Tag hexapeptide [48 articles] Export

Recent papers classified by the tag hexapeptide.

	Conformational entropy of alanine versus glycine in protein denatured states [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 8. (20 February 2007), pp. 2661-2666. by Kathryn A. Scott, Darwin O. V. Alonso, Satoshi Sato, Alan R. Fersht, Valerie Daggett posted to free_energy hexapeptide glycine conformational_entropy alanine by Diego_Prada on 2009-09-17 12:38:50 as
	Refined kinetic transition networks for the GB1 hairpin peptide [My Copy] Phys. Chem. Chem. Phys., Vol. 11, No. 18. (2009), pp. 3341-3354. by Joanne M. Carr, David J. Wales posted to free_energy beta-hairpin first_passage hexapeptide protein_dynamics protein_folding qha reaction_paths short-peptides transition_path transition_states by Diego_Prada on 2009-07-02 11:55:15 as
	A Probabilistic Model of RNA Conformational Space [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (19 June 2009), e1000406. by Jes Frellsen, Ida Moltke, Martin Thiim, Kanti V. Mardia, Jesper Ferkinghoff-Borg, Thomas Hamelryck posted to free_energy beta-hairpin cmn dihedral hexapeptide short-peptides by Diego_Prada on 2009-06-19 10:09:14 as along with 4 people and 1 group physics phoenixzxl kshameer ppgardne Journal picks
	Multiscale Modelling in Molecular Dynamics: Biomolecular Conformations as Metastable States [My Copy] Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1 (2006), pp. 495-517. by E. Meerbach, E. Dittmer, I. Horenko, C. Schütte posted to free_energy ala5 cmn hexapeptide short-peptides by Diego_Prada on 2009-05-30 20:42:39 as
	Computing Best Transition Pathways in High-Dimensional Dynamical Systems: Application to the Alpha[sub L] ≤ftrightharpoons Beta ≤ftrightharpoons Alpha[sub R] Transitions in Octaalanine [My Copy] Multiscale Modeling & Simulation, Vol. 5, No. 2. (2006), pp. 393-419. by Frank Noé, Marcus Oswald, Gerhard Reinelt, Stefan Fischer, Jeremy C. Smith posted to transition_path stochastic_processes statistical_mechanics markov hexapeptide aux by Diego_Prada on 2009-05-29 19:05:53 as
	Folding Pathways and Rates for the Three-Stranded β-Sheet Peptide Beta3s using Discrete Path Sampling [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 29. (1 July 2008), pp. 8760-8769. by Joanne M. Carr, David J. Wales posted to free_energy beta-hairpin hexapeptide protein_folding short-peptides by Diego_Prada on 2009-04-30 12:10:50 as
	Conformational states and folding pathways of peptides revealed by principal-independent component analyses [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 67, No. 3. (2007), pp. 579-592. by Phuong H. Nguyen posted to articulo hexapeptide pca by Diego_Prada on 2009-03-21 17:37:12 as
	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
	The free energy landscape and dynamics of met-enkephalin [My Copy] The Journal of Chemical Physics, Vol. 119, No. 18. (2003), pp. 9947-9955. by David A. Evans, David J. Wales posted to free_energy plos markov hexapeptide chapt_cmn aux by Diego_Prada on 2009-02-17 15:55:06 as
	Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a β-Hairpin Peptide [My Copy] J. Phys. Chem. B, Vol. 108, No. 21. (27 May 2004), pp. 6582-6594. by W. C. Swope, J. W. Pitera, F. Suits, et al.M. Pitman, M. Eleftheriou, B. G. Fitch, R. S. Germain, A. Rayshubski, T. J. C. Ward, Y. Zhestkov, R. Zhou posted to beta-hairpin hexapeptide markov md stochastic_processes by Diego_Prada on 2009-02-16 11:17:38 as along with 1 person toerst
