Tag nma [151 articles] Export

Recent papers classified by the tag nma.

	Hydrogen bonding in protein circular dichroism calculations [My Copy] Journal of Molecular Structure: THEOCHEM, Vol. 506, No. 1-3. (14 July 2000), pp. 161-167. by N. Besley posted to nma hydrogen_bonds by loison on 2009-11-17 13:17:49 as
	Can Conformational Change Be Described by Only a Few Normal Modes? [My Copy] Biophys. J., Vol. 90, No. 5. (1 March 2006), pp. 1583-1593. by Paula Petrone, Vijay S. Pande posted to nma by ahmetbakan on 2009-10-19 01:49:21 as along with 12 people and 7 groups csrocha BragilMassoud barry dimka aqeel shuns yongzhao xdeupi choonpeng joergkurtwegner daevans LamBras structural_bioinformatics Bioinformatics TSRI_MGL Molecular-Modelling Drug-Design Cheminformatics LabCompMed
	The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 34. (25 August 2009), pp. 14349-14354. by Ahmet Bakan, Ivet Bahar posted to nma flexibility essential-dynamics enm anm by ahmetbakan on 2009-10-18 19:11:57 as along with 6 people and 1 group mittinatten apaydin anuragsethi jmccammon okapi boris_aguilar McCammon
	A force field for virtual atom molecular mechanics of proteins [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 37. (15 September 2009), pp. 15667-15672. by Anil Korkut, Wayne A. Hendrickson posted to nma force_field coarse_grain by barry to the group structural_bioinformatics on 2009-09-28 19:29:39 as along with 1 person and 1 group jmccammon McCammon
	Theoretical analysis of twist/bend ratio and mechanical moduli of bacterial flagellar hook and filament. [My Copy] Biophys J, Vol. 86, No. 5. (May 2004), pp. 3204-3210. by Terence C. Flynn, Jianpeng Ma posted to nma enm by abovell on 2009-08-26 18:52:44 as along with 1 person aqeel
	A Natural Coarse Graining for Simulating Large Biomolecular Motion [My Copy] Vol. 91, No. 6. (15 September 2006), pp. 2115-2120. by Holger Gohlke, M. F. Thorpe posted to enm first froda nma protein_dynamics protein_flexibility by fl on 2009-07-13 09:47:21 as
	Inelastic neutron scattering from damped collective vibrations of macromolecules [My Copy] Chemical Physics, Vol. 261, No. 1-2. (1 November 2000), pp. 1-24. by G. Kneller posted to friction langevin nma protein-dynamics by abovell on 2009-07-10 16:50:43 as along with 1 person apaydin
	Harmonicity in slow protein dynamics [My Copy] Chemical Physics, Vol. 261, No. 1-2. (1 November 2000), pp. 25-37. by K. Hinsen posted to friction nma protein-dynamics by abovell on 2009-07-10 16:46:09 as along with 4 people and 1 group Diego_Prada apaydin sobolevnrm saravan baker-group
	Langevin modes of macromolecules [My Copy] The Journal of Chemical Physics, Vol. 85, No. 12. (1986), pp. 7334-7348. by Gene Lamm, Attila Szabo posted to friction langevin nma protein-dynamics by abovell on 2009-07-10 16:40:21 as along with 1 person apaydin
	On the Compression of Low Rank Matrices [My Copy] SIAM Journal on Scientific Computing, Vol. 26, No. 4. (2005), pp. 1389-1404. by H. Cheng, Z. Gimbutas, P. G. Martinsson, V. Rokhlin posted to hessian nma by abovell on 2009-07-08 18:12:05 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 2008 conformation ensembles networks nma perturbation protein structural_model structure by klexa on 2009-06-29 15:33:43 as along with 5 people and 2 groups pansapiens abovell sobolevnrm oteri middledomain baker-group Structural Biology Group TorVergata
