ssomani's library 123 articles Export

	Unorthodox uses of Bennett's acceptance ratio method [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Gerhard König, Stefan Bruckner, Stefan Boresch posted to free_energy by ssomani on 2009-11-03 21:14:49 as along with 2 people agrossfield RamuAnandakrishnan
	Interaction between large spheres immersed in small spheres: remarkable effects due to a trace amount of medium-sized spheres [My Copy] Chemical Physics Letters, Vol. 353, No. 3-4. (19 February 2002), pp. 259-269. by M. Kinoshita posted to housekeepingaug09 by ssomani on 2009-08-20 21:51:28 as
	Dynamics of Water Confined in the Interdomain Region of a Multidomain Protein† [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 8. (1 March 2006), pp. 3704-3711. by Lan Hua, Xuhui Huang, Ruhong Zhou, B. J. Berne posted to water-ref housekeepingaug09 by ssomani on 2009-08-20 21:44:28 as
	Dielectric breakdown of cell membranes. [My Copy] Biophysical journal, Vol. 14, No. 11. (November 1974), pp. 881-899. by U. Zimmermann, G. Pilwat, F. Riemann posted to no-tag by ssomani on 2008-11-25 03:21:34 as along with 1 person Scis0000002
	Understanding ensemble protein folding at atomic detail [My Copy] PNAS, Vol. 103, No. 47. (21 November 2006), pp. 17747-17752. by Isaac A. Hubner, Eric J. Deeds, Eugene I. Shakhnovich posted to md_simulation by ssomani on 2008-10-24 23:40:31 as along with 2 people aalibes choonpeng
	Calculation of stress in atomistic simulation [My Copy] Modelling and Simulation in Materials Science and Engineering, Vol. 12, No. 4. (2004), pp. S319-S332. by J. A. Zimmerman, E. B. Webbiii, J. J. Hoyt, R. E. Jones, P. A. Klein, D. J. Bammann posted to elasticity stat-mech by ssomani on 2008-10-06 23:42:40 as
	Hybrid Monte Carlo [My Copy] Physics Letters B, Vol. 195, No. 2. (3 September 1987), pp. 216-222. by Simon Duane, A. D. Kennedy, Brian J. Pendleton, Duncan Roweth posted to md_simulation by ssomani on 2008-09-25 23:54:06 as along with 3 people carmenrg carmenrodrig fghorow
	Dihedral angle principal component analysis of molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 126, No. 24. (2007) by Alexandros Altis, Phuong Nguyen, Rainer Hegger, Gerhard Stock posted to md_simulation pca recons torsion_angles by ssomani on 2008-08-26 18:33:42 as
	Numerical Recipes in C: The Art of Scientific Computing [My Copy] (30 October 1992) by William H. Press, Brian P. Flannery, Saul A. Teukolsky, William T. Vetterling posted to recons by ssomani on 2008-08-26 17:03:52 as along with 22 people and 1 group tienholin anitabanerji howardjp kumar_physics gagnon_d gi0rgi0ne nilsma toerst tovrstra 6rheology kenenglish arne ihaque rpadams slh dpollard danielaugot cherrie amcmorl phla8271 cvq sheephat EisenLab
	The Equilibrium Theory of Classical Fluids [My Copy] by H. L. Frisch, J. L. Lebowitz posted to recons by ssomani on 2008-08-26 16:22:36 as
	Theory of Simple Liquids, Third Edition [My Copy] (03 April 2006) by Jean-Pierre Hansen, I. R. Mcdonald posted to recons by ssomani on 2008-08-23 20:51:25 as along with 3 people chiufanlee kkims waitonhill
	Pattern Recognition and Machine Learning (Information Science and Statistics) [My Copy] (01 October 2007) by Christopher M. Bishop posted to recons by ssomani on 2008-07-24 03:20:01 as along with 54 people and 6 groups fjanoos pjmaybank emailhy pingmei bklynbam gavin1332 ecome psychorav mircea longtop resilla bertelsen ocs sugarexpletive bgibson tkf mthomure emre haiyeong h-chi brian sbarthelme bayes mboehmer paulclinger thefillm stibor ppeeling yaroslavvb sdvillal nojhan gkvas paulinus ajylha helsley hawkes zeppe poluxmoon librain kohei-h brianmc napvasconcelos teesid robotact Hoertnagl matjes eddymier delip markusd filippone singhsh pprett rwilliamson Dukhat Tracking Methods EvolutionaryComputation Metaheuristics Optimization contact-id MuSAMA
	Molecular recognition: A simple dinaphthyridine receptor for urea [My Copy] Tetrahedron Letters, Vol. 38, No. 9. (3 March 1997), pp. 1619-1622. by Shyamaprosad Goswami, Rakhi Mukherjee posted to recons by ssomani on 2008-06-24 22:35:01 as
	ICM - A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation [My Copy] Journal of Computational Chemistry, Vol. 15, No. 5. (7 September 2004), pp. 488-506. by Ruben Abagyan, Maxim Totrov, Dmitry Kuznetsov posted to recons by ssomani on 2008-06-16 14:11:37 as along with 2 people and 1 group P2324548 okarsligil Bioinformatics
	Possible generalization of Boltzmann-Gibbs statistics [My Copy] J. Stat. Physics, Vol. 52 (1988) by C. Tsallis posted to stat-mech by ssomani on 2008-06-13 01:59:30 as along with 1 person and 1 group ciga Computational_Information_Geometry
	All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins† [My Copy] The Journal of Physical Chemistry B, Vol. 102, No. 18. (1 April 1998), pp. 3586-3616. by A. D. MacKerell, D. Bashford, Bellott, et al.R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus posted to recons by ssomani on 2008-06-11 06:57:52 as along with 12 people jmparks dsmueller rpetrenko jrperillaj Diego_Prada oceanwind dfgreen mkrishna timg dimka ttjoseph papatonyhill
	Equilibrium and Nonequilibrium Statistical Mechanics [My Copy] by Radu Balescu posted to recons stat-mech by ssomani on 2008-06-11 06:49:08 as