	Transition networks for modeling the kinetics of conformational change in macromolecules [My Copy] Current Opinion in Structural Biology In Theory and simulation / Macromolecular assemblages, Vol. 18, No. 2. (April 2008), pp. 154-162. by F NOE,, S FISCHER, posted to chapt_cmn cmn hexapeptide markov networks plos by Diego_Prada on 2009-02-11 18:08:45 as along with 6 people and 3 groups ckmyo aqeel barry sobolevnrm paulschlesinger toerst structural_bioinformatics baker-group McCammon
	Reaction path study of conformational transitions and helix formation in a tetrapeptide [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 86, No. 18. (1989), pp. 6963-6967. by R. Czerminski, R. Elber posted to hexapeptide secondary_structure short-peptides by Diego_Prada on 2008-12-18 19:37:34 as
	Collective vibrations of an alpha-helix. A molecular dynamics study. [My Copy] Biophys. J., Vol. 59, No. 4. (1 April 1991), pp. 795-804. by J. Pleiss, F. Jahnig posted to hexapeptide by Diego_Prada on 2008-12-16 16:31:22 as along with 1 person saravan
	Coarse Master Equations for Peptide Folding Dynamics [My Copy] J. Phys. Chem. B (31 January 2008) by N. V. Buchete, G. Hummer posted to chapt_cmn hexapeptide markov plos stochastic_processes by Diego_Prada on 2008-12-16 16:27:49 as along with 3 people and 1 group apaydin ruvido sobolevnrm baker-group
	Are Current Molecular Dynamics Force Fields too Helical? [My Copy] Biophys. J., Vol. 95, No. 1. (1 July 2008), pp. L07-9. by Robert B. Best, Nicolae-Viorel Buchete, Gerhard Hummer posted to force-fields hexapeptide by Diego_Prada on 2008-12-16 16:08:06 as along with 3 people dmobley loison middledomain
	A Microscopic View of Helix Propagation: N and C-terminal Helix Growth in Alanine Helices [My Copy] Journal of Molecular Biology, Vol. 259, No. 3. (14 June 1996), pp. 560-572. by W. Young, Brooks posted to hexapeptide by Diego_Prada on 2008-12-16 13:12:21 as
	Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 97, No. 20. (2000), pp. 10786-10791. by Franc Avbelj, Peizhi Luo, Robert L. Baldwin posted to hexapeptide by Diego_Prada on 2008-12-16 13:10:20 as
	Helix design, prediction and stability [My Copy] Current Opinion in Biotechnology, Vol. 6, No. 4. (1995), pp. 382-386. by V. Muñoz posted to experimental hexapeptide by Diego_Prada on 2008-12-16 13:08:41 as
	Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions [My Copy] Protein Sci, Vol. 3, No. 5. (1 May 1994), pp. 843-852. by A. Chakrabartty, T. Kortemme, R. L. Baldwin posted to hexapeptide by Diego_Prada on 2008-12-16 13:05:47 as
	Polyproline II structure in a sequence of seven alanine residues. [My Copy] Proc Natl Acad Sci U S A, Vol. 99, No. 14. (9 July 2002), pp. 9190-9195. by Z. Shi, C. A. Olson, G. D. Rose, R. L. Baldwin, N. R. Kallenbach posted to hexapeptide by Diego_Prada on 2008-12-16 13:03:57 as along with 1 person allmensch
	Statistical Prediction and Molecular Dynamics Simulation [My Copy] Biophys. J. (1 August 2008), biophysj.108.131623. by Ben Cooke, Scott Schmidler posted to hexapeptide by Diego_Prada on 2008-12-16 12:53:39 as along with 3 people joseph_x_zhou agrossfield paulschlesinger
	Unusual compactness of a polyproline type II structure. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 33. (16 August 2005), pp. 11698-11703. by B. Zagrovic, J. Lipfert, E. J. Sorin, et al.I. S. Millett, W. F. van Gunsteren, S. Doniach, V. S. Pande posted to experimental force-fields hexapeptide by Diego_Prada on 2008-12-16 12:51:37 as along with 1 person allmensch