	Normal mode analysis with simplified models to investigate the global dynamics of biological systems. [My Copy] Protein Pept Lett, Vol. 10, No. 2. (April 2003), pp. 119-132. by F. Tama posted to enm nma protein-dynamics review by abovell on 2009-06-25 16:13:09 as along with 1 person BragilMassoud
	Temperature Dependence of Normal Mode Reconstructions of Protein Dynamics [My Copy] Physical Review Letters, Vol. 102, No. 21. (2009), 218104. by Francesco Piazza, Paolo, Fabio Cecconi posted to go-model journal-club nma by abovell on 2009-06-24 16:01:04 as along with 6 people and 1 group dchen agrossfield paulschlesinger cecconi_fabio Diego_Prada kdesmond2 smc-infm
	BlockMaster: Partitioning Protein Kinase Structures Using Normal-Mode Analysis† [My Copy] The Journal of Physical Chemistry A, Vol. 113, No. 26. (2 July 2009), pp. 7528-7534. by Marina Shudler, Masha Y. Niv posted to domain_motions kinases nma by barry to the group McCammon on 2009-06-16 02:37:53 as along with 3 people carlosjavierna sobolevnrm paulschlesinger
	Coarse-graining of protein structures for the normal mode studies [My Copy] Journal of Computational Chemistry, Vol. 28, No. 8. (2007), pp. 1400-1410. by Kilho Eom, Seung-Chul Baek, Jung-Hee Ahn, Sungsoo Na posted to nma protein-dynamics by abovell on 2009-06-15 19:47:11 as along with 2 people aqeel choonpeng
	AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules [My Copy] Computer Physics Communications, Vol. 91, No. 1-3. (02 September 1995), pp. 1-41. by D Pearlman, posted to amber force-field nma protein-dynamics by abovell on 2009-06-15 18:35:41 as along with 3 people rdf papatonyhill gruppo
	Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit. [My Copy] The Journal of chemical physics, Vol. 129, No. 21. (7 December 2008) by H. L. Woodcock, W. Zheng, A. Ghysels, Y. Shao, J. Kong, B. R. Brooks posted to enm hydration-layer nma protein-dynamics water-dynamics by abovell on 2009-05-28 16:07:10 as
	Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis [My Copy] Physical Review Letters, Vol. 77, No. 9. (1996), 1905. by Monique M. Tirion posted to nma protein-dynamics by abovell on 2009-05-25 19:06:23 as along with 4 people and 1 group akraemer joseph_x_zhou aqeel Diego_Prada protein_Dyn
	Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. [My Copy] Proc Natl Acad Sci U S A, Vol. 100, No. 22. (28 October 2003), pp. 12570-12575. by O. Miyashita, J. N. Onuchic, P. G. Wolynes posted to nma nonlinear-nma protein-dynamics by abovell on 2009-05-25 19:01:13 as along with 3 people and 2 groups kjell aqeel joseph_x_zhou biophysics protein_Dyn
	Simple Energy Landscape Model for the Kinetics of Functional Transitions in Proteins [My Copy] The Journal of Physical Chemistry B, Vol. 109, No. 5. (1 February 2005), pp. 1959-1969. by Osamu Miyashita, Peter G. Wolynes, Jose N. Onuchic posted to nma nonlinear-nma protein-dynamics by abovell on 2009-05-25 18:26:05 as along with 2 people xdeupi aqeel
	Analysis of domain motions by approximate normal mode calculations [My Copy] Proteins: Structure, Function, and Genetics, Vol. 33, No. 3. (9 March 1999), pp. 417-429. by Konrad Hinsen posted to nma protein-dynamics by abovell on 2009-05-25 18:19:46 as along with 5 people and 3 groups BragilMassoud barry shadowman aqeel yongzhao structural_bioinformatics Bioinformatics TSRI_MGL
