saravan's library 195 articles Export

	Intrinsic motions along an enzymatic reaction trajectory. [My Copy] Nature, Vol. 450, No. 7171. (6 December 2007), pp. 838-844. by Katherine A. Henzler-Wildman, Vu Thai, Ming Lei, et al.Maria Ott, Magnus Wolf-Watz, Tim Fenn, Ed Pozharski, Mark A. Wilson, Gregory A. Petsko, Martin Karplus, Christian G. Hübner, Dorothee Kern posted to no-tag by saravan on 2009-11-22 05:01:58 as along with 12 people and 1 group ahmetbakan xdeupi ubcg08l ruvido barry aqeel ebeutler cactus sobolevnrm paulschlesinger jlh64 yalexeev baker-group
	Coarse-grained models for proteins [My Copy] Current Opinion in Structural Biology, Vol. 15, No. 2. (April 2005), pp. 144-150. by V. Tozzini posted to no-tag by saravan on 2009-11-22 05:01:47 as along with 10 people flbarroso krapnik RamuAnandakrishnan baaden aqeel ltrabuco simone cottrell choonpeng iantunbridge
	Dynamic personalities of proteins [My Copy] Nature, Vol. 450, No. 7172. (12 December 2007), pp. 964-972. by Katherine Henzler-Wildman, Dorothee Kern posted to no-tag by saravan on 2009-11-22 05:01:43 as along with 19 people and 1 group victorclaessen Diego_Prada xdeupi viktor21614 ruvido barry pavanghatty chad_davis allmensch choonpeng rsantana cjeans sobolevnrm wilbur mijam kjell phoenixzxl higueruelo GeeSharpMinor baker-group
	(NMR) input structure is translated into a geometric description of Predicting free energy changes using the complex, and starting from random coordinates, 300–600 struc- structural ensembles tures both of the mutant and the wild type are generated by iteratively correcting the coordinates until all geometric constraints are fulfilled. Then an energy function based on physical chemistry (force field) and an efficient continuum solvent approach, the solution of the Poisson-Boltzmann equation and a term for nonpolar solvation2, is averaged over the generated structural ensembles (Supplementary Methods online). The free energy is approximated by [My Copy] posted to no-tag by saravan on 2009-11-04 08:39:17 as
	The Thermodynamic Influence of Trapped Water Molecules on a Protein–Ligand Interaction* [My Copy] posted to no-tag by saravan on 2009-11-04 08:37:19 as
	simulation of complete viral cell [My Copy] posted to no-tag by saravan on 2009-11-04 08:35:26 as
	Detection of Functional Modes in Protein Dynamics Jochen S. Hub, Bert L. de Groot* [My Copy] posted to no-tag by saravan on 2009-11-04 08:31:13 as
	Mechanical properties of the icosahedral shell of southern bean mosaic virus: a molecular dynamics study [My Copy] posted to no-tag by saravan on 2009-11-04 08:15:27 as
	Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach. [My Copy] Biophysical journal, Vol. 94, No. 9. (1 May 2008), pp. 3461-3474. by L. Zhou, S. A. Siegelbaum posted to no-tag by saravan on 2009-07-30 13:39:39 as along with 3 people and 1 group flbarroso choonpeng joseph_x_zhou protein_Dyn
	Transconformations of the SERCA1 Ca-ATPase: a normal mode study. [My Copy] Biophysical journal, Vol. 85, No. 4. (October 2003), pp. 2186-2197. by N. Reuter, K. Hinsen, J. J. Lacapère posted to no-tag by saravan on 2009-07-30 13:37:30 as along with 1 person edvin
	THz time domain spectroscopy of biomolecular conformational modes. [My Copy] Physics in medicine and biology, Vol. 47, No. 21. (7 November 2002), pp. 3797-3805. by A. Markelz, S. Whitmire, J. Hillebrecht, R. Birge posted to no-tag by saravan on 2009-07-30 13:36:07 as
	Molecular genetics of human color vision: the genes encoding blue, green, and red pigments [My Copy] Science, Vol. 232, No. 4747. (11 April 1986), pp. 193-202. by J. Nathans, D. Thomas, D. S. Hogness posted to no-tag by saravan on 2009-07-30 13:34:13 as