	Simulation of the folding equilibrium of alpha-helical peptides: a comparison of the generalized Born approximation with explicit solvent. [My Copy] Proc Natl Acad Sci U S A, Vol. 100, No. 24. (25 November 2003), pp. 13934-13939. by H. Nymeyer, A. E. García posted to force-fields hexapeptide short-peptides by Diego_Prada on 2008-12-16 12:49:08 as along with 2 people fjc1 RamuAnandakrishnan
	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
	Characterization of non-alpha helical conformations in Ala peptides [My Copy] Polymer, Vol. 45, No. 2. (January 2004), pp. 669-676. by A. E. García posted to hexapeptide by Diego_Prada on 2008-12-16 12:10:36 as along with 1 person diasc
	Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 5. (5 March 2002), pp. 2782-2787. by A. E. García, K. Y. Sanbonmatsu posted to hexapeptide by Diego_Prada on 2008-12-16 11:58:14 as along with 2 people pavanghatty GermanErlenkamp
	Simulations of the pressure and temperature unfolding of an α-helical peptide [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 19. (10 May 2005), pp. 6765-6770. by Dietmar Paschek, S. Gnanakaran, Angel E. García posted to hexapeptide by Diego_Prada on 2008-12-16 11:54:14 as
	Eigenvalue spectrum of the master equation for hierarchical dynamics of complex systems [My Copy] Phys. Chem. Chem. Phys., Vol. 4, No. 20. (2002), pp. 5052-5058. by Yaakov Levy, Joshua Jortner, Stephen R. Berry posted to hexapeptide markov by Diego_Prada on 2008-12-16 11:45:00 as
	Helix-coil transition of alanine peptides in water: Force field dependence on the folded and unfolded structures [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 59, No. 4. (1 June 2005), pp. 773-782. by S. Gnanakaran, Angel E. García posted to hexapeptide by Diego_Prada on 2008-12-16 11:22:12 as along with 2 people chemrahul82 allmensch
	Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis [My Copy] The Journal of Chemical Physics, Vol. 128, No. 24. (2008) by Alexandros Altis, Moritz Otten, Phuong H. Nguyen, Rainer Hegger, Gerhard Stock posted to free_energy articulo dpca hexapeptide pca by Diego_Prada on 2008-12-16 11:16:42 as along with 2 people scampos agrossfield
	Helix Unfolding and Intramolecular Hydrogen Bond Dynamics in Small α-Helices in Explicit Solvent [My Copy] J. Phys. Chem. B, Vol. 106, No. 41. (17 October 2002), pp. 10748-10752. by C. J. Margulis, H. A. Stern, B. J. Berne posted to free_energy hexapeptide protein_folding by Diego_Prada on 2008-10-17 12:45:54 as
	Helix nucleation kinetics from molecular simulations in explicit solvent [My Copy] Proteins: Structure, Function, and Genetics, Vol. 42, No. 1. (2001), pp. 77-84. by Gerhard Hummer, Angel E. García, Shekhar Garde posted to free_energy hexapeptide protein_folding by Diego_Prada on 2008-10-17 12:42:01 as
	Structure and Dynamics of the Homologous Series of Alanine Peptides: A Joint Molecular Dynamics/NMR Study [My Copy] J. Am. Chem. Soc., Vol. 129, No. 5. (7 February 2007), pp. 1179-1189. by J. Graf, P. H. Nguyen, G. Stock, H. Schwalbe posted to dialanine hexapeptide by Diego_Prada on 2008-09-29 17:57:05 as
	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
	Energy landscape of a small peptide revealed by dihedral angle principal component analysis [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 58, No. 1. (2005), pp. 45-52. by Yuguang Mu, Phuong H. Nguyen, Gerhard Stock posted to articulo dpca hexapeptide md pca by Diego_Prada on 2008-09-24 12:25:09 as
	Heteropolymer freezing and design: Towards physical models of protein folding [My Copy] Reviews of Modern Physics, Vol. 72, No. 1. (1 January 2000), 259. by Vijay S. Pande, Alexander Y. Grosberg, Toyoichi Tanaka posted to free_energy hexapeptide hp_model protein_folding proteins review by Diego_Prada on 2008-08-19 22:25:55 as