	How to describe protein motion without amino acid sequence and atomic coordinates. [My Copy] Proc Natl Acad Sci U S A, Vol. 99, No. 13. (25 June 2002), pp. 8620-8625. by D. Ming, Y. Kong, M. A. Lambert, Z. Huang, J. Ma posted to enm nma protein-dynamics by abovell on 2009-05-25 18:08:06 as along with 1 person aqeel
	A comparative study of motor-protein motions by using a simple elastic-network model. [My Copy] Proc Natl Acad Sci U S A, Vol. 100, No. 23. (11 November 2003), pp. 13253-13258. by W. Zheng, S. Doniach posted to enm nma protein-dynamics by abovell on 2009-05-25 18:01:47 as along with 5 people and 2 groups barry aqeel shuns barry2 qwermish structural_bioinformatics Bioinformatics
	Effects of Surface Water on Protein Dynamics Studied by a Novel Coarse-Grained Normal Mode Approach [My Copy] Vol. 94, No. 9. (1 May 2008), pp. 3461-3474. by Lei Zhou, Steven A. Siegelbaum posted to explicit-water hydration-layer nma protein-dynamics water-dynamics by abovell on 2009-05-25 17:46:33 as along with 1 person saravan
	Molecular Mechanics of the alpha-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior. [My Copy] PLoS computational biology, Vol. 5, No. 5. (May 2009) by J. Golji, R. Collins, M. R. Mofrad posted to alpha_actinin cytoskeleton md_simulation nma by barry to the group McCammon on 2009-05-18 20:09:50 as
	Structure-based protein NMR assignments using native structural ensembles [My Copy] Journal of Biomolecular NMR, Vol. 40, No. 4. (April 2008), pp. 263-276. by Mehmet Apaydın, Vincent Conitzer, Bruce Donald posted to assignments nma nmr resonance sba by apaydin on 2009-04-28 09:42:20 as along with 1 person rph
	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 allosteric nma protein_dynamics by barry on 2009-04-23 03:03:19 as along with 5 people and 1 group skywalkerus02 agrossfield ubcg08l higueruelo sobolevnrm baker-group
	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 nma by barry on 2009-04-21 08:32:54 as along with 1 person and 1 group sobolevnrm baker-group
	Improved Theoretical π−π* Absorption and Circular Dichroic Spectra of Helical Polypeptides Using New Polarizabilities of Atoms and NC‘O Chromophores [My Copy] The Journal of Physical Chemistry, Vol. 100, No. 45. (1 January 1996), pp. 17825-17834. by Kimberly A. Bode, Jon Applequist posted to nma by loison on 2009-04-08 16:37:26 as
	Kerr constants of amides and peptides [My Copy] Biopolymers, Vol. 12, No. 5. (1973), pp. 1137-1148. by R. T. Ingwall, E. A. Czurylo, P. J. Flory posted to nma by loison on 2009-04-08 16:30:55 as
	Charge equilibration for molecular dynamics simulations [My Copy] The Journal of Physical Chemistry, Vol. 95, No. 8. (1 April 1991), pp. 3358-3363. by Anthony K. Rappe, William A. Goddard posted to nma by loison on 2009-04-08 16:16:43 as along with 1 person dsmueller
	Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes [My Copy] J. Chem. Theory Comput., Vol. 3, No. 6. (13 November 2007), pp. 1878-1889. by W. Xie, J. Pu, A. D. Mackerell, J. Gao posted to nma by loison on 2009-04-08 16:14:51 as along with 2 people tovrstra middledomain
	Group Polarizability Model for Molecular Mechanics Energy Functions [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 6. (1 November 2007), pp. 2120-2127. by Kim Palmo, Samuel Krimm posted to nma by loison on 2009-04-08 16:07:27 as