	Exact and approximate expressions for the three-particle direct correlation function and some related functions [My Copy] Physical Review A, Vol. 33, No. 2. (1 February 1986), 1338. by J. A. Hernando posted to no-tag by ssomani on 2008-06-11 06:42:55 as
	Markov Processes: An Introduction for Physical Scientists [My Copy] (08 October 1991) by Daniel T. Gillespie posted to recons by ssomani on 2008-06-10 06:07:18 as along with 1 person fbaroni
	Probability Theory: The Logic of Science (Vol 1) [My Copy] (09 June 2003) by E. T. Jaynes posted to recons by ssomani on 2008-06-10 05:47:46 as along with 13 people and 2 groups csferrie NitinCR shangyung gtaralds jarlet sbarthelme livingthingdan gyuli wnpx spirit_of_numenor nathanielvirgo robertoalamino MBFalcon ComplexAdaptiveSystems DSTO-CAS
	Extraction of configurational entropy from molecular simulations via an expansion approximation. [My Copy] The Journal of chemical physics, Vol. 127, No. 2. (14 July 2007) by B. J. Killian, J. Yundenfreund Kravitz, M. K. Gilson posted to recons by ssomani on 2008-06-05 20:21:08 as
	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 on 2006-07-24 20:11:45 as along with 1 group structure-bii
	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 on 2006-07-13 02:59:47 as along with 1 group structure-bii
	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 on 2006-07-10 03:29:17 as along with 1 person and 1 group softsimu structure-bii
	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 on 2006-07-09 17:17:45 as along with 1 group structure-bii
	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 on 2006-07-09 05:02:05 as along with 1 group structure-bii
	Solution structure of p53 core domain: Structural basis for its instability. [My Copy] Proc Natl Acad Sci U S A (6 February 2006) by José Manuel Pérez M. Cañadillas, Henning Tidow, Stefan M V M. Freund, Trevor J J. Rutherford, Hwee Ching C. Ang, Alan R R. Fersht posted to water-ref by ssomani on 2006-07-09 04:41:19 as along with 1 person and 1 group anita structure-bii
	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 on 2006-07-08 21:14:46 as along with 1 group structure-bii
	The statistical-thermodynamic basis for computation of binding affinities: a critical review. [My Copy] Biophys J, Vol. 72, No. 3. (March 1997), pp. 1047-1069. by M. K. Gilson, J. A. Given, B. L. Bush, J. A. McCammon posted to stat-mech by ssomani on 2006-07-06 04:25:02 as along with 3 people and 2 groups dfgreen hmk cchang structure-bii Chang group
	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 on 2006-07-04 19:33:15 as along with 1 group structure-bii
	Protein stability and ligand binding: new paradigms from in-silico experiments. [My Copy] Biophys Chem, Vol. 115, No. 2-3. (1 April 2005), pp. 295-302. by C. S. Verma, S. Fischer posted to no-tag by ssomani on 2006-07-04 19:29:35 as along with 2 people and 1 group blackbart ruvido structure-bii
	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 on 2006-07-04 05:03:07 as along with 1 person and 1 group aqeel structure-bii
	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 on 2006-07-04 05:00:29 as along with 1 group structure-bii
	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 on 2006-07-04 04:59:13 as along with 1 group structure-bii
	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 on 2006-07-04 04:55:30 as along with 3 people and 1 group chemrahul82 baaden simone structure-bii
	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 on 2006-07-04 04:54:37 as along with 1 group structure-bii
	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 on 2006-07-04 04:54:06 as along with 1 group structure-bii
	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 on 2006-07-04 04:35:10 as along with 2 people and 1 group timg higueruelo structure-bii
	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 on 2006-07-04 04:34:17 as along with 3 people and 1 group Martin8223 flbarroso mschofie structure-bii
	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 on 2006-07-04 04:32:56 as along with 1 group structure-bii
	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 on 2006-07-04 04:32:08 as along with 1 group structure-bii
	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 on 2006-07-04 04:30:03 as along with 1 person and 1 group GermanErlenkamp structure-bii
	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 on 2006-07-04 04:28:41 as along with 1 group structure-bii
	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 on 2006-07-04 04:28:04 as along with 1 person and 1 group ruvido structure-bii
	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 on 2006-07-04 04:26:58 as along with 1 person and 1 group Lombardo_7 structure-bii
	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 on 2006-07-04 04:24:47 as along with 1 group structure-bii
	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 on 2006-07-04 04:17:54 as along with 2 people and 2 groups flbarroso brocktice structure-bii 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 on 2006-07-04 04:08:31 as along with 1 group structure-bii
	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 on 2006-07-04 03:54:41 as along with 1 group structure-bii
	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 on 2006-07-04 03:52:46 as along with 1 person and 1 group blackbart structure-bii