Diego_Prada's md [41 articles] Export

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	Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 6. (1 November 2007), pp. 2312-2334. by Jianyin Shao, Stephen W. Tanner, Nephi Thompson, Thomas E. Cheatham posted to protein_dynamics md communities clustering beta-hairpin by Diego_Prada on 2009-09-19 15:52:15 as along with 10 people and 3 groups karinaecomp anuragsethi scampos oteri barry daevans sobolevnrm LamBras allmensch GermanErlenkamp Structural Biology Group TorVergata structural_bioinformatics baker-group
	Dynamic personalities of proteins [My Copy] Nature, Vol. 450, No. 7172. (12 December 2007), pp. 964-972. by Katherine Henzler-Wildman, Dorothee Kern posted to proteins protein_folding protein_dynamics md free-energy by Diego_Prada on 2009-09-19 15:39:20 as along with 19 people and 1 group victorclaessen saravan xdeupi viktor21614 ruvido barry pavanghatty chad_davis allmensch choonpeng rsantana cjeans sobolevnrm wilbur mijam kjell phoenixzxl higueruelo GeeSharpMinor baker-group
	Two-state protein folding kinetics through all-atom molecular dynamics based sampling. [My Copy] Frontiers in bioscience : a journal and virtual library, Vol. 14 (2009), pp. 2801-2828. by P. G. Bolhuis posted to free-energy md protein_dynamics by Diego_Prada on 2009-05-30 19:31:01 as
	Multidimensional Langevin modeling of biomolecular dynamics [My Copy] The Journal of Chemical Physics, Vol. 130, No. 3. (2009), 034106. by Rainer Hegger, Gerhard Stock posted to lanvegin md methods pca short-peptides by Diego_Prada on 2009-05-30 19:16:19 as along with 1 person and 1 group sobolevnrm baker-group
	HOW WELL CAN SIMULATION PREDICT PROTEIN FOLDING KINETICS AND THERMODYNAMICS? [My Copy] Annual Review of Biophysics and Biomolecular Structure, Vol. 34, No. 1. (29 October 2005), pp. 43-69. by Christopher D. Snow, Eric J. Sorin, Young M. Rhee, Vijay S. Pande posted to md methods protein_folding statistical_mechanics stochastic_processes by Diego_Prada on 2009-04-30 12:01:14 as along with 9 people amphibina flbarroso doktornoe dgront blackbart allmensch saunders evanse toerst
	Kemp elimination catalysts by computational enzyme design [My Copy] Nature, Vol. 453, No. 7192. (19 March 2008), pp. 190-195. by Daniela Rothlisberger, Olga Khersonsky, Andrew M. Wollacott, et al.Lin Jiang, Jason DeChancie, Jamie Betker, Jasmine L. Gallaher, Eric A. Althoff, Alexandre Zanghellini, Orly Dym, Shira Albeck, Kendall N. Houk, Dan S. Tawfik, David Baker posted to md md_history by Diego_Prada on 2009-04-05 18:36:59 as along with 12 people and 3 groups barmak7282 baiaixi whitead qbin1304 fralium apaydin jwm msuarezdiez austin cactus neils sobolevnrm Jiang Research Group Biocatalysis and Biotransformation baker-group
	Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 3. (16 January 2007), pp. 808-813. by Tom Young, Robert Abel, Byungchan Kim, Bruce J. Berne, Richard A. Friesner posted to md md_history water by Diego_Prada on 2009-04-05 18:33:39 as along with 5 people ubcg08l LamBras daevans jwagoner zwang
	Mechanism of Na+/H+ Antiporting [My Copy] Science, Vol. 317, No. 5839. (10 August 2007), pp. 799-803. by Isaiah T. Arkin, Huafeng Xu, Morten O. Jensen, et al.Eyal Arbely, Estelle R. Bennett, Kevin J. Bowers, Edmond Chow, Ron O. Dror, Michael P. Eastwood, Ravenna Flitman-Tene, Brent A. Gregersen, John L. Klepeis, Istvan Kolossvary, Yibing Shan, David E. Shaw posted to hot md md_history by Diego_Prada on 2009-04-05 18:30:28 as along with 6 people and 1 group allmensch sobolevnrm Jporci MMehrotra LamBras dimka baker-group
	Domain swapping is a consequence of minimal frustration [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 38. (2004), pp. 13786-13791. by Sichun Yang, Samuel S. Cho, Yaakov Levy, et al.Margaret S. Cheung, Herbert Levine, Peter G. Wolynes, José N. Onuchic posted to gnm go md md_history by Diego_Prada on 2009-04-05 18:27:24 as along with 1 person apaydin
	Design of a novel globular protein fold with atomic-level accuracy. [My Copy] Science (New York, N.Y.), Vol. 302, No. 5649. (21 November 2003), pp. 1364-1368. by Brian Kuhlman, Gautam Dantas, Gregory C. Ireton, Gabriele Varani, Barry L. Stoddard, David Baker posted to md md_history by Diego_Prada on 2009-04-05 18:24:02 as along with 10 people bmduggan kgutwin onufriev apaydin dfgreen jwm hmk heymiki kevinchannon ca3295
