Group: structural_bioinformatics - with tag nma [32 articles] Export

Recent papers posted by members of the structural_bioinformatics group with tag nma

	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
	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 coarse_grain nma by barry to the group structural_bioinformatics on 2008-10-05 19:05:40 as along with 6 people and 4 groups sobolevnrm aqeel apaydin ruvido agrossfield skoddet baker-group Nielsen group McCammon Bioinformatics
	Representing receptor flexibility in ligand docking through relevant normal modes. [My Copy] J Am Chem Soc, Vol. 127, No. 26. (6 July 2005), pp. 9632-9640. by C. N. Cavasotto, J. A. Kovacs, R. A. Abagyan posted to docking nma by barry to the group structural_bioinformatics on 2007-09-27 19:13:39 as along with 6 people and 2 groups BragilMassoud apaydin aqeel yongzhao kazemi LamBras Bioinformatics TSRI_MGL
	Signal Propagation in Proteins and Relation to Equilibrium Fluctuations [My Copy] PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e172. by Chakra Chennubhotla, Ivet Bahar posted to allosteric correlated_motions nma protein_dynamics protein_structure time_series_analysis by barry to the group structural_bioinformatics on 2007-09-22 23:29:36 as along with 1 person and 1 group apaydin Bioinformatics
	Analysis of Domain Movements in Glutamine-Binding Protein with Simple Models [My Copy] Biophys. J., Vol. 92, No. 4. (15 February 2007), pp. 1326-1335. by Ji G. Su, Xiong Jiao, Ting G. Sun, Chun H. Li, Wei Z. Chen, Cun X. Wang posted to nma domain_motions by barry to the group structural_bioinformatics on 2007-09-13 18:57:46 as along with 1 group Bioinformatics
	How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. [My Copy] Biophys J, Vol. 88, No. 3. (March 2005), pp. 1552-1559. by T. Haliloglu, O. Keskin, B. Ma, R. Nussinov posted to protein_structure protein_protein nma by barry to the group structural_bioinformatics on 2007-09-13 18:55:42 as along with 4 people and 1 group baaden aqeel eweaver choonpeng Bioinformatics
	Evolutionary Conservation of Protein Backbone Flexibility [My Copy] Journal of Molecular Evolution, Vol. 63, No. 4. (14 October 2006), pp. 448-457. by Sandra Maguid, Sebastián Fernández-Alberti, Gustavo Parisi, Julián Echave posted to protein_structure protein_dynamics nma by barry to the group structural_bioinformatics on 2007-09-05 01:48:20 as along with 4 people and 1 group gisle jlh64 edvin tny Bioinformatics
	Association of putative concave protein-binding sites with the fluctuation behavior of residues. [My Copy] Protein Sci, Vol. 15, No. 10. (October 2006), pp. 2265-2277. by A. Ertekin, R. Nussinov, T. Haliloglu posted to protein_protein protein_dynamics nma by barry to the group structural_bioinformatics on 2007-09-04 20:13:14 as along with 1 person and 1 group aqeel Bioinformatics
	Characterization of Protein Conformational States by Normal-Mode Frequencies [My Copy] J. Am. Chem. Soc. (23 August 2007) by B. A. Hall, S. L. Kaye, A. Pang, R. Perera, P. C. Biggin posted to protein_structure pca nma md_simulation clustering by barry to the group structural_bioinformatics on 2007-08-27 19:15:41 as along with 7 people and 2 groups Diego_Prada Scis0000002 ubcg08l aqeel choonpeng sobolevnrm LamBras Bioinformatics baker-group
	How Well Can We Understand Large-Scale Protein Motions Using Normal Modes of Elastic Network Models? [My Copy] Biophys J (4 May 2007) by Lei Yang, Guang Song, Robert L L. Jernigan posted to protein_structure protein_dynamics nma correlated_motions by barry to the group structural_bioinformatics on 2007-08-13 19:53:33 as along with 3 people and 1 group aqeel choonpeng willpitt Bioinformatics
	Equilibration of experimentally determined protein structures for molecular dynamics simulation [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 74, No. 6. (2006) by Emily B. Walton, Krystyn J. Vanvliet posted to nma md_simulation by barry to the group structural_bioinformatics on 2007-04-27 17:32:57 as along with 1 group Bioinformatics
