Diego_Prada's short-peptides [62 articles] Export

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	Network Structure of Protein Folding Pathways [My Copy] (7 May 2007) by Erzsebet Ravasz, S. Gnanakaran, Zoltan Toroczkai posted to short-peptides free-energy cmn by Diego_Prada on 2009-09-17 16:11:59 as
	Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations [My Copy] PLoS Comput Biol, Vol. 5, No. 7. (10 July 2009), e1000428. by Lucy R. Allen, Sergei V. Krivov, Emanuele Paci posted to dihedral free-energy short-peptides by Diego_Prada on 2009-07-10 11:52:24 as along with 2 people zwang melo_mcr
	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 beta-hairpin first_passage free-energy 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 beta-hairpin cmn dihedral free-energy 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 ala5 cmn free-energy hexapeptide short-peptides by Diego_Prada on 2009-05-30 20:42:39 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
	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 beta-hairpin free-energy hexapeptide protein_folding short-peptides by Diego_Prada on 2009-04-30 12:10:50 as
	Likelihood-Based Estimation of Multidimensional Langevin Models and Its Application to Biomolecular Dynamics [My Copy] Multiscale Modeling & Simulation, Vol. 7, No. 2. (2008), pp. 731-773. by Illia Horenko, Christof Schütte posted to free-energy langevin short-peptides statistical_mechanics stochastic_processes by Diego_Prada on 2009-03-07 12:46:38 as along with 1 person gardenes
	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 coarse-grained dialanine free-energy short-peptides by Diego_Prada on 2009-03-04 12:12:11 as
	Foldamer dynamics expressed via Markov state models. II. State space decomposition [My Copy] The Journal of Chemical Physics, Vol. 123, No. 11. (2005) by Sidney P. Elmer, Sanghyun Park, Vijay S. Pande posted to free-energy markov short-peptides stochastic_processes by Diego_Prada on 2009-03-03 12:09:47 as
	Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water [My Copy] The Journal of Chemical Physics, Vol. 123, No. 11. (2005) by Sidney P. Elmer, Sanghyun Park, Vijay S. Pande posted to free-energy markov short-peptides stochastic_processes by Diego_Prada on 2009-03-03 12:06:39 as along with 1 person toerst
	alpha/3<SUB><FONT SIZE='-1'>10</FONT></SUB>-Helix transitions in alpha-methylalanine homopeptides: Conformational transition pathway and potential of mean force [My Copy] Biopolymers, Vol. 34, No. 1. (1994), pp. 75-90. by Shawn E. Huston, Garland R. Marshall posted to short-peptides by Diego_Prada on 2008-12-21 20:05:46 as
	Alpha-helix and beta-hairpin Folding from experiment, analytical theory and molecular dynamics simulations. [My Copy] Current protein & peptide science, Vol. 3, No. 2. (April 2002), pp. 191-200. by O. V. Galzitskaya, J. Higo, A. V. Finkelstein posted to beta-hairpin short-peptides by Diego_Prada on 2008-12-19 16:10:00 as
	The Mechanism of alpha-Helix Formation by Peptides [My Copy] Annual Review of Biophysics and Biomolecular Structure, Vol. 21, No. 1. (1992), pp. 95-118. by Martin J. Scholtz, Robert L. Baldwin posted to short-peptides by Diego_Prada on 2008-12-19 11:58:05 as
	Free energy landscape of a biomolecule in dihedral principal component space: sampling convergence and correspondence between structures and minima. [My Copy] Proteins, Vol. 67, No. 3. (15 May 2007), pp. 569-578. by G. G. Maisuradze, D. M. Leitner posted to articulo pca short-peptides by Diego_Prada on 2008-12-19 11:25:15 as along with 2 people scampos onufriev
	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
