Group: structure-bii - with tag water-ref [97 articles] Export

Recent papers posted by members of the structure-bii group with tag water-ref

	Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. [My Copy] J Am Chem Soc, Vol. 126, No. 24. (23 June 2004), pp. 7683-7689. by D. Hamelberg, J. A. McCammon posted to water-ref by ssomani to the group structure-bii on 2006-07-24 20:11:45 as
	Bovine tuberculosis - Another view from down under. [My Copy] Vet J (20 June 2006) by G W W. de Lisle, B M M. Buddle, D M M. Collins posted to water-ref by ssomani to the group structure-bii on 2006-07-13 02:59:47 as
	Water dynamics and dewetting transitions in the small mechanosensitive channel MscS. [My Copy] Biophys J, Vol. 86, No. 5. (May 2004), pp. 2883-2895. by A. Anishkin, S. Sukharev posted to water-ref by ssomani to the group structure-bii on 2006-07-10 03:29:17 as along with 1 person softsimu
	Does picosecond protein dynamics have survival value? [My Copy] Trends Biochem Sci, Vol. 24, No. 7. (July 1999), pp. 253-255. by M. Brunori, F. Cutruzzolà, C. Savino, C. Travaglini-Allocatelli, B. Vallone, Q. H. Gibson posted to water-ref by ssomani to the group structure-bii on 2006-07-09 17:17:45 as
	Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 46. (15 November 2005), pp. 16668-16671. by M. D. Collins, G. Hummer, M. L. Quillin, B. W. Matthews, S. M. Gruner posted to water-ref by ssomani to the group structure-bii on 2006-07-09 05:02:05 as
	Topological frustration and the folding of interleukin-1 beta. [My Copy] J Mol Biol, Vol. 357, No. 3. (31 March 2006), pp. 986-996. by S. Gosavi, L. L. Chavez, P. A. Jennings, J. N. Onuchic posted to water-ref by ssomani to the group structure-bii on 2006-07-08 21:14:46 as
	Discovery of new ligand binding pathways in myoglobin by random mutagenesis. [My Copy] Nat Struct Biol, Vol. 1, No. 4. (April 1994), pp. 226-229. by X. Huang, S. G. Boxer posted to water-ref by ssomani to the group structure-bii on 2006-07-04 19:33:15 as
	The Mechanism and Pathway of pH Induced Swelling in Cowpea Chlorotic Mottle Virus [My Copy] Journal of Molecular Biology, Vol. 318, No. 3. (03 May 2002), pp. 733-747. by Florence Tama, Charles L. Brooks III posted to water-ref by ssomani to the group structure-bii on 2006-07-04 05:03:07 as along with 1 person aqeel
	Internal mobility of the basic pancreatic trypsin inhibitor in solution: a comparison of NMR spin relaxation measurements and molecular dynamics simulations. [My Copy] J Mol Biol, Vol. 246, No. 2. (17 February 1995), pp. 356-365. by P. E. Smith, R. C. van Schaik, T. Szyperski, K. Wüthrich, W. F. van Gunsteren posted to water-ref by ssomani to the group structure-bii on 2006-07-04 05:00:29 as
	Using buried water molecules to explore the energy landscape of proteins. [My Copy] Nat Struct Biol, Vol. 3, No. 6. (June 1996), pp. 505-509. by V. P. Denisov, J. Peters, H. D. Hörlein, B. Halle posted to water-ref by ssomani to the group structure-bii on 2006-07-04 04:59:13 as
	Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations [My Copy] Proteins: Structure, Function, and Genetics, Vol. 11, No. 3. (1991), pp. 205-217. by Toshiko Ichiye, Martin Karplus posted to water-ref by ssomani to the group structure-bii on 2006-07-04 04:55:30 as along with 3 people chemrahul82 baaden simone
	Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty acid-binding protein. [My Copy] Proteins, Vol. 47, No. 4. (1 June 2002), pp. 534-545. by D. Bakowies, W. F. Van Gunsteren posted to water-ref by ssomani to the group structure-bii on 2006-07-04 04:54:37 as
	Water penetration and escape in proteins. [My Copy] Proteins, Vol. 38, No. 3. (15 February 2000), pp. 261-272. by A. E. García, G. Hummer posted to water-ref by ssomani to the group structure-bii on 2006-07-04 04:54:06 as
	X-ray crystal structure of a small antagonist peptide bound to interleukin-1 receptor type 1. [My Copy] J Biol Chem, Vol. 275, No. 47. (24 November 2000), pp. 36927-36933. by G. P. Vigers, D. J. Dripps, C. K. Edwards, B. J. Brandhuber posted to water-ref by ssomani to the group structure-bii on 2006-07-04 04:35:10 as along with 2 people timg higueruelo
	PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations [My Copy] Nucl. Acids Res., Vol. 32, No. suppl_2. (1 July 2004), pp. W665-667. by Todd J. Dolinsky, Jens E. Nielsen, J. Andrew Mccammon, Nathan A. Baker posted to water-ref by ssomani to the group structure-bii on 2006-07-04 04:34:17 as along with 3 people Martin8223 flbarroso mschofie
	Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities. [My Copy] Biophys J, Vol. 89, No. 1. (July 2005), pp. 465-474. by C. Bossa, A. Amadei, I. Daidone, et al.M. Anselmi, B. Vallone, M. Brunori, A. Di Nola posted to water-ref by ssomani to the group structure-bii on 2006-07-04 04:32:56 as
	Modulating functional loop movements: the role of highly conserved residues in the correlated loop motions. [My Copy] Chembiochem, Vol. 5, No. 2. (6 February 2004), pp. 224-230. by K. Gunasekaran, R. Nussinov posted to water-ref by ssomani to the group structure-bii on 2006-07-04 04:32:08 as
	Efficient evaluation of binding free energy using continuum electrostatics solvation. [My Copy] J Med Chem, Vol. 47, No. 23. (4 November 2004), pp. 5791-5797. by D. Huang, A. Caflisch posted to water-ref by ssomani to the group structure-bii on 2006-07-04 04:30:03 as along with 1 person GermanErlenkamp
	Liquid-vapor oscillations of water in hydrophobic nanopores. [My Copy] Proc Natl Acad Sci U S A, Vol. 100, No. 12. (10 June 2003), pp. 7063-7068. by O. Beckstein, M. S. Sansom posted to water-ref by ssomani to the group structure-bii on 2006-07-04 04:28:41 as
	Dynamics of confined water molecules. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 9. (1 March 2005), pp. 3202-3207. by J. J. Gilijamse, A. J. Lock, H. J. Bakker posted to water-ref by ssomani to the group structure-bii on 2006-07-04 04:28:04 as along with 1 person ruvido
	Molecular dynamics study of water penetration in staphylococcal nuclease. [My Copy] Proteins, Vol. 60, No. 3. (15 August 2005), pp. 433-449. by A. Damjanović, B. García-Moreno, E. E. Lattman, A. E. García posted to water-ref by ssomani to the group structure-bii on 2006-07-04 04:26:58 as along with 1 person Lombardo_7
	Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. [My Copy] J Am Chem Soc, Vol. 104, No. 17. (1980), pp. 4546-4559. by G. Lipari, A. Szabo posted to water-ref by ssomani to the group structure-bii on 2006-07-04 04:24:47 as
	Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. [My Copy] Nature, Vol. 431, No. 7010. (14 October 2004), pp. 830-834. by S. Y. Noskov, S. Bernèche, B. Roux posted to water-ref by ssomani to the group structure-bii on 2006-07-04 04:17:54 as along with 2 people and 1 group flbarroso brocktice TulaneCEP
	Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain. [My Copy] Biophys J, Vol. 85, No. 1. (July 2003), pp. 61-69. by W. Guo, S. Lampoudi, J. E. Shea posted to water-ref by ssomani to the group structure-bii on 2006-07-04 04:08:31 as
	Crystallographic structures of the M and N intermediates of bacteriorhodopsin: assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff base. [My Copy] J Mol Biol, Vol. 330, No. 3. (11 July 2003), pp. 553-570. by B. Schobert, L. S. Brown, J. K. Lanyi posted to water-ref by ssomani to the group structure-bii on 2006-07-04 03:54:41 as
	Statistical and molecular dynamics studies of buried waters in globular proteins. [My Copy] Proteins, Vol. 60, No. 3. (15 August 2005), pp. 450-463. by S. Park, J. G. Saven posted to water-ref by ssomani to the group structure-bii on 2006-07-04 03:52:46 as along with 1 person blackbart
	MHC-peptide binding is assisted by bound water molecules. [My Copy] J Mol Biol, Vol. 338, No. 2. (23 April 2004), pp. 419-435. by P. M. Petrone, A. E. Garcia posted to water-ref by ssomani to the group structure-bii on 2006-07-04 03:18:24 as along with 3 people and 1 group sobolevnrm fjc1 jteyra baker-group
	Electrostatics of nanosystems: Application to microtubules and the ribosome [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 98, No. 18. (28 August 2001), pp. 10037-10041. by Nathan A. Baker, David Sept, Simpson Joseph, Michael J. Holst, J. Andrew McCammon posted to water-ref by ssomani to the group structure-bii on 2006-07-04 03:17:09 as along with 7 people nickolay ras Martin8223 flbarroso gane5h qwermish mschofie
	Water conduction through the hydrophobic channel of a carbon nanotube. [My Copy] Nature, Vol. 414, No. 6860. (8 November 2001), pp. 188-190. by G. Hummer, J. C. Rasaiah, J. P. Noworyta posted to water-ref by ssomani to the group structure-bii on 2006-04-28 17:02:53 as along with 4 people kentsis james1 softsimu Hdeu
	Solvation Thermodynamics [My Copy] (30 September 1987) by Arieh Y. Ben-Naim posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:34:40 as