	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 free-energy md md_history methods statistical_mechanics stochastic_processes by Diego_Prada on 2009-04-05 18:20:54 as along with 11 people and 1 group jrperillaj edws stephenbond dfgreen A_Coletta_Thesis sunnytov dgront sikorski jwagoner bransfop allmensch Structural Biology Group TorVergata
	Energetics of ion conduction through the K+ channel. [My Copy] Nature, Vol. 414, No. 6859. (1 November 2001), pp. 73-77. by S. Bernèche, B. Roux posted to md md_history by Diego_Prada on 2009-04-05 18:18:36 as along with 2 people and 1 group dimka brocktice TulaneCEP
	Replica-exchange molecular dynamics method for protein folding [My Copy] Chemical Physics Letters, Vol. 314, No. 1-2. (26 November 1999), pp. 141-151. by Y. Sugita posted to md md_history methods statistical_mechanics stochastic_processes by Diego_Prada on 2009-04-05 17:41:37 as along with 8 people and 1 group chemrahul82 tovrstra oteri Sylvain_Prigent andreasauerwein dgront allmensch rulix Structural Biology Group TorVergata
	Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. [My Copy] Science (New York, N.Y.), Vol. 282, No. 5389. (23 October 1998), pp. 740-744. by Y. Duan, P. A. Kollman posted to md md_history by Diego_Prada on 2009-04-05 17:38:31 as along with 6 people flbarroso doktornoe j3xucite allmensch RamuAnandakrishnan choonpeng
	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 md_history by Diego_Prada on 2009-04-05 17:36:40 as along with 1 person yxue
	Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions [My Copy] Journal of Molecular Biology, Vol. 268, No. 1. (25 April 1997), pp. 209-225. by K. Simons posted to md md_history by Diego_Prada on 2009-04-05 17:26:19 as along with 12 people and 2 groups chemrahul82 paddydu reyez guxiyou ana jwm vavi wouterboomsma j3xucite hmk mijam joule structural_bioinformatics Bioinformatics
	Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. [My Copy] Science, Vol. 271, No. 5251. (16 February 1996), pp. 997-999. by H. Grubmüller, B. Heymann, P. Tavan posted to md md_history by Diego_Prada on 2009-04-05 17:24:31 as along with 2 people TheoBioPhys choonpeng
	Role of hydration and water structure in biological and colloidal interactions [My Copy] Nature, Vol. 379, No. 6562. (18 January 1996), pp. 219-225. by Jacob Israelachvili, Hakan Wennerstrom posted to md md_history water by Diego_Prada on 2009-04-05 17:20:25 as along with 1 person anyscientist
	A method to explore transition paths in macromolecules. Applications to hemoglobin and phosphoglycerate kinase [My Copy] Computer Physics Communications, Vol. 91, No. 1-3. (02 September 1995), pp. 263-273. by C. Guilbert, D. Perahia, L. Mouawad posted to md md_history rmsd by Diego_Prada on 2009-04-05 17:18:35 as along with 1 person oteri
	Accurate simulation of protein dynamics in solution. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 85, No. 20. (October 1988), pp. 7557-7561. by M. Levitt, R. Sharon posted to md md_history by Diego_Prada on 2009-04-05 17:15:41 as
	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
	Computer simulation of protein folding [My Copy] Nature, Vol. 253, No. 5494. (27 February 1975), pp. 694-698. by Michael Levitt, Arieh Warshel posted to md md_history by Diego_Prada on 2009-04-05 16:57:56 as
	Equation of State Calculations by Fast Computing Machines [My Copy] The Journal of Chemical Physics, Vol. 21, No. 6. (1953), pp. 1087-1092. by Nicholas Metropolis, Arianna W. Rosenbluth, Marshall N. Rosenbluth, Augusta H. Teller, Edward Teller posted to mc md md_history by Diego_Prada on 2009-04-05 16:52:28 as along with 26 people eyliu zhaidong philipppixel iantunbridge wei flbarroso LGNR mcbla mrkn jjray muraken scalptob ppeeling gale82 Jarosik apostola chad_davis tobin mkurc rabio gcalda Akimasa Bc91 guxiyou petermilner naegele
	Full correlation analysis of conformational protein dynamics [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 70, No. 9999. (2007), pp. 1294-1312. by Oliver F. Lange, Helmut Grubmüller posted to articulo md mutual-information pca by Diego_Prada on 2009-03-21 17:32:53 as along with 7 people and 1 group anuragsethi jeargle softsimu barry choonpeng sobolevnrm LamBras baker-group