	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
	beta-Hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solution [My Copy] Journal of Peptide Science, Vol. 10, No. 9. (2004), pp. 546-565. by Clara M. Santiveri, Ángeles M. Jiménez, Manuel Rico, Wilfred F. van Gunsteren, Xavier Daura posted to beta-hairpin short-peptides by Diego_Prada on 2008-12-15 13:02:27 as
	Characterization of the Stereochemical Selectivity of β-Hairpin Formation by Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 109, No. 3. (1 January 2005), pp. 1281-1288. by Patricia Soto, Ronen Zangi posted to beta-hairpin experimental short-peptides by Diego_Prada on 2008-12-15 12:30:06 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
	Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ16–22, Aβ16–35, and Aβ10–35): Sequence effects [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 22. (29 October 2002), pp. 14126-14131. by Buyong Ma, Ruth Nussinov posted to amyloids short-peptides by Diego_Prada on 2008-12-11 19:15:09 as
	Folding dynamics and mechanism of \|[beta]\|-hairpin formation [My Copy] Nature, Vol. 390, No. 6656. (13 November 1997), pp. 196-199. by Victor Munoz, Peggy A. Thompson, James Hofrichter, William A. Eaton posted to beta-hairpin short-peptides by Diego_Prada on 2008-12-11 16:32:00 as along with 1 person dgront
	Chemical, physical, and theoretical kinetics of an ultrafast folding protein [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 48. (2 December 2008), pp. 18655-18662. by Jan Kubelka, Eric R. Henry, Troy Cellmer, James Hofrichter, William A. Eaton posted to protein_folding short-peptides by Diego_Prada on 2008-12-11 16:29:33 as along with 3 people zwang operon RamuAnandakrishnan
	Understanding the key factors that control the rate of Î²-hairpin folding [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 45. (9 November 2004), pp. 15915-15920. by Deguo Du, Yongjin Zhu, Cheng-Yen Huang, Feng Gai posted to beta-hairpin short-peptides by Diego_Prada on 2008-12-11 16:10:28 as along with 2 people kjell allmensch
	Kinetic studies of β-sheet protein folding [My Copy] Current Opinion in Structural Biology, Vol. 8, No. 1. (February 1998), pp. 86-92. by A. P. Capaldi, S. E. Radford posted to amyloids short-peptides by Diego_Prada on 2008-12-08 12:48:37 as along with 1 person chiufanlee
	From Computer Simulations to Human DiseaseEmerging Themes in Protein Folding [My Copy] Cell, Vol. 97, No. 3. (30 April 1999), pp. 291-298. by S. E. Radford, C. M. Dobson posted to amyloids protein_folding short-peptides by Diego_Prada on 2008-12-08 12:42:35 as along with 1 person flbarroso
	Experimental investigation of protein folding and misfolding [My Copy] Methods, Vol. 34, No. 1. (September 2004), pp. 4-14. by C. Dobson posted to amyloids protein_folding short-peptides by Diego_Prada on 2008-12-08 12:30:48 as
	Principles of protein folding, misfolding and aggregation [My Copy] Seminars in Cell & Developmental Biology, Vol. 15, No. 1. (February 2004), pp. 3-16. by C. Dobson posted to amyloids protein_folding short-peptides by Diego_Prada on 2008-12-08 12:28:03 as along with 1 person pjkiley
	Protein folding and misfolding [My Copy] Nature, Vol. 426, No. 6968. (18 December 2003), pp. 884-890. by Christopher M. Dobson posted to amyloids protein_folding short-peptides by Diego_Prada on 2008-12-08 12:24:54 as along with 8 people and 1 group onufriev chiufanlee penka allmensch choonpeng anyscientist dougjoemartin Ema Nie