	Electric Field and Temperature Effects on Water in Carbon Nanotubes [My Copy] J.Chem. Phys., Vol. 121 (2004), 7955. by S. Vaitheeswaran, J. C. Rasaiah, G. Hummer posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:22:27 as
	Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A. [My Copy] Science, Vol. 305 (2004), pp. 1587-1594. by S. Khademi, 3rd J. O'Connell, J. Remis, Robles Y. Colmenares, L. J. Miercke, R. M. Stroud posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	Hydrophobic Collapse in Multidomain Protein Folding [My Copy] Science, Vol. 305 (2004), pp. 1605-1609. by Ruhong Zhou, Xuhui Huang, Claudio J. Margulis, Bruce J. Berne posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	The Role of Small Intraprotein Cavities in the Catalytic Cycle of Bacteriorhodopsin [My Copy] Biophys. J., Vol. 85 (2003) by R. Friedman, R. Nachliel, M. Gutman posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	Properties of the protein matrix revealed by the free energy of cavity formation [My Copy] Structure (London), Vol. 4 (1996), pp. 1517-1529. by J. P. Kocher, M. Prevost, S. J. Wodak, Lee posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	The interleukin 1 receptor: ligand interactions and signal transduction [My Copy] Cytokine Growth Factor Rev., Vol. 9 (1998) by P. E. Auron posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	Solvent interaction of a Hsp70 chaperone substrate-binding domain investigated with water-NOE NMR experiments [My Copy] Biochemistry, Vol. 42 (2003), pp. 11100-11108. by S. Cai, S. Y. Stevens, A. P. Budor, E. R. Zuiderweg posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	Thermodynamics Stability of Water Molecules in the Bacteriorhodopsin Proton Channel: A Molecular Dynamics Free Energy Perturbation Study. [My Copy] Biophys. J., Vol. 72 (1996), pp. 670-681. by B. Roux, M. Nina, R. Pomes, J. C. Smith posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	A Molecular Dynamics Study of Thermodynamic and Structural Aspects of the Hydration of Cavities in Proteins [My Copy] Biopolymers, Vol. 31 (1991), pp. 919-931. by R. C. Wade, M. H. Mazor, J. A. Mccammon, F. A. Quiocho posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	How do the GTPases really work? [My Copy] Nature Structural Biology, Vol. 2 (1995), pp. 3-6. by Rolf Hilgenfeld posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	Hydrophobicity: Two faces of water [My Copy] Nature, Vol. 417 (2002) by David Chandler posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands [My Copy] Nature, Vol. 431 (2004), pp. 830-834. by Roux posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	Refinement of X-Ray Data on Dual Cosubstrate Specificity of CK2 Kinase by Free Energy Calculations Based on Molecular Dynamics Simulation [My Copy] Proteins, Vol. 58 (2005), pp. 511-517. by Piotr Setny, Maciej Geller posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	Detailed hydration maps of benzene and cyclohexane reveal distinct water structures [My Copy] J. Phys. Chem. B, Vol. 108 (2004), pp. 13492-13500. by T. M. Raschke, M. Levitt posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	Aromatic Rings Act as Hydrogen Bond Acceptors [My Copy] J. Mol. Biol., Vol. 201 (1988), pp. 751-754. by M. Levitt, M. F. Perutz posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	Analysis of solvent structure in proteins using neutron D2O-H2O solvent maps: pattern of primary and secondary hydration of trypsin [My Copy] Proteins, Vol. 12 (1992), pp. 223-236. by A. A. Kossiakoff, M. D. Sintchak, J. Shpungin, L. G. Presta posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	High apparent dielectric constants in the interior of a protein reflect water penetration [My Copy] Biophysical J., Vol. 79 (2000), pp. 1610-1620. by J. J. Dwyer, A. G. Gittis, D. A. Karp, et al.E. E. Lattman, D. S. Spencer, W. E. Stites, Garcia B. E. Moreno posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules [My Copy] Nat. Struct. Biol., Vol. 4 (1997), pp. 396-404. by G. Otting, E. Liepinsh, B. Halle, U. Frey posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	Water-protein interactions: Theory and experiment [My Copy] Ann. Rev. Biophys. Biophys. Chem., Vol. 20 (1991), pp. 577-600. by M. M. Teeter posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as
	Water: now you see it, now you don't [My Copy] Structure, Vol. 1 (1993), pp. 223-226. by M. Levitt, B. H. Park posted to water-ref by ssomani to the group structure-bii on 2006-04-28 16:18:35 as

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