Diego_Prada's Karplus:M [25 articles] Export Sort

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	One-Dimensional Barrier-Preserving Free-Energy Projections of a β-sheet Miniprotein: New Insights into the Folding Process [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 29. (1 July 2008), pp. 8701-8714. by Sergei V. Krivov, Stefanie Muff, Amedeo Caflisch, Martin Karplus posted to free_energy cmn by Diego_Prada on 2009-12-19 19:09:09 as along with 1 person ruvido
	Enthalpic Contribution to Protein Stability: Insights from Atom-Based Calculations and Statistical Mechanics [My Copy] In Advances in Protein Chemistry Volume 47, Vol. 47 (1995), pp. 231-306. by T. Lazaridis, G. Archontis, M. Karplus posted to free_energy protein_folding by Diego_Prada on 2009-11-27 19:52:33 as along with 1 person flbarroso
	Conjugate peak refinement: an algorithm for finding reaction paths and accurate transition states in systems with many degrees of freedom [My Copy] Chemical Physics Letters, Vol. 194, No. 3. (26 June 1992), pp. 252-261. by S. Fischer, M. Karplus posted to free_energy transition_path reaction_paths problems_fel_dof methods by Diego_Prada on 2009-11-23 17:38:17 as along with 1 person ckmyo
	Cis-Trans Imide Isomerization of the Proline Dipeptide [My Copy] Journal of the American Chemical Society, Vol. 116, No. 26. (1 December 1994), pp. 11931-11937. by Stefan Fischer, Roland L. Dunbrack, Martin Karplus posted to transition_path problems_fel_dof amino by Diego_Prada on 2009-11-23 17:09:55 as
	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
	A hierarchy of timescales in protein dynamics is linked to enzyme catalysis [My Copy] Nature (18 November 2007) by Katherine A. Henzler-Wildman, Ming Lei, Vu Thai, Jordan S. Kerns, Martin Karplus, Dorothee Kern posted to struct_decorr proteins protein_dynamics collective_motions allostery active_site by Diego_Prada on 2009-09-19 15:45:21 as along with 9 people and 1 group ruvido tmmurali allmensch cactus sobolevnrm jlh64 RamuAnandakrishnan dmobley chenway baker-group
	A method for determining reaction paths in large molecules: Application to myoglobin [My Copy] Chemical Physics Letters, Vol. 139 (1987), pp. 375-380. by R. Elber, M. Karplus posted to reaction_paths transition_path by Diego_Prada on 2009-06-08 20:43:50 as
	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 force-fields by Diego_Prada on 2009-05-01 20:39:49 as along with 12 people jmparks dsmueller rpetrenko jrperillaj oceanwind dfgreen mkrishna timg dimka ttjoseph papatonyhill ssomani
	Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. [My Copy] Proc Natl Acad Sci U S A, Vol. 80, No. 21. (November 1983), pp. 6571-6575. by B. Brooks, M. Karplus posted to gnm md_history by Diego_Prada on 2009-04-05 17:12:49 as along with 5 people mkrishna baaden lna aqeel saravan
	Dynamical theory of activated processes in globular proteins [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 79, No. 13. (July 1982), pp. 4035-4039. by S. H. Northrup, M. R. Pear, C. Y. Lee, J. A. Mccammon, M. Karplus posted to free_energy md md_history by Diego_Prada on 2009-04-05 17:10:15 as
	Dynamics of ligand binding to heme proteins [My Copy] Journal of Molecular Biology, Vol. 132, No. 3. (15 August 1979), pp. 343-368. by D. A. Case, M. Karplus posted to md md_history by Diego_Prada on 2009-04-05 17:04:14 as along with 1 person ruvido
	Diffusive reaction dynamics on invariant free energy profiles [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 37. (16 September 2008), pp. 13841-13846. by Sergei V. Krivov, Martin Karplus posted to free_energy articulo by Diego_Prada on 2009-03-21 17:44:16 as
	Protein Folding: A Perspective from Theory and Experiment [My Copy] Angewandte Chemie International Edition, Vol. 37, No. 7. (1998), pp. 868-893. by Christopher M. Dobson, Andrej Scaronali, Martin Karplus posted to free_energy protein_folding proteins by Diego_Prada on 2008-08-19 19:50:01 as along with 1 person dsmueller
	Understanding protein folding via free-energy surfaces from theory and experiment [My Copy] Trends in Biochemical Sciences, Vol. 25, No. 7. (1 July 2000), pp. 331-339. by Aaron R. Dinner, Andrej Sali, Lorna J. Smith, Christopher M. Dobson, M. Karplus posted to free_energy protein_folding by Diego_Prada on 2008-08-19 19:34:59 as
	The Levinthal paradox: yesterday and today [My Copy] Folding and Design, Vol. 2, No. Supplement 1. (June 1997), pp. S69-S75. by Martin Karplus posted to protein_folding by Diego_Prada on 2008-08-19 19:28:28 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
	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
	Solvation - molecular-dynamics study of a dipeptide in water [My Copy] J. Am. Chem. Soc., Vol. 101, No. 8. (1979), pp. 1913-1937. by P. J. Rossky, M. Karplus posted to chapt_cmn dialanine plos by Diego_Prada on 2008-08-03 16:10:28 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
	Importance of Metastable States in the Free Energy Landscapes of Polypeptide Chains [My Copy] Physical Review Letters, Vol. 99, No. 17. (2007) by Stefan Auer, Mark A. Miller, Sergei V. Krivov, Christopher M. Dobson, Martin Karplus, Michele Vendruscolo posted to free_energy hot by Diego_Prada on 2008-02-19 10:53:07 as
	Free energy disconnectivity graphs: Application to peptide models [My Copy] The Journal of Chemical Physics, Vol. 117, No. 23. (2002), pp. 10894-10903. by Sergei V. Krivov, Martin Karplus posted to free_energy plos chapt_cmn aux by Diego_Prada on 2008-02-19 10:28:36 as
	Potential Energy Surfaces and Conformational Transitions in Biomolecules: A Successive Confinement Approach Applied to a Solvated Tetrapeptide [My Copy] Physical Review Letters, Vol. 88, No. 3. (2 January 2002), 038101. by Sergei V. Krivov, Sergei F. Chekmarev, Martin Karplus posted to free_energy by Diego_Prada on 2008-02-19 10:26:36 as
	One-Dimensional Free-Energy Profiles of Complex Systems: Progress Variables that Preserve the Barriers. [My Copy] J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, Vol. 110, No. 25. (29 June 2006), pp. 12689-12698. by S. V. Krivov, M. Karplus posted to free_energy by Diego_Prada on 2008-02-19 10:24:24 as
	Hidden complexity of free energy surfaces for peptide (protein) folding. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 41. (12 October 2004), pp. 14766-14770. by S. V. Krivov, M. Karplus posted to free_energy proteins plos chapt_cmn aux by Diego_Prada on 2008-02-19 10:22:29 as along with 4 people apaydin dimka bilab Fernando_FF
	The Meaning of Component Analysis: Decomposition of the Free Energy in Terms of Specific Interactions [My Copy] Journal of Molecular Biology, Vol. 254, No. 5. (15 December 1995), pp. 801-807. by S. Boresch, M. Karplus posted to free_energy pca by Diego_Prada on 2008-02-19 10:11:40 as along with 1 person dmobley

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