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	Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 44. (4 November 2008), pp. 16928-16933. by Lan Hua, Ruhong Zhou, D. Thirumalai, B. J. Berne posted to md urea by yxue on 2009-08-10 21:22:57 as along with 2 people abende qshao
	Structural details of urea binding to barnase: a molecular dynamics analysis [My Copy] Structure, Vol. 7, No. 5. (15 May 1999), pp. 477-S2. by Amedeo Caflisch, Martin Karplus posted to md urea by yxue on 2009-08-10 21:21:49 as
	Computer Simulation of Urea−Water Mixtures: A Test of Force Field Parameters for Use in Biomolecular Simulation [My Copy] The Journal of Physical Chemistry B, Vol. 108, No. 3. (1 January 2004), pp. 1065-1071. by Lorna J. Smith, Herman J. C. Berendsen, Wilfred F. van Gunsteren posted to md urea by yxue on 2009-08-10 21:20:29 as along with 1 person dsmueller
	Computational methods for generating models of denatured and partially folded proteins [My Copy] Methods, Vol. 34, No. 1. (September 2004), pp. 144-150. by L. Smith posted to md unfolded_protein by yxue on 2009-07-22 04:22:49 as along with 3 people flbarroso karbak allmensch
	Scalable molecular dynamics with NAMD [My Copy] Journal of Computational Chemistry, Vol. 26, No. 16. (December 2005), pp. 1781-1802. by James C. Phillips, Rosemary Braun, Wei Wang, et al.James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kalé, Klaus Schulten posted to md namd by yxue on 2009-07-17 20:44:28 as along with 20 people and 5 groups krapnik pjkiley flbarroso r2s2 grondina rpetrenko oteri oceanwind dfgreen vahmurk gisle dimka jwm ttjoseph sangeetha yoel_rf bilab wilsoros sobolevnrm ibuch Radiation_Damage Stressosome Bioinformatics insilicodrug baker-group
	General Framework for Studying the Dynamics of Folded and Nonfolded Proteins by NMR Relaxation Spectroscopy and MD Simulation [My Copy] Journal of the American Chemical Society, Vol. 124, No. 16. (1 April 2002), pp. 4522-4534. by Jeanine J. Prompers, Rafael Bruschweiler posted to md thesis ubiquitin by yxue on 2009-07-10 03:33:48 as along with 2 people rpetrenko jlh64
	Calculation of the mutual diffusion coefficient by equilibrium and nonequilibrium molecular dynamics [My Copy] International Journal of Thermophysics, Vol. 7, No. 2. (21 March 1986), pp. 305-317. by J. Erpenbeck, J. Kincaid posted to md thesis by yxue on 2009-06-29 08:02:46 as
	Molecular Dynamics and NMR Spin Relaxation in Proteins [My Copy] Accounts of Chemical Research, Vol. 35, No. 6. (1 June 2002), pp. 325-331. by David A. Case posted to md model_free order_parameter by yxue on 2009-06-08 23:28:02 as along with 1 person thegoose
	A Theory of Protein Dynamics to Predict NMR Relaxation [My Copy] Biophys. J., Vol. 93, No. 12. (15 December 2007), pp. 4128-4140. by Esther Caballero-Manrique, Jenelle K. Bray, William A. Deutschman, Frederick W. Dahlquist, Marina G. Guenza posted to md relaxation_theory by yxue on 2009-06-06 00:02:51 as along with 1 person and 1 group sobolevnrm baker-group
	CHARMM Force Field Parameters for Nitroalkanes and Nitroarenes [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 1. (1 January 2008), pp. 107-115. by Jeffery B. Klauda, Bernard R. Brooks posted to md paramdev by yxue on 2009-05-20 02:05:48 as
	CHARMMing: A New, Flexible Web Portal for CHARMM [My Copy] J. Chem. Inf. Model. (13 August 2008) by Benjamin T. Miller, Rishi P. Singh, Jeffery B. Klauda, Milan Hodošček, Bernard R. Brooks, Lee H. Woodcock posted to md paramdev by yxue on 2009-05-01 02:35:30 as along with 3 people and 1 group jmccammon middledomain reyez McCammon
	Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures [My Copy] Journal of Computational Chemistry, Vol. 25, No. 2. (30 January 2004), pp. 265-284. by Michael Feig, Alexey Onufriev, Michael S. Lee, Wonpil Im, David A. Case, Charles L. Brooks posted to gborn implicit_solvent md by yxue on 2009-04-24 02:40:05 as along with 4 people itolokh allmensch stephenbond Lombardo_7
	Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations [My Copy] Journal of Computational Chemistry, Vol. 27, No. 6. (2006), pp. 719-729. by Jana Chocholouscaronová, Michael Feig posted to gbsw2 implicit_solvent md by yxue on 2009-04-24 01:51:11 as along with 1 person boris_aguilar