	Principal component analysis for protein folding dynamics [My Copy] Journal of Molecular Biology (15 October 2008) by G. Maisuradze, A. Liwo, H. Scheraga posted to articulo dpca md pca by Diego_Prada on 2009-03-21 17:04:23 as along with 4 people and 1 group scampos phoenixzxl barry paulschlesinger structural_bioinformatics
	Coarse Master Equation from Bayesian Analysis of Replica Molecular Dynamics Simulations† [My Copy] The Journal of Physical Chemistry B, Vol. 109, No. 14. (1 April 2005), pp. 6479-6484. by Saravanapriyan Sriraman, Ioannis G. Kevrekidis, Gerhard Hummer posted to md non_markovian by Diego_Prada on 2009-03-06 16:22:29 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
	Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory [My Copy] J. Phys. Chem. B, Vol. 108, No. 21. (27 May 2004), pp. 6571-6581. by W. C. Swope, J. W. Pitera, F. Suits posted to chapt_cmn free-energy markov md plos protein_dynamics stochastic_processes by Diego_Prada on 2009-02-16 11:14:57 as along with 2 people mtw apaydin
	termostato2 [My Copy] posted to md methods protein_dynamics by Diego_Prada on 2008-12-18 18:00:09 as
	Peptide Folding: When Simulation Meets Experiment [My Copy] Angewandte Chemie International Edition, Vol. 38, No. 1-2. (1999), pp. 236-240. by Xavier Daura, Karl Gademann, Bernhard Jaun, Dieter Seebach, Wilfred F. van Gunsteren, Alan E. Mark posted to beta-hairpin md protein_dynamics short-peptides by Diego_Prada on 2008-12-15 12:06:57 as along with 2 people dsmueller jteyra
	Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 35. (1 September 2006), pp. 17616-17626. by Berk Hess, Nico F. A. van der Vegt posted to md methods by Diego_Prada on 2008-12-10 12:26:36 as along with 6 people and 1 group softsimu arnaucordomi krapnik flbarroso Marine ashaytan Molecular dynamics in MSU
	Simulating replica exchange simulations of protein folding with a kinetic network model [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 39. (25 September 2007), pp. 15340-15345. by Weihua Zheng, Michael Andrec, Emilio Gallicchio, Ronald M. Levy posted to cmn markov md methods by Diego_Prada on 2008-11-29 15:56:08 as along with 1 person zwang
	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
	Dihedral angle principal component analysis of molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 126, No. 24. (2007) by Alexandros Altis, Phuong H. Nguyen, Rainer Hegger, Gerhard Stock posted to articulo dpca md pca protein_dynamics by Diego_Prada on 2008-09-24 11:39:38 as along with 4 people and 1 group scampos barry ruvido nh structural_bioinformatics
	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
	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
	GROMACS: fast, flexible, and free. [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1701-1718. by David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. Berendsen posted to chapt_cmn md by Diego_Prada on 2008-08-01 18:26:15 as along with 20 people and 2 groups arifor krapnik r2s2 janneb dsmueller oteri choonpeng sebk dimka jwm ttjoseph bilab rabio Dinler tji softsimu ashaytan robertvacha sunnytov A_Coletta_Thesis Radiation_Damage Stressosome
	Comparison of simple potential functions for simulating liquid water [My Copy] The Journal of Chemical Physics, Vol. 79, No. 2. (1983), pp. 926-935. by William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura, Roger W. Impey, Michael L. Klein posted to chapt_cmn md water by Diego_Prada on 2008-08-01 18:05:06 as along with 17 people and 1 group jmparks fralium bmduggan kulinskii ibuch Lombardo_7 paddydu dfgreen softsimu mleis ttjoseph ffranca easybakemuffin ashaytan RamuAnandakrishnan r2s2 pavanghatty CMB
	Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids [My Copy] Journal of the American Chemical Society, Vol. 118, No. 45. (1 January 1996), pp. 11225-11236. by William L. Jorgensen, David S. Maxwell, Julian Tirado-Rives posted to chapt_cmn force-fields md opls by Diego_Prada on 2008-08-01 17:47:35 as along with 9 people dimka snichols15 flbarroso tovrstra dfgreen sunnytov BragilMassoud loison softsimu

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plos	47
md	41
communities	38
markov	35
stochastic_processes	34
gnm	32
cmn	31
pca	30
protein_dynamics	29
amino	28
protein_folding	28
amyloids	27
dialanine	27
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articulo	21
complex_systems	21
transition_path	19
coarse-grained	18
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