Group: baker-group - with tag quasiharmonic_models [42 articles] Export

Recent papers posted by members of the baker-group group with tag quasiharmonic_models

	Modeling the Mechanical Response of Proteins to Anisotropic Deformation [My Copy] ChemPhysChem, Vol. 10, No. 1. (2009), pp. 115-118. by Sophie Sacquin-Mora, Richard Lavery posted to quasiharmonic_models by sobolevnrm to the group baker-group on 2009-05-28 12:32:12 as
	Frequency-resolved communication maps for proteins and other nanoscale materials [My Copy] The Journal of Chemical Physics, Vol. 130, No. 19. (2009), 195101. by David M. Leitner posted to allostery quasiharmonic_models by sobolevnrm to the group baker-group on 2009-05-20 12:46:21 as along with 2 people and 2 groups biblioteca_babel barry structural_bioinformatics McCammon
	The subspace iteration method in protein normal mode analysis [My Copy] Journal of Computational Chemistry, Vol. 31, No. 1. (2010), pp. 66-74. by Reza S. Sedeh, Mark Bathe, Klaus-Jürgen Bathe posted to mathematics quasiharmonic_models by sobolevnrm to the group baker-group on 2009-05-01 12:13:58 as along with 1 person agrossfield
	Computational Methods for Predicting Sites of Functionally Important Dynamics [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Adam D. Schuyler, Heather A. Carlson, Eva L. Feldman posted to bioinformatics quasiharmonic_models structure by sobolevnrm to the group baker-group on 2009-04-21 12:31:19 as along with 5 people skywalkerus02 agrossfield ubcg08l higueruelo barry
	Biomolecular motion characterization by a self-distribution-function procedure in elastic incoherent neutron scattering [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 4. (2009), 041915. by Salvatore Magazù, Giacomo Maisano, Federica Migliardo, Antonio Benedetto posted to experimental_methodology quasiharmonic_models by sobolevnrm to the group baker-group on 2009-04-20 12:37:51 as
	Linear response theory in dihedral angle space for protein structural change upon ligand binding [My Copy] Journal of Computational Chemistry, Vol. 30, No. 16. (2009), pp. 2602-2608. by Satoshi Omori, Sotaro Fuchigami, Mitsunori Ikeguchi, Akinori Kidera posted to allostery protein-ligand_interactions quasiharmonic_models by sobolevnrm to the group baker-group on 2009-04-20 12:35:29 as along with 2 people barry RamuAnandakrishnan
	Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL [My Copy] PLoS Comput Biol, Vol. 5, No. 4. (17 April 2009), e1000360. by Zheng Yang, Peter Májek, Ivet Bahar posted to allostery quasiharmonic_models by sobolevnrm to the group baker-group on 2009-04-20 12:33:47 as along with 2 people and 1 group barry jmccammon McCammon
	Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: A case study of antibodies [My Copy] BMC Structural Biology, Vol. 7 (17 May 2007), 31. by Ozlem Keskin posted to allostery quasiharmonic_models by sobolevnrm to the group baker-group on 2009-04-03 12:49:07 as along with 4 people skywalkerus02 aqeel choonpeng medic0747
	Multivariate frequency domain analysis of protein dynamics [My Copy] The Journal of Chemical Physics, Vol. 130, No. 12. (2009), 124104. by Yasuhiro Matsunaga, Sotaro Fuchigami, Akinori Kidera posted to quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-27 11:57:11 as along with 1 person barry
	In silico Relationship between Configurational Entropy and Soft Degrees of Freedom in Proteins and Peptides [My Copy] Physical Review Letters, Vol. 102, No. 11. (2009), 118108. by Da W. Li, Rafael Brüschweiler posted to free_energy quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-26 11:37:09 as along with 2 people anna_yershova Diego_Prada
	Classical Simulation of Quantum Energy Flow in Biomolecules [My Copy] Physical Review Letters, Vol. 102, No. 11. (2009), 118301. by Gerhard Stock posted to quantum_mechanics quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-26 11:36:51 as along with 2 people biblioteca_babel paulschlesinger
	Analysis of Correlations between Energy and Residue Fluctuations in Native Proteins and Determination of Specific Sites for Binding [My Copy] Physical Review Letters, Vol. 102, No. 8. (2009) by Turkan Haliloglu, Burak Erman posted to protein-ligand_interactions quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-26 11:36:12 as along with 1 person scratchmandoo
	Automatic identification of discrete substates in proteins: singular value decomposition analysis of time-averaged crystallographic refinements. [My Copy] Proteins, Vol. 22, No. 4. (August 1995), pp. 311-321. by T. D. Romo, J. B. Clarage, D. C. Sorensen, G. N. Phillips posted to quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-25 11:37:54 as
	Building alternate protein structures using the elastic network model [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by Qingyi Yang, Kim A. Sharp posted to enhanced_sampling quasiharmonic_models structure_prediction by sobolevnrm to the group baker-group on 2009-03-25 11:36:50 as along with 5 people and 1 group pansapiens klexa abovell oteri middledomain Structural Biology Group TorVergata