	Flexibility, Conformation Spaces, and Bioactivity [My Copy] J. Phys. Chem. B, Vol. 104, No. 9. (9 March 2000), pp. 2123-2135. by O. M. Becker, Y. Levy, O. Ravitz posted to free_energy hexapeptide by Diego_Prada on 2008-08-19 20:36:56 as
	Aspects of Protein Reaction Dynamics: Deviations from Simple Behavior [My Copy] The Journal of Physical Chemistry B, Vol. 104, No. 1. (1 January 2000), pp. 11-27. by Martin Karplus posted to free_energy complex_systems hexapeptide protein_folding by Diego_Prada on 2008-08-19 19:25:56 as along with 3 people proposals ruvido yalexeev
	Geometric versus topological clustering: an insight into conformation mapping. [My Copy] Proteins, Vol. 27, No. 2. (February 1997), pp. 213-226. by O. M. Becker posted to free_energy plos hexapeptide chapt_cmn aux by Diego_Prada on 2008-08-19 18:55:05 as
	The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics [My Copy] The Journal of Chemical Physics, Vol. 106, No. 4. (1997), pp. 1495-1517. by Oren M. Becker, Martin Karplus posted to free_energy hexapeptide aux by Diego_Prada on 2008-08-19 18:38:50 as along with 2 people chiufanlee nigham
	Quantitative visualization of a macromolecular potential energy "funnel" [My Copy] Journal of Molecular Structure: THEOCHEM In World Congress of Theoretically Oriented Chemists, Vol. 398-399 (30 June 1997), pp. 507-516. by Oren M. Becker posted to free_energy articulo hexapeptide by Diego_Prada on 2008-08-19 18:00:05 as
	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
	Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 4. (2006), pp. 898-913. by Phuong H. Nguyen posted to free_energy hexapeptide pca by Diego_Prada on 2008-07-04 18:29:56 as along with 2 people nickolay ladab
	Energy landscapes of conformationally constrained peptides [My Copy] The Journal of Chemical Physics, Vol. 114, No. 2. (2001), pp. 993-1009. by Yaakov Levy, Oren M. Becker posted to free_energy hexapeptide by Diego_Prada on 2008-07-04 17:33:07 as
	Dynamics of hierarchical folding on energy landscapes of hexapeptides [My Copy] The Journal of Chemical Physics, Vol. 115, No. 22. (2001), pp. 10533-10547. by Yaakov Levy, Joshua Jortner, Oren M. Becker posted to free_energy hexapeptide by Diego_Prada on 2008-07-04 17:30:57 as
	Effect of Conformational Constraints on the Topography of Complex Potential Energy Surfaces [My Copy] Physical Review Letters, Vol. 81, No. 5. (1998), 1126. by Yaakov Levy, Oren M. Becker posted to free_energy hexapeptide aux by Diego_Prada on 2008-07-04 17:20:57 as
	Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states. [My Copy] J Chem Phys, Vol. 126, No. 15. (21 April 2007) by F. Noé, I. Horenko, C. Schütte, J. C. Smith posted to chapt_cmn hexapeptide markov plos protein_dynamics by Diego_Prada on 2008-03-30 16:22:35 as along with 3 people barmak7282 choonpeng toerst

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protein_folding	6
articulo	5
aux	5
chapt_cmn	5
plos	5
beta-hairpin	4
force-fields	4
pca	4
cmn	3
experimental	3
stochastic_processes	3
b3lyp	2
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dpca	2
md	2
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pelmenschikov_siegbahn_06_nickel	2
protein_dynamics	2
statistical_mechanics	2
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ala5	1
alanine	1
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first_passage	1
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