	The Formation of Straight and Twisted Filaments from Short Tau Peptides [My Copy] J. Biol. Chem., Vol. 279, No. 26. (25 June 2004), pp. 26868-26875. by Warren J. Goux, Lauren Kopplin, Anh D. Nguyen, et al.Kathryn Leak, Marni Rutkofsky, Vasanthi D. Shanmuganandam, Deepak Sharma, Hideyo Inouye, Daniel A. Kirschner posted to amyloids short-peptides by Diego_Prada on 2008-12-08 12:16:59 as along with 1 person chiufanlee
	Structural and Thermodynamic Approach to Peptide Immunogenicity [My Copy] PLoS Comput Biol, Vol. 4, No. 11. (21 November 2008), e1000231. by Carlos J. Camacho, Yasuhiro Katsumata, Dana P. Ascherman posted to short-peptides by Diego_Prada on 2008-12-02 16:20:58 as along with 1 person VGreiff
	Linking folding with aggregation in Alzheimer's beta-amyloid peptides [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 43. (23 October 2007), pp. 16880-16885. by Jana Khandogin, Charles L. Brooks posted to amyloids short-peptides by Diego_Prada on 2008-11-29 18:39:50 as along with 3 people and 1 group scampos onufriev sobolevnrm baker-group
	Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein G [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 16. (1999), pp. 9062-9067. by Vijay S. Pande, Daniel S. Rokhsar posted to short-peptides by Diego_Prada on 2008-11-29 18:36:58 as
	Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation [My Copy] Protein Sci, Vol. 11, No. 10. (1 October 2002), pp. 2335-2350. by Buyong Ma, Ruth Nussinov posted to amyloids short-peptides by Diego_Prada on 2008-11-29 18:26:27 as along with 1 person chiufanlee
	The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35 [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 9. (29 April 2003), pp. 5154-5159. by Jörg Gsponer, Urs Haberthür, Amedeo Caflisch posted to amyloids short-peptides by Diego_Prada on 2008-11-29 18:14:21 as
	Investigating the Mechanism of Peptide Aggregation: Insights from Mixed MonteCarlo-Molecular Dynamics Simulations [My Copy] Biophys. J. (8 February 2008), biophysj.107.121061. by Massimiliano Meli, Giulia Morra, Giorgio Colombo posted to short-peptides by Diego_Prada on 2008-11-29 18:10:25 as along with 1 person paulschlesinger
	Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: Antiparallel versus parallel association [My Copy] Biochemical and Biophysical Research Communications, Vol. 377, No. 4. (26 December 2008), pp. 1036-1041. by L. Vitagliano, L. Esposito, C. Pedone, A. Desimone posted to short-peptides by Diego_Prada on 2008-11-29 18:05:13 as
	Identification of amyloid fibril-forming segments based on structure and residue-based statistical potential [My Copy] Bioinformatics, Vol. 23, No. 17. (1 September 2007), pp. 2218-2225. by Zhuqing Zhang, Hao Chen, Luhua Lai posted to amyloids short-peptides by Diego_Prada on 2008-11-29 18:02:11 as along with 1 person bobychan
	Temperature-Induced Dissociation of Abeta Monomers from Amyloid Fibril [My Copy] Biophys. J., Vol. 95, No. 4. (15 August 2008), pp. 1758-1772. by Takako Takeda, Dmitri K. Klimov posted to amyloids short-peptides by Diego_Prada on 2008-11-29 17:57:28 as along with 1 person chiufanlee
	A systematic screen of β2-microglobulin and insulin for amyloid-like segments [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 11. (14 March 2006), pp. 4079-4082. by Magdalena I. Ivanova, Michael J. Thompson, David Eisenberg posted to amyloids short-peptides by Diego_Prada on 2008-11-29 17:53:54 as
	Ile-Phe Dipeptide Self-Assembly: Clues to Amyloid Formation [My Copy] Biophys. J., Vol. 92, No. 5. (1 March 2007), pp. 1732-1741. by Natalia S. de Groot, Teodor Parella, Francesc X. Aviles, Josep Vendrell, Salvador Ventura posted to short-peptides by Diego_Prada on 2008-11-29 17:47:27 as