	A Sequential Molecular Mechanics/Quantum Mechanics Study of the Electronic Spectra of Amides [My Copy] Journal of the American Chemical Society, Vol. 126, No. 41. (1 October 2004), pp. 13502-13511. by Nicholas A. Besley, Mark T. Oakley, Alexander J. Cowan, Jonathan D. Hirst posted to nma by loison on 2009-04-08 15:50:48 as
	A polarizable electrostatic model of the N-methylacetamide dimer [My Copy] Journal of Computational Chemistry, Vol. 22, No. 16. (2001), pp. 1933-1943. by B. Mannfors, N. G. Mirkin, K. Palmo, S. Krimm posted to nma by loison on 2009-04-08 15:48:44 as
	Coupling between Normal Modes Drives Protein Conformational Dynamics: Illustrations Using Allosteric Transitions in Myosin II [My Copy] Biophysical Journal, Vol. 96, No. 6. (18 March 2009), pp. 2128-2137. by Wenjun Zheng, D. Thirumalai posted to myosin nma by barry on 2009-03-20 23:48:11 as
	Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. [My Copy] J Mol Biol, Vol. 181, No. 3. (5 February 1985), pp. 423-447. by M. Levitt, C. Sander, P. S. Stern posted to collective_modes nma nma_protein_early_articles by mkrishna on 2009-02-05 05:08:33 as along with 2 people pavanghatty saravan
	Dynamics of a Small Globular Protein in Terms of Low-Frequency Vibrational Modes [My Copy] PNAS, Vol. 80, No. 12. (15 June 1983), pp. 3696-3700. by Nobuhiro Go, Tosiyuki Noguti, Testuo Nishikawa posted to coupling nma nma_protein_early_articles vet vibration by mkrishna on 2009-02-05 04:12:33 as along with 2 people aqeel saravan
	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 groel nma sca by barry to the group McCammon on 2009-01-23 02:57:06 as along with 1 person and 1 group sobolevnrm baker-group
	Generalising and Symbolising Ordnance Survey Base Scale Data to Create a Prototype 1:50 000 Scale Vector Map [My Copy] Cartographic Journal, The, Vol. 44, No. 3. (August 2007), pp. 251-257. by Revell, Patrick, Regnauld, Nicolas, Thom, Stuart posted to generalisation nma symbolisation by jgaffuri to the group Geomatics on 2009-01-06 01:53:11 as
	Automatic Amalgamation of Buildings for Producing Ordnance Survey 1:50 000 Scale Maps [My Copy] Cartographic Journal, The, Vol. 44, No. 3. (August 2007), pp. 239-250. by Regnauld, Nicolas, Revell, Patrick posted to algorithm amalgamation building generalisation nma by jgaffuri to the group Geomatics on 2009-01-06 01:52:00 as
	Creating a hydrographic network from its cartographic representation: a case study using Ordnance Survey MasterMap data [My Copy] International Journal of Geographical Information Science, Vol. 20, No. 6. (July 2006), pp. 611-631. by Regnauld, Nicolas, Mackaness, William posted to generalisation hydrography nma by jgaffuri to the group Geomatics on 2009-01-06 01:38:09 as
	A Data Model for Multi-scale Topographical Data [My Copy] Headway in Spatial Data Handling In Headway in Spatial Data Handling (2008), pp. 233-254. by J. E. Stoter, J. M. Morales, R. L. G. Lemmens, et al.B. M. Meijers, van Oosterom, C. W. Quak, H. T. Uitermark, L. Brink edited by Anne Ruas, Christopher Gold posted to generalisation multi-representation nma ocl by jgaffuri on 2008-12-31 13:59:13 as along with 1 person Saerdna
	Ab Initio Study of the Effect of Solvation on the Electronic Spectra of Formamide and N-Methylacetamide [My Copy] The Journal of Physical Chemistry A, Vol. 102, No. 52. (1 December 1998), pp. 10791-10797. by Nicholas A. Besley, Jonathan D. Hirst posted to formamide nma solvation theory by loison on 2008-12-15 09:59:09 as