	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 md review by yxue on 2009-04-24 01:01:32 as along with 8 people saravan onufriev adilson_mohr yalexeev baaden aqeel RamuAnandakrishnan LamBras
	Molecular Dynamics and NMR Spin Relaxation in Proteins [My Copy] Accounts of Chemical Research, Vol. 35, No. 6. (2002), pp. 325-331. by David A. Case posted to md review by yxue on 2009-04-24 00:44:10 as
	Modeling and Studying Proteins with Molecular Dynamics [My Copy] Methods in Enzymology, Vol. 383 (2004), pp. 28-47. by Robert Schleif posted to md review by yxue on 2009-04-24 00:40:08 as
	Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins [My Copy] Chemical Reviews, Vol. 106, No. 5. (1 May 2006), pp. 1589-1615. by Stewart A. Adcock, J. Andrew Mccammon posted to md review by yxue on 2009-04-23 23:48:15 as along with 5 people flbarroso tovrstra aqeel higueruelo LamBras
	Characterization of the Protein Unfolding Processes Induced by Urea and Temperature☆ [My Copy] Biophysical Journal, Vol. 94, No. 6. (March 2008), pp. 2241-2251. by A. Rocco posted to md unfolded_protein urea by yxue on 2009-04-22 01:51:55 as
	Molecular dynamics simulations of the native and partially folded states of ubiquitin: influence of methanol cosolvent, pH, and temperature on the protein structure and dynamics. [My Copy] Protein science : a publication of the Protein Society, Vol. 16, No. 6. (June 2007), pp. 1101-1118. by D. B. Kony, P. H. Hünenberger, W. F. van Gunsteren posted to md unfolded_protein by yxue on 2009-04-21 18:21:40 as
	Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. [My Copy] Physical chemistry chemical physics : PCCP, Vol. 10, No. 4. (28 January 2008), pp. 471-481. by J. Chen, C. L. Brooks posted to implicit_solvent md unfolded_protein by yxue on 2009-04-21 03:02:00 as along with 2 people flbarroso choonpeng
	Calculation of Protein Heat Capacity from Replica-Exchange Molecular Dynamics Simulations with Different Implicit Solvent Models [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 47. (27 November 2008), pp. 15064-15073. by In-Chul Yeh, Michael S. Lee, Mark A. Olson posted to gbsw2 implicit_solvent md unfolded_protein by yxue on 2009-04-21 02:56:42 as
	Force Fields for Protein Simulations [My Copy] Advances in Protein Chemistry, Vol. 66 (2003), pp. 27-85. by Jay W. Ponder, David A. Case posted to force_field md by yxue on 2009-04-21 00:08:44 as
	Protein Folding and Unfolding at Atomic Resolution [My Copy] Cell, Vol. 108, No. 4. (22 February 2002), pp. 573-582. by Alan R. Fersht, Valerie Daggett posted to md unfolded_protein by yxue on 2009-04-18 04:50:06 as along with 2 people flbarroso choonpeng
	Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 97, No. 25. (5 December 2000), pp. 13518-13522. by U. Mayor, C. M. Johnson, V. Daggett, A. R. Fersht posted to md unfolded_protein by yxue on 2009-04-18 04:49:31 as along with 2 people dsmueller doktornoe
	Methods for molecular dynamics simulations of protein folding/unfolding in solution [My Copy] Methods, Vol. 34, No. 1. (September 2004), pp. 112-120. by David A. Beck, Valerie Daggett posted to md unfolded_protein by yxue on 2009-04-18 04:47:51 as along with 2 people karbak choonpeng
	A model of the molten globule state from molecular dynamics simulations [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 89, No. 11. (1 June 1992), pp. 5142-5146. by V. Daggett, M. Levitt posted to md unfolded_protein by yxue on 2009-04-18 04:46:55 as
	Thermal denaturing of mutant lysozyme with both the OPLSAA and the CHARMM force fields. [My Copy] J Am Chem Soc, Vol. 128, No. 41. (18 October 2006), pp. 13388-13395. by M. Eleftheriou, R. S. Germain, A. K. Royyuru, R. Zhou posted to md unfolded_protein by yxue on 2009-04-18 04:43:50 as along with 3 people saravan allmensch choonpeng
	Molecular Dynamics Study of the Structure, Flexibility and Dynamics of Thermostable L1 Lipase at High Temperatures [My Copy] The Protein Journal by Abedi, Abdul, Mahiran Basri, Abu Salleh, Donald Jacobs, Abdul posted to md unfolded_protein by yxue on 2009-04-18 04:40:46 as
