jrperillaj's library 38 articles Export

	THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method [My Copy] Journal of Computational Chemistry, Vol. 13, No. 8. (1992), pp. 1011-1021. by Shankar Kumar, John M. Rosenberg, Djamal Bouzida, Robert H. Swendsen, Peter A. Kollman posted to no-tag by jrperillaj on 2009-09-28 20:48:44 as along with 11 people and 1 group edws Diego_Prada stephenbond dfgreen A_Coletta_Thesis sunnytov dgront sikorski jwagoner bransfop allmensch Structural Biology Group TorVergata
	Weighted-ensemble Brownian dynamics simulations for protein association reactions [My Copy] Biophysical Journal, Vol. 70, No. 1. (January 1996), pp. 97-110. by G. Huber posted to no-tag by jrperillaj on 2009-06-19 18:48:45 as
	Determination of a Transition State at Atomic Resolution from Protein Engineering Data [My Copy] Journal of Molecular Biology, Vol. 324, No. 1. (15 November 2002), pp. 151-163. by Emanuelel Paci, Michele Vendruscolo, Christopher M. Dobson, Martin Karplus posted to no-tag by jrperillaj on 2009-06-19 18:37:18 as
	Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems [My Copy] The Journal of Chemical Physics, Vol. 110, No. 8. (1999), pp. 3697-3702. by Massimo Marchi, Pietro Ballone posted to no-tag by jrperillaj on 2009-06-19 18:27:53 as
	Comparison of Three Perturbation Molecular Dynamics Methods for Modeling Conformational Transitions [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 5. (12 May 2009), pp. 1304-1314. by He Huang, Elif Ozkirimli, Carol B. Post posted to no-tag by jrperillaj on 2009-06-19 18:20:27 as
	Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 46. (13 November 2007), pp. 18043-18048. by Bin W. Zhang, David Jasnow, Daniel M. Zuckerman posted to no-tag by jrperillaj on 2009-06-19 17:44:23 as along with 2 people and 1 group sobolevnrm RamuAnandakrishnan baker-group
	Statistical mechanics of chemical equilibria and intramolecular structures of nonrigid molecules in condensed phases [My Copy] The Journal of Chemical Physics, Vol. 65, No. 8. (1976), pp. 2925-2940. by David Chandler, Lawrence R. Pratt posted to no-tag by jrperillaj on 2009-06-15 21:12:06 as
	Substrate Induced Population Shifts and Stochastic Gating in the PBCV-1 mRNA Capping Enzyme [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Robert V. Swift, Andrew J. Mccammon posted to no-tag by jrperillaj on 2009-06-15 20:49:30 as along with 1 person and 1 group sobolevnrm baker-group
	Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation [My Copy] Current Opinion in Structural Biology In Catalysis and regulation / Proteins, Vol. 17, No. 6. (December 2007), pp. 633-640. by Ivet Bahar, Chakra Chennubhotla, Dror Tobi posted to no-tag by jrperillaj on 2009-06-15 20:48:16 as along with 10 people and 4 groups allmensch barry aqeel ruvido cactus sobolevnrm jennifermbui higueruelo LamBras jmccammon structural_bioinformatics Bioinformatics baker-group McCammon
	Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 47. (20 November 2007), pp. 18496-18501. by Karunesh Arora, Charles L. Brooks posted to no-tag by jrperillaj on 2009-06-15 20:45:43 as along with 7 people and 2 groups xdeupi barry allmensch cactus sobolevnrm jlh64 karunesh structural_bioinformatics baker-group
	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 jrperillaj on 2009-06-11 17:26:49 as along with 8 people and 1 group rodrigofaccioli mmuecke medic0747 flbarroso xavierprat saravan sobolevnrm dimka baker-group
	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 no-tag by jrperillaj on 2009-06-11 17:24:42 as along with 12 people jmparks dsmueller rpetrenko Diego_Prada oceanwind dfgreen mkrishna timg dimka ttjoseph papatonyhill ssomani
	Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide [My Copy] The Journal of Chemical Physics, Vol. 123, No. 13. (2005), 134109. by Weiqing Ren, Eric V. Eijnden, Paul Maragakis, E. Weinan posted to no-tag by jrperillaj on 2009-06-04 19:50:42 as
	Transition path sampling of cavitation between molecular scale solvophobic surfaces [My Copy] The Journal of Chemical Physics, Vol. 113, No. 18. (2000), pp. 8154-8160. by Peter G. Bolhuis, David Chandler posted to no-tag by jrperillaj on 2009-06-04 19:22:23 as
	A statistical method for identifying transition states in high dimensional problems [My Copy] The Journal of Chemical Physics, Vol. 85, No. 9. (1986), pp. 5045-5048. by Lawrence R. Pratt posted to no-tag by jrperillaj on 2009-06-03 22:52:00 as along with 1 person Diego_Prada
	Adaptive search with stochastic acceptance probabilities for global optimization [My Copy] Operations Research Letters, Vol. 36, No. 3. (May 2008), pp. 285-290. by A. Ghate, R. Smith posted to no-tag by jrperillaj on 2009-04-20 22:22:35 as
	Transition events in butane simulations: Similarities across models [My Copy] The Journal of Chemical Physics, Vol. 116, No. 6. (2002), pp. 2586-2591. by Daniel M. Zuckerman, Thomas B. Woolf posted to no-tag by jrperillaj on 2009-04-20 16:24:15 as
	An algorithm for the location of transition states [My Copy] Journal of Computational Chemistry, Vol. 7, No. 4. (1986), pp. 385-395. by Jon Baker posted to no-tag by jrperillaj on 2009-04-20 16:10:19 as
	On finding transition states [My Copy] The Journal of Chemical Physics, Vol. 75, No. 6. (1981), pp. 2800-2806. by Charles J. Cerjan, William H. Miller posted to no-tag by jrperillaj on 2009-04-20 16:09:08 as along with 1 person and_ped10
	Efficient Generation of Feasible Pathways for Protein Conformational Transitions [My Copy] Vol. 83, No. 3. (1 September 2002), pp. 1620-1630. by Moon K. Kim, Robert L. Jernigan, Gregory S. Chirikjian posted to no-tag by jrperillaj on 2009-04-16 20:36:34 as
	Sampling protein conformations and pathways [My Copy] Journal of Computational Chemistry, Vol. 25, No. 9. (5 April 2004), pp. 1133-1148. by Ming Lei, Maria I. Zavodszky, Leslie A. Kuhn, M. F. Thorpe posted to no-tag by jrperillaj on 2009-04-16 20:34:43 as along with 9 people Scis0000002 fl aqeel blackbart smenor ruvido nh higueruelo apaydin
	Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor. [My Copy] Structure, Vol. 5, No. 8. (15 August 1997), pp. 997-1015. by F. A. Quiocho, J. C. Spurlino, L. E. Rodseth posted to no-tag by jrperillaj on 2009-04-16 01:22:23 as along with 2 people nigham papatonyhill
	Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis. [My Copy] Biochemistry, Vol. 31, No. 44. (10 November 1992), pp. 10657-10663. by A. J. Sharff, L. E. Rodseth, J. C. Spurlino, F. A. Quiocho posted to no-tag by jrperillaj on 2009-04-16 01:21:49 as
	Molecular replacement solution of the structure of apolactoferrin, a protein displaying large-scale conformational change. [My Copy] Acta crystallographica. Section B, Structural science, Vol. 47 ( Pt 6) (1 December 1991), pp. 998-1004. by G. E. Norris, B. F. Anderson, E. N. Baker posted to no-tag by jrperillaj on 2009-04-16 01:15:39 as along with 1 person nigham
	A note on two problems in connexion with graphs [My Copy] Numerische Mathematik, Vol. 1, No. 1. (1 December 1959), pp. 269-271. by E. W. Dijkstra posted to no-tag by jrperillaj on 2009-04-06 20:51:58 as along with 7 people Diego_Prada Borelli ben500 hp2oo1 antonkratz mpotamias dylanwalker
	Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures. [My Copy] Protein science : a publication of the Protein Society, Vol. 16, No. 6. (June 2007), pp. 1032-1041. by M. J. Borrok, L. L. Kiessling, K. T. Forest posted to ggbp by jrperillaj on 2009-03-31 01:33:04 as
	Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein. [My Copy] Science (New York, N.Y.), Vol. 242, No. 4883. (2 December 1988), pp. 1290-1295. by N. K. Vyas, M. N. Vyas, F. A. Quiocho posted to ggbp by jrperillaj on 2009-03-31 01:30:33 as
	The third IgG-binding domain from streptococcal protein G. An analysis by X-ray crystallography of the structure alone and in a complex with Fab. [My Copy] Journal of molecular biology, Vol. 243, No. 5. (11 November 1994), pp. 906-918. by J. P. Derrick, D. B. Wigley posted to 1igd by jrperillaj on 2009-03-31 01:23:45 as
	Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures. [My Copy] Biochemistry, Vol. 31, No. 40. (13 October 1992), pp. 9665-9672. by H. Gouda, H. Torigoe, A. Saito, M. Sato, Y. Arata, I. Shimada posted to 1bdc by jrperillaj on 2009-03-31 01:22:26 as
	Crystal structures of S100A6 in the Ca(2+)-free and Ca(2+)-bound states: the calcium sensor mechanism of S100 proteins revealed at atomic resolution. [My Copy] Structure (London, England : 1993), Vol. 10, No. 4. (April 2002), pp. 557-567. by L. R. Otterbein, J. Kordowska, C. Witte-Hoffmann, C. L. Wang, R. Dominguez posted to s100 by jrperillaj on 2009-03-31 01:17:48 as
	Transition path sampling and the calculation of rate constants [My Copy] The Journal of Chemical Physics, Vol. 108, No. 5. (1998), pp. 1964-1977. by Christoph Dellago, Peter G. Bolhuis, Félix S. Csajka, David Chandler posted to no-tag by jrperillaj on 2009-03-30 23:17:12 as along with 2 people tovrstra ruvido
	A temperature-dependent nudged-elastic-band algorithm [My Copy] The Journal of Chemical Physics, Vol. 118, No. 21. (2003), pp. 9563-9571. by Ramon Crehuet, Martin J. Field posted to no-tag by jrperillaj on 2009-03-30 23:08:09 as
	Mechanism of a Molecular Valve in the Halorhodopsin Chloride Pump [My Copy] Vol. 13, No. 4. (1 April 2005), pp. 617-627. by Andreea D. Gruia, Ana-Nicoleta Bondar, Jeremy C. Smith, Stefan Fischer posted to no-tag by jrperillaj on 2009-03-30 23:03:48 as
	Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model1 [My Copy] Journal of Molecular Biology, Vol. 284, No. 3. (04 December 1998), pp. 835-848. by Michael Schaefer, Christian Bartels, Martin Karplus posted to ace2 by jrperillaj on 2009-03-30 20:06:13 as
	Path corrected functionals of stochastic trajectories: towards relative free energy and reaction coordinate calculations [My Copy] Chemical Physics Letters, Vol. 289, No. 5-6. (19 June 1998), pp. 433-441. by T. Woolf posted to no-tag by jrperillaj on 2009-03-30 19:21:02 as
	Rapid Determination of Multiple Reaction Pathways in Molecular Systems: The Soft-Ratcheting Algorithm [My Copy] (27 Sep 2002) by Daniel M. Zuckerman, Thomas B. Woolf posted to no-tag by jrperillaj on 2009-03-25 18:18:40 as
	Open-State Conformation of the KcsA K+ Channel: Monte Carlo Normal Mode Following Simulations [My Copy] Structure, Vol. 15, No. 12. (13 December 2007), pp. 1654-1662. by G. Miloshevsky, P. Jordan posted to no-tag by jrperillaj on 2009-03-23 22:16:57 as
	The Open State Gating Mechanism of Gramicidin A Requires Relative Opposed Monomer Rotation and Simultaneous Lateral Displacement [My Copy] Structure, Vol. 14, No. 8. (August 2006), pp. 1241-1249. by G. Miloshevsky, P. Jordan posted to no-tag by jrperillaj on 2009-03-23 22:16:29 as

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