	Ab Initio and Empirical Model MD Simulation Studies of Solvent Effects on the Properties of N-Methylacetamide along a cis−trans Isomerization Pathway [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 27. (1 July 2006), pp. 13523-13538. by Yves A. Mantz, Helene Gerard, Radu Iftimie, Glenn J. Martyna posted to nma solvation theory by loison on 2008-12-15 09:52:06 as
	Key interactions in integrin ectodomain responsible for global conformational change detected by elastic network normal-mode analysis. [My Copy] Biophysical journal, Vol. 95, No. 6. (15 September 2008), pp. 2895-2908. by Atsushi Matsumoto, Tetsuji Kamata, Junichi Takagi, Kenji Iwasaki, Kei Yura posted to integrin nma by choonpeng on 2008-11-25 03:07:01 as along with 2 people tprpip aqeel
	Collective motions in Glucosamine-6-phosphate Synthase: Influence of Ligand Binding and role in Ammonia Channelling and Opening of the Fructose Phosphate Binding Site. [My Copy] Journal of molecular biology (19 October 2008) by Nicolas Floquet, Philippe Durand, Bernard Maigret, Bernard Badet, Marie-Ange A. Badet-Denisot, David Perahia posted to nma by barry on 2008-11-07 01:36:09 as
	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 nma protein by ruvido on 2008-10-15 10:02:41 as along with 6 people and 5 groups sobolevnrm aqeel apaydin agrossfield skoddet barry baker-group Nielsen group structural_bioinformatics McCammon Bioinformatics
	Normal Modes and Essential Dynamics [My Copy] Molecular Modeling of Proteins, Vol. 443 (2008), pp. 89-106. by Steven Hayward, Bert L. Groot posted to nma protein by ruvido on 2008-10-13 14:43:31 as along with 4 people and 1 group arybakov csrocha LamBras higueruelo structural_bioinformatics
	Use of normal modes for structural modeling of proteins: the case study of rat heme oxygenase 1 [My Copy] European Biophysics Journal, Vol. 37, No. 7. (2008), pp. 1157-1165. by Jean-Didier Marechal, David Perahia posted to nma protein_structure_modeling by aqeel on 2008-09-30 14:05:03 as

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protein_dynamics	58
protein_structure	54
protein	23
structure	20
domain_motions	18
pca	18
md_simulation	14
protein-dynamics	14
docking	12
flexibility	11
review	11
dynamics	10
enm	10
myosin	9
structure_flexible	9
coarse-grained	8
kinesin	8
molecular_motors	8
allosteric	7
coarse_grain	7
generalisation	7
correlated_motions	6
multiple_structure_comparison	6
protein_protein	6
structure_core	6
web_server	6
2008	5
allostery	5
clustering	4
kinases	4
nachr	4
2005	3
2006	3
adh	3
bioinf_methods	3
ctbp	3
dynamic_similarity	3
f1atpase	3
flexible_protein	3
force_field	3
friction	3
nmr	3
protein-folding	3
protein_sequence	3
replica_exchange	3
time_series_analysis	3
web-server	3
xf	3
algorithm	2
alpha_actinin	2
amalgamation	2
anm	2
binding	2
building	2
cavities	2
coarse-graining	2
conformation	2
cytoskeleton	2
enzymes	2
first	2
groel	2
hydration-layer	2
hydrography	2
internal_coordinates	2
langevin	2
math	2
metabolomics	2
nma_protein_early_articles	2
nonlinear-nma	2
pocket	2
sca	2
screening	2
solvation	2
symbolisation	2
theory	2
water-dynamics	2
coupling	1
enzyme	1
hinge_motion	1
hydrogen_bonds	1
integrin	1
klein	1
md	1
mine	1
multi-representation	1
ocl	1
ppi	1
protein-docking	1
protein-domains	1
protein_structure_modeling	1
qc	1
regulation	1
residue	1
ribosome	1
sba	1
shape	1
signaling	1
skeleton	1
structural_model	1
surface	1

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