Tag dialanine [27 articles] Export Sort

Recent papers classified by the tag dialanine.

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	Simulation of activation free energies in molecular systems [My Copy] The Journal of Chemical Physics, Vol. 105, No. 5. (1996), pp. 1902-1921. by Eyal Neria, Stefan Fischer, Martin Karplus posted to transition_path problems_fel_dof force-fields dialanine alanine by Diego_Prada on 2009-11-23 16:30:50 as along with 1 person timg
	Weighted ensemble dynamics simulations for detecting metastable states [My Copy] (2 Dec 2009) by Linchen Gong, Xin Zhou posted to free_energy dialanine cmn by Diego_Prada on 2009-11-19 11:53:58 as along with 1 person Fernando_FF
	Unravelling the Conformational Dynamics of the Aqueous Alanine Dipeptide with First-Principle Molecular Dynamics [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 30. (30 July 2009), pp. 10059-10062. by M. P. Gaigeot posted to dialanine cpmd by loison on 2009-10-28 13:38:38 as along with 3 people and 2 groups jmccammon whitead carlosjavierna McCammon Jiang Research Group
	Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine ldquodipeptidesrdquo (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 50, No. 3. (15 February 2003), pp. 451-463. by Hao Hu, Marcus Elstner, Jan Hermans posted to amino dialanine force-fields by Diego_Prada on 2009-07-26 16:12:40 as along with 3 people flbarroso paddydu allmensch
	In silico Relationship between Configurational Entropy and Soft Degrees of Freedom in Proteins and Peptides [My Copy] Physical Review Letters, Vol. 102, No. 11. (2009), 118108. by Da W. Li, Rafael Brüschweiler posted to free_energy cmn dialanine dihedral dpca entropy qha by Diego_Prada on 2009-06-03 11:08:23 as along with 2 people and 1 group anna_yershova sobolevnrm baker-group
	Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide [My Copy] Chemical Physics Letters, Vol. 466, No. 4-6. (04 December 2008), pp. 105-115. by Birgit Strodel, David J. Wales posted to free_energy amino articulo coarse-grained dialanine hexapeptide statistical_mechanics by Diego_Prada on 2009-03-07 12:18:52 as
	Absolute free energies estimated by combining pre-calculated molecular fragment libraries [My Copy] (30 Jan 2009) by Xin Zhang, Artem B. Mamonov, Daniel M. Zuckerman posted to free_energy coarse-grained dialanine short-peptides by Diego_Prada on 2009-03-04 12:12:11 as
	Conformational Dynamics of Trialanine in Water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS Force Fields to NMR and Infrared Experiments [My Copy] J. Phys. Chem. B, Vol. 107, No. 21. (29 May 2003), pp. 5064-5073. by Y. G. Mu, D. S. Kosov, G. Stock posted to dialanine experimental force-fields hexapeptide short-peptides by Diego_Prada on 2008-12-16 12:24:41 as along with 1 person yalexeev
	Conformational Dynamics of Trialanine in Water: A Molecular Dynamics Study [My Copy] The Journal of Physical Chemistry B, Vol. 106, No. 20. (1 May 2002), pp. 5294-5301. by Yuguang Mu, Gerhard Stock posted to dialanine hexapeptide short-peptides by Diego_Prada on 2008-12-16 12:21:08 as
	Structure and Dynamics of the Homologous Series of Alanine Peptides: A Joint Molecular Dynamics/NMR Study [My Copy] Journal of the American Chemical Society, Vol. 129, No. 5. (1 February 2007), pp. 1179-1189. by Jurgen Graf, Phuong H. Nguyen, Gerhard Stock, Harald Schwalbe posted to dialanine hexapeptide by Diego_Prada on 2008-09-29 17:57:05 as along with 1 person Vadikus
	How Complex Is the Dynamics of Peptide Folding? [My Copy] Physical Review Letters, Vol. 98, No. 2. (2007) by Rainer Hegger, Alexandros Altis, Phuong H. Nguyen, Gerhard Stock posted to free_energy complex_systems dialanine hexapeptide by Diego_Prada on 2008-09-29 17:54:18 as
	A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. Phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests. [My Copy] Journal of biomolecular structure & dynamics, Vol. 7, No. 3. (December 1989), pp. 421-453. by I. K. Roterman, M. H. Lambert, K. D. Gibson, H. A. Scheraga posted to chapt_cmn alanine amino dialanine plos by Diego_Prada on 2008-08-03 18:21:35 as
	The alanine dipeptide free energy surface in solution [My Copy] J. Chem. Phys., Vol. 111 (September 1999), pp. 5568-5579. by P. E. Smith posted to chapt_cmn dialanine plos by Diego_Prada on 2008-08-03 11:24:04 as