	Structure and Dynamics of Parallel beta-Sheets, Hydrophobic Core, and Loops in Alzheimer's Abeta Fibrils [My Copy] Biophys. J., Vol. 92, No. 9. (1 May 2007), pp. 3032-3039. by Nicolae-Viorel Buchete, Gerhard Hummer posted to amyloids short-peptides by Diego_Prada on 2008-11-29 17:33:48 as
	All-Atom Computer Simulations of Amyloid Fibrils Disaggregation [My Copy] Biophys. J. (29 August 2008), biophysj.108.131672. by Jun Wang, Chunhu Tan, Hai-Feng Chen, Ray Luo posted to amyloids short-peptides by Diego_Prada on 2008-11-29 17:26:57 as along with 2 people chiufanlee paulschlesinger
	Unzipping the mysteries of amyloid fiber formation [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 13. (30 March 2004), pp. 4335-4336. by Andrew D. Miranker posted to amyloids short-peptides by Diego_Prada on 2008-11-29 17:23:06 as
	A conserved trimerization motif controls the topology of short coiled coils [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 39. (2005), pp. 13891-13896. by Richard A. Kammerer, Dirk Kostrewa, Pavlos Progias, et al.Srinivas Honnappa, David Avila, Ariel Lustig, Fritz K. Winkler, Jean Pieters, Michel O. Steinmetz posted to short-peptides by Diego_Prada on 2008-11-29 17:16:21 as along with 1 person kgutwin
	Molecular basis of coiled-coil formation [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 17. (24 April 2007), pp. 7062-7067. by Michel O. Steinmetz, Ilian Jelesarov, William M. Matousek, et al.Srinivas Honnappa, Wolfgang Jahnke, John H. Missimer, Sabine Frank, Andrei T. Alexandrescu, Richard A. Kammerer posted to short-peptides by Diego_Prada on 2008-11-29 17:03:45 as along with 2 people krapnik kgutwin
	Configurational entropy elucidates the role of salt-bridge networks in protein thermostability. [My Copy] Protein Sci, Vol. 16, No. 7. (July 2007), pp. 1349-1359. by J. H. Missimer, M. O. Steinmetz, R. Baron, et al.F. K. Winkler, R. A. Kammerer, X. Daura, W. F. van Gunsteren posted to short-peptides by Diego_Prada on 2008-11-29 16:01:54 as along with 1 person choonpeng
	Stability and Structure of Oligomers of the Alzheimer Peptide Abeta16-22: From the Dimer to the 32-Mer [My Copy] Biophys. J., Vol. 91, No. 9. (1 November 2006), pp. 3217-3229. by Ute F. Rohrig, Alessandro Laio, Nazario Tantalo, Michele Parrinello, Roberto Petronzio posted to amyloids short-peptides by Diego_Prada on 2008-11-29 15:59:16 as

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free-energy	87
networks	66
short-peptides	62
chapt_cmn	61
hexapeptide	48
plos	47
md	41
communities	38
markov	35
stochastic_processes	34
cmn	29
pca	29
protein_dynamics	29
protein_folding	27
amino	26
amyloids	26
md_history	26
dialanine	25
gnm	25
articulo	21
complex_systems	21
coarse-grained	18
hp_model	16
beta-hairpin	15
dpca	15
proteins	15
methods	14
transition_path	13
water	13
chapt_amino	12
force-fields	12
statistical_mechanics	12
clustering	8
experimental	8
first_passage	8
reaction_paths	7
transition_states	7
active_site	6
glass_transition	6
mutual-information	6
struct_decorr	6
glycine	5
hot	5
kramers	5
langevin	5
mios	5
out_of_equilibrium	5
rmsd	5
secondary_structure	5
allostery	4
entropy	4
kinetic_models	4
mc	4
percolation	4
qha	4
collective_motions	3
dihedral	3
energy_landscape	3
rol_nodes	3
work_theorem	3
ala5	2
alanine	2
bayesian_analysis	2
fca	2
funnels	2
go	2
information	2
irreversibility	2
lanvegin	2
leas_action	2
non_markovian	2
statistics	2
wavelets	2
chain_interactions	1
conformational_entropy	1
discrete_breathers	1
enkaphalin	1
flagellum	1
hurst_exponent	1
information_theory	1
latex	1
markov_state_models	1
mpi	1
nmr	1
nonequilibrium	1
opls	1
pendiente	1
protein_flexibility	1
relaxation_processes	1
review	1
statistical_models	1
t_dependence	1

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