	Exploring the common dynamics of homologous proteins. Application to the globin family. [My Copy] Biophys J, Vol. 89, No. 1. (July 2005), pp. 3-13. by S. Maguid, S. Fernandez-Alberti, L. Ferrelli, J. Echave posted to protein_structure protein_dynamics nma by barry to the group structural_bioinformatics on 2007-01-19 21:54:41 as along with 5 people and 1 group aqeel gisle Einat jlh64 edvin Bioinformatics
	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 protein_dynamics by barry to the group structural_bioinformatics on 2006-08-17 20:10:25 as along with 12 people and 6 groups ahmetbakan csrocha BragilMassoud dimka aqeel shuns yongzhao xdeupi choonpeng joergkurtwegner daevans LamBras Bioinformatics TSRI_MGL Molecular-Modelling Drug-Design Cheminformatics LabCompMed
	The Contribution of Vibrational Entropy to Molecular Association : The Dimerization of Insulin [My Copy] Journal of Molecular Biology, Vol. 238, No. 3. (5 May 1994), pp. 405-414. by Bruce Tidor, Martin Karplus posted to nma protein_dynamics by barry to the group structural_bioinformatics on 2006-08-17 19:35:30 as along with 1 person and 1 group dfgreen Bioinformatics
	Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. [My Copy] Structure, Vol. 13, No. 4. (April 2005), pp. 565-577. by W. Zheng, B. R. Brooks, S. Doniach, D. Thirumalai posted to nma protein_dynamics protein_sequence protein_structure by barry to the group structural_bioinformatics on 2006-08-15 19:16:49 as along with 1 group Bioinformatics
	Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mode. [My Copy] J Biol Chem, Vol. 261, No. 32. (15 November 1986), pp. 15273-15280. by F. Colonna-Cesari, D. Perahia, M. Karplus, H. Eklund, C. I. Brädén, O. Tapia posted to adh ctbp nma by barry to the group structural_bioinformatics on 2006-08-15 02:25:29 as along with 1 group Bioinformatics
	Channel Opening Motion of [alpha]7 Nicotinic Acetylcholine Receptor as Suggested by Normal Mode Analysis [My Copy] Journal of Molecular Biology, Vol. 355, No. 2. (13 January 2006), pp. 310-324. by Xiaolin Cheng, Benzhuo Lu, Barry Grant, Richard J. Law, Andrew J. Mccammon posted to nachr nma by ana to the group structural_bioinformatics on 2006-04-03 21:01:16 as along with 2 people and 1 group sdbneuro barry Bioinformatics
	iGNM: a database of protein functional motions based on Gaussian Network Model. [My Copy] Bioinformatics, Vol. 21, No. 13. (1 July 2005), pp. 2978-2987. by L. W. Yang, X. Liu, C. J. Jursa, et al.M. Holliman, A. J. Rader, H. A. Karimi, I. Bahar posted to nma protein_dynamics protein_structure by barry to the group structural_bioinformatics on 2006-03-06 22:07:42 as along with 3 people and 2 groups baaden yongzhao choonpeng Bioinformatics TSRI_MGL
	Elastic Properties of Proteins: Insight on the Folding Process and Evolutionary Selection of Native Structures [My Copy] Journal of Molecular Biology, Vol. 321, No. 5. (30 August 2002), pp. 909-921. by Cristian Micheletti, Gianluca Lattanzi, Amos Maritan posted to nma protein_dynamics by barry to the group structural_bioinformatics on 2005-10-11 00:52:55 as along with 2 people and 1 group Einat Diego_Prada Bioinformatics
	Conformational sampling for the impatient. [My Copy] Biophys Chem, Vol. 107, No. 3. (15 February 2004), pp. 213-220. by K. Tai posted to nma protein_dynamics replica_exchange by barry to the group structural_bioinformatics on 2005-10-08 00:57:29 as along with 3 people and 2 groups baaden yongzhao dgront Bioinformatics TSRI_MGL
	MolMovDB: analysis and visualization of conformational change and structural flexibility. [My Copy] Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 478-482. by N. Echols, D. Milburn, M. Gerstein posted to nma protein_dynamics protein_structure by barry to the group structural_bioinformatics on 2005-10-08 00:56:13 as along with 3 people and 5 groups nigham yongzhao joergkurtwegner Bioinformatics TSRI_MGL Molecular-Modelling Drug-Design Cheminformatics
	Hierarchical clustering of the correlation patterns: New method of domain identification in proteins. [My Copy] Biophys Chem (24 August 2005) by S O O. Yesylevskyy, V N N. Kharkyanen, A P P. Demchenko posted to domain_motions nma pca protein_dynamics by barry to the group structural_bioinformatics on 2005-10-08 00:55:14 as along with 2 people and 2 groups yongzhao choonpeng Bioinformatics TSRI_MGL