	Statistical thermodynamics of residue fluctuations in native proteins [My Copy] The Journal of Chemical Physics, Vol. 130, No. 9. (2009), 095103. by Osman N. Yogurtcu, Mert Gur, Burak Erman posted to quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-25 11:36:38 as along with 1 person agrossfield
	Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach [My Copy] The Journal of Chemical Physics, Vol. 130, No. 8. (2009), 084107. by A. Ghysels, D. Van Neck, B. R. Brooks, V. Van Speybroeck, M. Waroquier posted to molecular_simulation quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-25 11:31:29 as along with 1 person barry
	Principal Component Analysis of Native Ensembles of Biomolecular Structures (PCA_NEST): Insights into Functional Dynamics [My Copy] Bioinformatics (15 January 2009), btp023. by Lee-Wei Yang, Eran Eyal, Ivet Bahar, Akio Kitao posted to quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-24 12:24:32 as along with 4 people agomez carlosjavierna apaydin ahmetbakan
	Localizing normal modes in large molecules [My Copy] The Journal of Chemical Physics, Vol. 130, No. 8. (2009) by Christoph R. Jacob, Markus Reiher posted to quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-24 12:24:21 as along with 1 person dlimmer
	Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Manuel Rueda, Giovanni Bottegoni, Ruben Abagyan posted to protein-ligand_interactions quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-23 11:56:04 as along with 1 person reyez
	Conformational Motions of HIV-1 Protease Identified Using Reversible Digitally Filtered Molecular Dynamics [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Adrian P. Wiley, Sarah L. Williams, Jonathan W. Essex posted to clustering molecular_simulation quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-23 11:51:27 as
	Iterative cluster-NMA: A tool for generating conformational transitions in proteins. [My Copy] Proteins, Vol. 74, No. 3. (15 February 2009), pp. 760-776. by A. D. Schuyler, R. L. Jernigan, P. K. Qasba, B. Ramakrishnan, G. S. Chirikjian posted to enhanced_sampling quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-22 14:02:45 as along with 1 person aqeel
	StoneHinge: hinge prediction by network analysis of individual protein structures. [My Copy] Protein science : a publication of the Protein Society, Vol. 18, No. 2. (February 2009), pp. 359-371. by K. S. Keating, S. C. Flores, M. B. Gerstein, L. A. Kuhn posted to clustering enhanced_sampling quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-22 14:02:38 as along with 1 person and 1 group barry structural_bioinformatics
	Multiscale characterization of protein conformational ensembles [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 4. (2009), pp. 837-851. by Amarda Shehu, Lydia E. Kavraki, Cecilia Clementi posted to clustering quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-20 11:46:47 as along with 4 people and 2 groups anuragsethi okapi barry apaydin structural_bioinformatics McCammon
	Allostery Wiring Diagrams in the Transitions that Drive the GroEL Reaction Cycle. [My Copy] Journal of molecular biology (24 December 2008) by Riina Tehver, Jie Chen, D Thirumalai posted to allostery quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-19 12:07:27 as along with 1 person and 1 group barry McCammon
	Instantaneous Normal Modes and the Protein Glass Transition [My Copy] Biophysical Journal, Vol. 96, No. 2. (21 January 2009), pp. 476-484. by R. Schulz, M. Krishnan, I. Daidone, J. Smith posted to quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-18 11:28:41 as
	Multidimensional Langevin modeling of biomolecular dynamics [My Copy] The Journal of Chemical Physics, Vol. 130, No. 3. (2009), 034106. by Rainer Hegger, Gerhard Stock posted to diffusion kinetics multiscale quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-18 11:28:11 as along with 1 person Diego_Prada
	Similarity Measures for Protein Ensembles [My Copy] PLoS ONE, Vol. 4, No. 1. (15 January 2009), e4203. by Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg posted to bioinformatics clustering molecular_simulation quasiharmonic_models structure by sobolevnrm to the group baker-group on 2009-03-18 11:22:13 as along with 9 people and 2 groups skywalkerus02 anuragsethi klexa apaydin gane5h barry jmccammon reyez biehl structural_bioinformatics McCammon
	The Static Modes: An alternative approach for the treatment of macro- and bio-molecular induced-fit flexibility [My Copy] The European Physical Journal E: Soft Matter and Biological Physics by M. Brut, A. Estève, G. Landa, G. Renvez, Djafari posted to quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-13 11:25:53 as
	Spectral methods in machine learning and new strategies for very large datasets. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 2. (13 January 2009), pp. 369-374. by M. A. Belabbas, P. J. Wolfe posted to clustering mathematics quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-13 11:25:33 as along with 3 people TRHvidsten rdiaz mhamada