	Dynamic Coupling between the SH2 and SH3 Domains of c-Src and Hck Underlies Their Inactivation by C-Terminal Tyrosine Phosphorylation [My Copy] Cell, Vol. 105, No. 1. (06 April 2001), pp. 115-126. by Matthew A. Young, Stefania Gonfloni, Giulio Superti-Furga, Benoit Roux, John Kuriyan posted to no-tag by saravan on 2009-07-30 10:28:58 as along with 2 people choonpeng carlescorbi
	Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase. [My Copy] Biophysical journal, Vol. 81, No. 2. (August 2001), pp. 715-724. by K. Tai, T. Shen, U. Börjesson, M. Philippopoulos, J. A. McCammon posted to no-tag by saravan on 2009-07-30 10:25:47 as along with 1 person fralium
	Properties of water molecules in the active site gorge of acetylcholinesterase from computer simulation. [My Copy] Biophysical journal, Vol. 82, No. 5. (May 2002), pp. 2671-2682. by R. H. Henchman, K. Tai, T. Shen, J. A. McCammon posted to no-tag by saravan on 2009-07-30 10:23:51 as
	Validation of Protein Structure from Anisotropic Carbonyl Chemical Shifts in a Dilute Liquid Crystalline Phase [My Copy] Journal of the American Chemical Society, Vol. 120, No. 27. (1 July 1998), pp. 6836-6837. by Gabriel Cornilescu, John L. Marquardt, Marcel Ottiger, Ad Bax posted to no-tag by saravan on 2009-06-18 07:34:11 as
	Structure of ubiquitin refined at 1.8 A resolution. [My Copy] Journal of molecular biology, Vol. 194, No. 3. (5 April 1987), pp. 531-544. by S. Vijay-Kumar, C. E. Bugg, W. J. Cook posted to no-tag by saravan on 2009-06-18 07:30:34 as
	Transconformations of the SERCA1 Ca-ATPase: A Normal Mode Study [My Copy] Vol. 85, No. 4. (1 October 2003), pp. 2186-2197. by Nathalie Reuter, Konrad Hinsen, Jean-Jacques Lacapère posted to no-tag by saravan on 2009-06-18 00:42:51 as
	High-Resolution Terahertz Spectroscopy of Crystalline Trialanine: Extreme Sensitivity to β-Sheet Structure and Cocrystallized Water [My Copy] Journal of the American Chemical Society, Vol. 128, No. 17. (1 May 2006), pp. 5764-5775. by Karen Siegrist, Christine R. Bucher, Idan Mandelbaum, et al. Hight, Radhakrishnan Balu, Susan K. Gregurick, David F. Plusquellic posted to no-tag by saravan on 2009-06-18 00:38:33 as
	Conformational heterogeneity and low-frequency vibrational modes of proteins. [My Copy] Phys Chem Chem Phys, Vol. 8, No. 47. (21 December 2006), pp. 5543-5548. by E. Balog, J. C. Smith, D. Perahia posted to no-tag by saravan on 2009-06-02 01:47:15 as along with 1 person ruvido
	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 no-tag by saravan on 2009-06-02 01:42:35 as along with 1 person abovell
	Bacteriorhodopsin and rhodopsin studied by incoherent neutron scattering: dynamical properties of ground states and light activated intermediates [My Copy] Physica B Condensed Matter, Vol. 266 (May 1999), pp. 35-40. by J. fitter, S. A. W. verclas, R. E. lechner, et al.G. büldt, O. P. ernst, K. P. hofmann, N. A. dencher posted to no-tag by saravan on 2009-05-28 13:26:33 as
	Molecular-dynamics simulation evidences of a boson peak in protein hydration water [My Copy] Physical Review E, Vol. 57, No. 6. (Jun 1998), pp. R6277-R6280. by Alessandro Paciaroni, Anna R. Bizzarri, Salvatore Cannistraro posted to no-tag by saravan on 2009-05-28 12:52:08 as
	Slow Protein Dynamics to be Detected in Inelastic Neutron Scattering Spectra Studied by Molecular Simulation [My Copy] SLOW DYNAMICS IN COMPLEX SYSTEMS: 3rd International Symposium on Slow Dynamics in Complex Systems, Vol. 708, No. 1. (2004), pp. 358-359. by Yasumasa Joti, Akio Kitao, Nobuhiro Go edited by Michio Tokuyama, Irwin Oppenheim posted to no-tag by saravan on 2009-05-28 12:43:17 as