	Analysis of domain motions in large proteins [My Copy] Proteins: Structure, Function, and Genetics, Vol. 34, No. 3., pp. 369-382. by Konrad Hinsen, Aline Thomas, Martin J. Field posted to domain_motions nma by barry to the group structural_bioinformatics on 2005-10-08 00:53:28 as along with 3 people and 2 groups ubcg08l shadowman yongzhao Bioinformatics TSRI_MGL
	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 domain_motions nma by barry to the group structural_bioinformatics on 2005-10-08 00:53:06 as along with 5 people and 2 groups abovell BragilMassoud shadowman aqeel yongzhao Bioinformatics TSRI_MGL
	Coarse-grained normal mode analysis in structural biology [My Copy] Current Opinion in Structural Biology, Vol. 15, No. 5. (October 2005), pp. 586-592. by Ivet Bahar, Aj Rader posted to bioinf_methods nma review by barry to the group structural_bioinformatics on 2005-10-03 19:18:42 as along with 7 people and 1 group BragilMassoud apaydin aqeel shuns scis0000001 insectopalo higueruelo Bioinformatics
	Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin. [My Copy] Biophys J (6 May 2005) by Wenjun Zheng, Bernard R R. Brooks posted to kinesin molecular_motors myosin nma protein_dynamics protein_structure by barry to the group structural_bioinformatics on 2005-06-28 19:01:33 as along with 5 people and 1 group BragilMassoud baaden aqeel shuns qwermish Bioinformatics
	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 f1atpase kinesin molecular_motors myosin nma protein_dynamics by barry to the group structural_bioinformatics on 2005-06-24 23:29:09 as along with 5 people and 1 group abovell aqeel shuns barry2 qwermish Bioinformatics
	Tools and databases to analyze protein flexibility; approaches to mapping implied features onto sequences. [My Copy] Methods Enzymol, Vol. 374 (2003), pp. 544-584. by W. G. Krebs, J. Tsai, V. Alexandrov, J. Junker, R. Jansen, M. Gerstein posted to nma protein_structure structure_flexible web_server by ana to the group structural_bioinformatics on 2005-06-24 00:20:41 as along with 1 person and 1 group barry Bioinformatics
	Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. [My Copy] Proteins, Vol. 48, No. 4. (1 September 2002), pp. 682-695. by W. G. Krebs, V. Alexandrov, C. A. Wilson, N. Echols, H. Yu, M. Gerstein posted to nma protein_structure structure_flexible by ana to the group structural_bioinformatics on 2005-05-25 23:41:22 as along with 5 people and 2 groups apaydin barry aqeel yongzhao martainn Bioinformatics TSRI_MGL
	Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool. [My Copy] Protein Sci, Vol. 14, No. 3. (March 2005), pp. 633-643. by V. Alexandrov, U. Lehnert, N. Echols, D. Milburn, D. Engelman, M. Gerstein posted to nma protein_structure structure_flexible web_server by ana to the group structural_bioinformatics on 2005-05-25 23:40:39 as along with 2 people and 1 group barry aqeel Bioinformatics
	An analysis of core deformations in protein superfamilies. [My Copy] Biophys J, Vol. 88, No. 2. (February 2005), pp. 1291-1299. by A. Leo-Macias, P. Lopez-Romero, D. Lupyan, D. Zerbino, A. R. Ortiz posted to multiple_structure_comparison nma pca protein_structure structure_core by ana to the group structural_bioinformatics on 2005-05-11 00:41:04 as along with 8 people and 1 group dfdong apaydin barry lna dimka aqeel insectopalo edvin Bioinformatics
	Core deformations in protein families: a physical perspective. [My Copy] Biophys Chem, Vol. 115, No. 2-3. (1 April 2005), pp. 125-128. by A. Leo-Macias, P. Lopez-Romero, D. Lupyan, D. Zerbino, A. R. Ortiz posted to multiple_structure_comparison nma pca protein_structure structure_core by ana to the group structural_bioinformatics on 2005-04-20 23:52:01 as along with 3 people and 1 group lna dimka edvin Bioinformatics

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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
cgreview	1
collective_modes	1
computation	1
concoord	1
density	1
elnemo	1
ensembles	1
enzyme	1
froda	1
gnm	1
hessian	1
hinge_motion	1
md	1
mine	1
multi-representation	1
open	1
ppi	1
rcnma	1
regulation	1
structural_model	1
structure_refinement	1
surface	1
thesis	1
vibration	1

Group: structural_bioinformatics - with tag nma [32 articles] Export

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