	A temperature-dependent nudged-elastic-band algorithm [My Copy] J. Chem. Phys., Vol. 118 (June 2003), pp. 9563-9571. by R. Crehuet, M. J. Field posted to dialanine by Diego_Prada on 2008-08-01 21:04:03 as
	Reaction paths and free energy profiles for conformational transitions: An internal coordinate approach [My Copy] J. Chem. Phys., Vol. 95 (November 1991), pp. 7612-7625. by T. Lazaridis, D. J. Tobias, Brooks, M. E. Paulaitis posted to dialanine by Diego_Prada on 2008-08-01 20:59:59 as
	Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations [My Copy] Journal of Computational Chemistry, Vol. 18, No. 12. (1997), pp. 1450-1462. by Christian Bartels, Martin Karplus posted to dialanine md by Diego_Prada on 2008-08-01 20:53:13 as along with 1 person melo_mcr
	String method in collective variables: Minimum free energy paths and isocommittor surfaces [My Copy] The Journal of Chemical Physics, Vol. 125, No. 2. (2006), 024106. by Luca Maragliano, Alexander Fischer, Eric V. Eijnden, Giovanni Ciccotti posted to dialanine by Diego_Prada on 2008-08-01 20:37:12 as
	Stereochemistry of polypeptide chain configurations. [My Copy] Journal of molecular biology, Vol. 7 (July 1963), pp. 95-99. by G. N. Ramachandran, C. Ramakrishnan, V. Sasisekharan posted to chapt_amino amino dialanine proteins by Diego_Prada on 2008-08-01 20:33:15 as along with 7 people stharward kumar_physics yangjustinc reyez cen4ik jwm wouterboomsma
	Long-Time Conformational Transitions of Alanine Dipeptide in Aqueous Solution: Continuous and Discrete-State Kinetic Models [My Copy] J. Phys. Chem. B, Vol. 108, No. 50. (16 December 2004), pp. 19487-19495. by D. S. Chekmarev, T. Ishida, R. M. Levy posted to chapt_cmn dialanine plos by Diego_Prada on 2008-08-01 19:46:15 as
	Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations [My Copy] J. Chem. Phys., Vol. 118 (June 2003), pp. 10762-10773. by G. Hummer, I. G. Kevrekidis posted to chapt_cmn coarse-grained dialanine md plos by Diego_Prada on 2008-08-01 19:40:41 as
	Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations [My Copy] Multiscale Modeling & Simulation, Vol. 5, No. 4. (2006), pp. 1214-1226. by John D. Chodera, William C. Swope, Jed W. Pitera, Ken A. Dill posted to chapt_cmn dialanine markov md plos by Diego_Prada on 2008-08-01 19:30:32 as along with 2 people allmensch ucbcjbm
	Energy landscapes, global optimization and dynamics of the polyalanine Ac(ala)_8NHMe [My Copy] J. Chem. Phys., Vol. 114 (April 2001), pp. 6443-6454. by P. N. Mortenson, D. J. Wales posted to dialanine hexapeptide by Diego_Prada on 2008-08-01 19:23:19 as
	Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water [My Copy] The Journal of Chemical Physics, Vol. 110, No. 4. (1999), pp. 2099-2108. by Joannis Apostolakis, Philippe Ferrara, Amedeo Caflisch posted to chapt_cmn dialanine plos by Diego_Prada on 2008-08-01 19:00:45 as
	Automatic Method for Identifying Reaction Coordinates in Complex Systems [My Copy] J. Phys. Chem. B, Vol. 109, No. 14. (14 April 2005), pp. 6769-6779. by A. Ma, A. R. Dinner posted to chapt_cmn dialanine plos by Diego_Prada on 2008-08-01 18:54:53 as along with 2 people and 2 groups whitead A_Coletta_Thesis Jiang Research Group Structural Biology Group TorVergata
	Reaction coordinates of biomolecular isomerization. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 97, No. 11. (23 May 2000), pp. 5877-5882. by P. G. Bolhuis, C. Dellago, D. Chandler posted to chapt_cmn dialanine plos by Diego_Prada on 2008-08-01 18:49:48 as along with 3 people stephenbond paddydu doktornoe
	Conformational Study of the Alanine Dipeptide at the MP2 and DFT Levels [My Copy] J. Phys. Chem. A, Vol. 106, No. 13. (4 April 2002), pp. 3213-3218. by R. Vargas, J. Garza, B. P. Hay, D. A. Dixon posted to chapt_cmn dialanine plos by Diego_Prada on 2008-05-07 15:38:46 as
	From A to B in free energy space [My Copy] The Journal of Chemical Physics, Vol. 126, No. 5. (2007) by Davide Branduardi, Francesco L. Gervasio, Michele Parrinello posted to free_energy dialanine hot by Diego_Prada on 2008-02-19 10:14:26 as along with 4 people and 1 group A_Coletta_Thesis loison ruvido kdesmond Structural Biology Group TorVergata

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Tag dialanine [27 articles] Export Sort

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