	Terahertz Measurements of Protein Relaxational Dynamics [My Copy] Proceedings of the IEEE In Proceedings of the IEEE, Vol. 95, No. 8. (2007), pp. 1605-1610. by J. R. Knab, Jing-Yin Chen, Yunfen He, A. G. Markelz posted to no-tag by saravan on 2009-05-28 12:38:41 as
	Projection methods for obtaining intramolecular energy transfer rates from classical trajectory results: Application to 1,2-difluoroethane [My Copy] The Journal of Chemical Physics, Vol. 89, No. 9. (1988), pp. 5680-5691. by Lionel M. Raff posted to no-tag by saravan on 2009-05-28 12:36:02 as
	Magnetostructural Dynamics with the Extended Broken Symmetry Formalism: Antiferromagnetic [2Fe-2S] Complexes [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 8. (1 August 2008), pp. 1174-1188. by Nisanth N. Nair, Eduard Schreiner, Rodolphe Pollet, Volker Staemmler, Dominik Marx posted to no-tag by saravan on 2009-05-28 12:32:44 as along with 1 person ehesan
	Projection of monte carlo and molecular dynamics trajectories onto the normal mode axes: Human lysozyme [My Copy] Proteins: Structure, Function, and Genetics, Vol. 10, No. 2. (1991), pp. 106-116. by Tokio Horiuchi, Nobuhiro G&omacr; posted to no-tag by saravan on 2009-05-28 12:31:46 as
	Solvent mobility and the protein 'glass' transition. [My Copy] Nat Struct Biol, Vol. 7, No. 1. (January 2000), pp. 34-38. by D. Vitkup, D. Ringe, G. A. Petsko, M. Karplus posted to no-tag by saravan on 2009-05-28 07:11:43 as along with 4 people abovell naitsabes onufriev jteyra
	Weak temperature dependence of the free energy surface and folding pathways of structured peptides [My Copy] Proteins: Structure, Function, and Genetics, Vol. 47, No. 3. (2002), pp. 305-314. by Andrea Cavalli, Philippe Ferrara, Amedeo Caflisch posted to no-tag by saravan on 2009-05-27 10:17:54 as
	Analysis of a 10-ns Molecular Dynamics Simulation of Mouse Acetylcholinesterase [My Copy] Vol. 81, No. 2. (1 August 2001), pp. 715-724. by Kaihsu Tai, Tongye Shen, Ulf Börjesson, Marios Philippopoulos, Andrew J. Mccammon posted to no-tag by saravan on 2009-05-27 10:15:20 as
	Dynamic Coupling between the SH2 and SH3 Domains of c-Src and Hck Underlies Their Inactivation by C-Terminal Tyrosine Phosphorylation [My Copy] Vol. 105, No. 1. (6 April 2001), pp. 115-126. by Matthew A. Young, Stefania Gonfloni, Giulio Superti-Furga, Benoit Roux, John Kuriyan posted to no-tag by saravan on 2009-05-27 10:12:21 as
	Modeling the Bacterial Photosynthetic Reaction Center. 2. A Combined Quantum Mechanical/Molecular Mechanical Study of the Structure of the Cofactors in the Reaction Centers of Purple Bacteria [My Copy] The Journal of Physical Chemistry B, Vol. 103, No. 23. (1 June 1999), pp. 4906-4915. by Michael C. Hutter, Jason M. Hughes, Jeffrey R. Reimers, Noel S. Hush posted to no-tag by saravan on 2009-05-27 10:08:16 as
	Protein reaction kinetics in a room-temperature glass [My Copy] Science, Vol. 269, No. 5226. (18 August 1995), pp. 959-962. by S. J. Hagen, J. Hofrichter, W. A. Eaton posted to no-tag by saravan on 2009-05-27 10:03:56 as along with 1 person pavanghatty
	Molecular dynamics simulations of biomolecules. [My Copy] Nat Struct Biol, Vol. 9, No. 9. (September 2002), pp. 646-652. by M. Karplus, J. A. McCammon posted to no-tag by saravan on 2009-05-27 00:51:00 as along with 8 people yxue onufriev adilson_mohr yalexeev baaden aqeel RamuAnandakrishnan LamBras
	CHARMM: The biomolecular simulation program [My Copy] Journal of Computational Chemistry, Vol. 30, No. 10. (30 July 2009), pp. 1545-1614. by B. R. Brooks, C. L. Brooks, A. D. Mackerell, et al.L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus posted to no-tag by saravan on 2009-05-26 13:33:36 as along with 8 people and 1 group rodrigofaccioli mmuecke medic0747 flbarroso jrperillaj xavierprat sobolevnrm dimka baker-group