	Pattern recognition strategies for molecular surfaces. I. Pattern generation using fuzzy set theory [My Copy] Journal of Computational Chemistry, Vol. 23, No. 12. (2002), pp. 1176-1187. by Thomas E. Exner, Matthias Keil, Jürgen Brickmann posted to quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-13 11:21:27 as
	Conformational change of proteins arising from normal mode calculations [My Copy] Protein Eng., Vol. 14, No. 1. (1 January 2001), pp. 1-6. by F. Tama, Y. H. Sanejouand posted to quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-13 11:21:20 as along with 7 people sanejouand baaden aqeel ruvido martainn saravan nigham
	Vibrational normal-mode spectrum of globular proteins [My Copy] Physical Review B, Vol. 47, No. 21. (1 June 1993), 14559. by Daniel Ben-Avraham posted to quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-13 11:21:14 as
	Universal low-frequency vibrations of proteins from a simple interaction potential [My Copy] Physical Review E, Vol. 60, No. 4. (1 October 1999), 4593. by M. Nöllmann, P. Etchegoin posted to quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-13 11:21:05 as
	Flexibility and packing in proteins [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 3. (5 February 2002), pp. 1274-1279. by Bertil Halle posted to bioinformatics quasiharmonic_models structure by sobolevnrm to the group baker-group on 2009-03-13 11:20:58 as along with 7 people and 2 groups Diego_Prada edws barry ana aqeel allmensch hmk structural_bioinformatics Bioinformatics
	Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping [My Copy] Journal of Computational Chemistry, Vol. 30, No. 3. (2009), pp. 479-492. by Stephan Frickenhaus, Srinivasaraghavan Kannan, Martin Zacharias posted to clustering molecular_dynamics quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-12 12:31:39 as along with 3 people Diego_Prada scampos agrossfield
	Tork: Conformational analysis method for molecules and complexes [My Copy] Journal of Computational Chemistry, Vol. 24, No. 16. (2003), pp. 1987-1998. by Chia-En Chang, Michael K. Gilson posted to free_energy molecular_simulation quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-04 13:05:08 as
	A method for the analysis of domain movements in large biomolecular complexes [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Guru P. Poornam, Atsushi Matsumoto, Hisashi Ishida, Steven Hayward posted to clustering enhanced_sampling quasiharmonic_models by sobolevnrm to the group baker-group on 2009-02-28 21:52:03 as along with 1 person and 3 groups barry structural_bioinformatics McCammon Bioinformatics
	Perturbational formulation of principal component analysis in molecular dynamics simulation [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 78, No. 4. (2008) by Yohei M. Koyama, Tetsuya J. Kobayashi, Shuji Tomoda, Hiroki R. Ueda posted to allostery quasiharmonic_models by sobolevnrm to the group baker-group on 2009-02-10 12:58:11 as
	Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins [My Copy] Biophys. J., Vol. 95, No. 9. (1 November 2008), pp. 4183-4192. by Edward Lyman, Jim Pfaendtner, Gregory A. Voth posted to multiscale quasiharmonic_models by sobolevnrm to the group baker-group on 2009-01-27 12:33:16 as along with 1 person aqeel
	Coarse-graining protein structures with local multivariate features from molecular dynamics. [My Copy] The journal of physical chemistry. B, Vol. 112, No. 44. (6 November 2008), pp. 14026-14035. by Zhiyong Zhang, Willy Wriggers posted to clustering multiscale quasiharmonic_models by sobolevnrm to the group baker-group on 2009-01-26 12:48:57 as along with 1 person choonpeng
	A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (1 October 2008) by Mingyang Lu, Jianpeng Ma posted to quasiharmonic_models by sobolevnrm to the group baker-group on 2008-12-28 15:36:02 as along with 6 people and 4 groups aqeel apaydin ruvido agrossfield skoddet barry Nielsen group structural_bioinformatics McCammon Bioinformatics
	CONFORMATIONAL TRANSITION PATHWAYS EXPLORED BY MONTE CARLO SIMULATION INTEGRATED WITH COLLECTIVE MODES [My Copy] Biophys. J. (1 August 2008), biophysj.107.128447. by Nigar Kantarci-Carsibasi, Turkan Haliloglu, Pemra Doruker posted to allostery molecular_simulation quasiharmonic_models by sobolevnrm to the group baker-group on 2008-12-27 14:47:38 as along with 5 people paulschlesinger oteri viktor21614 sunhwan aqeel

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allostery	27
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molecular_simulation	25
mathematics	15
multiscale	15
structure	15
bioinformatics	14
enhanced_sampling	13
molecular_dynamics	9
protein-ligand_interactions	7
kinetics	6
diffusion	4
experimental_methodology	4
free_energy	4
correlated_mutations	3
graph_theory	3
quantum_mechanics	3
protein-protein_interactions	2
protein_folding	2
software	2
statistical_mechanics	2
structure_prediction	2
2009	1
acetylcholinesterase	1
conformation	1
disorder	1
dynamics	1
efficiency	1
helicase	1
metalloregulation	1
nmr	1
packing	1
protein	1
protein_engineering	1
statistics	1

Group: baker-group - with tag quasiharmonic_models [42 articles] Export

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