinsic motions along an enzymatic reaction trajectory
-
18026086
-
Intrinsic motions along an enzymatic reaction trajectory. K Henzler-Wildman V Thai M Lei M Ott M Wolf-Watz T Fenn E Pozharski M Wilson G Petsko M Karplus C Hübner D Kern, Nature 2007 450 7171 838 844 18026086
-
(2007)
Nature
, vol.450
, Issue.7171
, pp. 838-844
-
-
Henzler-Wildman, K.1
Thai, V.2
Lei, M.3
Ott, M.4
Wolf-Watz, M.5
Fenn, T.6
Pozharski, E.7
Wilson, M.8
Petsko, G.9
Karplus, M.10
Hübner, C.11
Kern, D.12
|