	Force Field Evaluation for Biomolecular Simulation: Free Enthalpies of Solvation of Polar and Apolar Compounds in Various Solvents [My Copy] ChemPhysChem, Vol. 7, No. 3. (2006), pp. 671-678. by Daan P. Geerke, Wilfred F. van Gunsteren posted to no-tag by saravan on 2009-05-26 10:52:51 as
	Computer simulation of DNA double-helix dynamics. [My Copy] Cold Spring Harbor symposia on quantitative biology, Vol. 47 Pt 1 (1983), pp. 251-262. by M. Levitt posted to no-tag by saravan on 2009-05-26 08:43:02 as
	-- Levitt 47: 251 -- [My Copy] posted to no-tag by saravan on 2009-05-26 08:34:00 as
	Dynamics of folded proteins [My Copy] Nature, Vol. 267, No. 5612. (16 June 1977), pp. 585-590. by Andrew J. Mccammon, Bruce R. Gelin, Martin Karplus posted to no-tag by saravan on 2009-05-26 07:27:27 as along with 1 person RamuAnandakrishnan
	Molecular dynamics of biological macromolecules: a brief history and perspective. [My Copy] Biopolymers, Vol. 68, No. 3. (March 2003), pp. 350-358. by M. Karplus posted to no-tag by saravan on 2009-05-25 22:36:30 as along with 1 person baaden
	Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin. [My Copy] Journal of molecular modeling, Vol. 15, No. 8. (August 2009), pp. 959-969. by Saravana Prakash P. Thirumuruganandham, Herbert M. Urbassek posted to no-tag by saravan on 2009-05-22 13:19:16 as along with 2 people xdeupi gcaltabiano
	MASKER: improved solvent-excluded molecular surface area estimations using Boolean masks. [My Copy] Protein Eng, Vol. 15, No. 12. (December 2002), pp. 959-965. by C. Bystroff posted to no-tag by saravan on 2009-05-21 05:06:13 as along with 3 people hryk BragilMassoud dgront
	Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations [My Copy] Journal of Computational Chemistry, Vol. 25, No. 8. (2004), pp. 1005-1014. by Olgun Guvench, Charles posted to no-tag by saravan on 2009-05-17 22:33:03 as along with 1 person mijam
	The Solvent-Excluding Surface as a descriptor of ionic channels: Gramicidin-A [My Copy] Journal of Molecular Structure: THEOCHEM, Vol. 426, No. 1-3. (09 March 1998), pp. 331-338. by J. Pascual-Ahuir posted to no-tag by saravan on 2009-05-09 05:15:04 as
	Explosive Boiling of Water Films Adjacent to Heated Surfaces: A Microscopic Description† [My Copy] The Journal of Physical Chemistry A, Vol. 105, No. 12. (1 March 2001), pp. 2748-2755. by Yusheng Dou, Leonid V. Zhigilei, Nicholas Winograd, Barbara J. Garrison posted to no-tag by saravan on 2009-05-08 10:52:54 as
	Analysis of double-stranded oligonucleotides by laser-induced liquid beam mass spectrometry [My Copy] International Journal of Mass Spectrometry and Ion Processes, Vol. 163, No. 1-2. (April 1997), pp. L1-L4. by W. Kleinekofort posted to no-tag by saravan on 2009-05-08 07:21:38 as
	Detection of intact hemoglobin from aqueous solution with laser desorption mass spectrometry [My Copy] Rapid Communications in Mass Spectrometry, Vol. 14, No. 10. (2000), pp. 859-861. by Andreas Wattenberg, Frank Sobott, Bernhard Brutschy posted to no-tag by saravan on 2009-05-08 07:18:29 as
	Studying noncovalent protein complexes in aqueous solution with laser desorption mass spectrometry [My Copy] International Journal of Mass Spectrometry, Vol. 203, No. 1-3. (26 December 2000), pp. 49-57. by A. Wattenberg posted to no-tag by saravan on 2009-05-08 07:17:30 as
	Relaxation Processes of Molecules on a Solution Surface Studied by the Two-Color Pump−Probe Ionization Technique [My Copy] The Journal of Physical Chemistry B, Vol. 103, No. 44. (1 November 1999), pp. 9540-9544. by Noriko Horimoto, Fumitaka Mafune, Tamotsu Kondow posted to no-tag by saravan on 2009-05-08 03:07:18 as

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