	Protein folding: bringing theory and experiment closer together [My Copy] Current Opinion in Structural Biology, Vol. 13, No. 1. (February 2003), pp. 82-87. by M. Vendruscolo posted to md unfolded_protein by yxue on 2009-04-17 04:44:55 as
	Protein molecular dynamics with the generalized born/ACE solvent model [My Copy] Proteins: Structure, Function, and Genetics, Vol. 45, No. 2. (01 November 2001), pp. 144-158. by Nicolas Calimet,, Michael Schaefer,, Thomas Simonson, posted to implicit_solvent md by yxue on 2009-04-06 23:33:59 as along with 2 people ckmyo onufriev
	Balancing Solvation and Intramolecular Interactions: Toward a Consistent Generalized Born Force Field [My Copy] Journal of the American Chemical Society, Vol. 128, No. 11. (1 March 2006), pp. 3728-3736. by Jianhan Chen, Wonpil Im, Charles L. Brooks posted to implicit_solvent md by yxue on 2009-04-06 23:23:48 as along with 5 people ckmyo oteri dfgreen onufriev bilab
	Exploring peptide energy landscapes: A test of force fields and implicit solvent models [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 57, No. 4. (2004), pp. 665-677. by Peter J. Steinbach posted to gborn implicit_solvent md by yxue on 2009-04-06 23:21:55 as
	Thermal unfolding molecular dynamics simulation of <I>Escherichia coli</I> dihydrofolate reductase: Thermal stability of protein domains and unfolding pathway [My Copy] Proteins: Structure, Function, and Genetics, Vol. 46, No. 3. (2002), pp. 308-320. by Yuk Y. Sham, Buyong Ma, Chung-Jung Tsai, Ruth Nussinov posted to md unfolded_protein by yxue on 2009-03-27 04:10:52 as along with 1 person choonpeng
	Molecular Dynamics Simulations of Protein Unfolding and Limited Refolding: Characterization of Partially Unfolded States of Ubiquitin in 60% Methanol and in Water [My Copy] Journal of Molecular Biology, Vol. 247, No. 3. (31 March 1995), pp. 501-520. by D. Alonso posted to md unfolded_protein by yxue on 2009-03-27 04:07:55 as
	Unfolding of Titin Immunoglobulin Domains by Steered Molecular Dynamics Simulation [My Copy] Biophysical Journal, Vol. 75, No. 2. (August 1998), pp. 662-671. by H. Lu, B. Isralewitz, A. Krammer, V. Vogel, K. Schulten posted to md unfolded_protein by yxue on 2009-03-27 04:05:15 as along with 1 person Diego_Prada
	Molecular dynamics simulations of urea and thermal-induced denaturation of S-peptide analogue [My Copy] Biophysical Chemistry, Vol. 89, No. 2-3. (15 February 2001), pp. 145-162. by Z. Zhang posted to md unfolded_protein by yxue on 2009-03-27 04:03:55 as
	Comparative Study of the Folding Free Energy Landscape of a Three-Stranded β-Sheet Protein with Explicit and Implicit Solvent Models [My Copy] The Journal of Physical Chemistry B, Vol. 104, No. 51. (1 December 2000), pp. 12378-12383. by Badry D. Bursulaya, Charles L. Brooks posted to gborn implicit_solvent md by yxue on 2009-03-26 04:40:23 as
	Benchmarking Implicit Solvent Folding Simulations of the Amyloid beta(10-35) Fragment [My Copy] J. Phys. Chem. B (19 March 2008) by A. Kent, A. K. Jha, J. E. Fitzgerald, K. F. Freed posted to gborn implicit_solvent md tinker unfolded_protein by yxue on 2009-03-26 04:39:09 as along with 2 people flbarroso dmobley
	Development of a Generalized Born Model Parametrization for Proteins and Nucleic Acids [My Copy] The Journal of Physical Chemistry B, Vol. 103, No. 18. (1 May 1999), pp. 3765-3773. by Brian N. Dominy, Charles L. Brooks posted to gborn implicit_solvent md by yxue on 2009-03-25 16:49:53 as
	Internal coordinates for molecular dynamics and minimization in structure determination and refinement. [My Copy] Journal of magnetic resonance (San Diego, Calif. : 1997), Vol. 152, No. 2. (October 2001), pp. 288-302. by C. D. Schwieters, G. M. Clore posted to pj-unfolded md ivm by yxue on 2008-08-24 22:27:45 as
	Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water [My Copy] Journal of Biomolecular NMR, Vol. 22, No. 4. (1 April 2002), pp. 317-331. by Bin Xia, Vickie Tsui, David A. Case, Jane H. Dyson, Peter E. Wright posted to implicit_solvent md by yxue on 2008-07-12 21:40:24 as

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