apaydin's folding [51 articles] Export

Recent papers added to apaydin's library classified by the tag folding. You can also see everyone's folding.

	How to mark off paths on the protein energy landscape [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 45. (10 November 2009), pp. 18879-18880. by Martin Gruebele posted to protein folding energy_landscape by apaydin on 2009-11-11 16:26:43 as
	Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 45. (10 November 2009), pp. 19011-19016. by Frank NoÃ©, Christof SchÃ¼tte, Eric Vanden-Eijnden, Lothar Reich, Thomas R. Weikl posted to protein folding by apaydin on 2009-11-11 16:18:08 as along with 1 person Diego_Prada
	Structural biology. Dynamic visions of enzymatic reactions. [My Copy] Science, Vol. 313, No. 5793. (15 September 2006), pp. 1586-1587. by M. Vendruscolo, C. M. Dobson posted to folding perspectives protein stochasticity by apaydin on 2009-05-20 07:13:25 as along with 2 people victorclaessen tny
	Shmygelska_Alena.pdf (application/pdf Object) [My Copy] by Shmygelska posted to ant colony folding optimization protein by apaydin on 2009-05-20 05:49:13 as
	Structural Interpretation of Paramagnetic Relaxation Enhancement-Derived Distances for Disordered Protein States [My Copy] Journal of Molecular Biology, Vol. 390, No. 3. (17 July 2009), pp. 467-477. by Debabani Ganguly, Jianhan Chen posted to denatured ensemble folding nmr pre protein by apaydin on 2009-05-19 09:59:22 as
	The folding mechanism of BBL: Plasticity of transition state structure observed within an ultrafast folding protein family [My Copy] by Hannes Neuweilera, Timothy, Trevor J. Rutherforda, et al.Christopher M. Johnsona, Mark D. Allena, Neil, Alan R. Fersht posted to folding protein transition_state_ensemble by apaydin on 2009-05-14 06:37:56 as
	Different members of a simple 3-helix bundle protein family have very different folding rates and fold by different mechanisms [My Copy] by Beth G. Wensleya, Martina Gärtner[1], Wan X. Chooa, Sarah Batey2, And posted to folding protein rate by apaydin on 2009-05-14 06:35:10 as
	msmbuilder [My Copy] by Pande posted to folding kinetics protein srs by apaydin on 2009-05-10 17:59:36 as
	Parameter optimization for the Gaussian model of protein folding [My Copy] Polymer, Vol. 43, No. 2. (January 2002), pp. 495-501. by A. Erkip posted to folding protein by apaydin on 2009-05-06 17:12:11 as
	Topological methods for exploring low-density states in biomolecular folding pathways. [My Copy] by Pande, Guibas posted to folding pathways protein topology by apaydin on 2009-04-26 10:06:28 as
	Relaxation Dispersion NMR Spectroscopy as a Tool for Detailed Studies of Protein Folding [My Copy] Vol. 96, No. 6. (18 March 2009), pp. 2045-2054. by Philipp Neudecker, Patrik Lundström, Lewis E. Kay posted to folding nmr protein by apaydin on 2009-03-20 10:02:36 as
	Rapid Sampling of Molecular Motions with Prior Information Constraints [My Copy] PLoS Comput Biol, Vol. 5, No. 2. (27 February 2009), e1000295. by Barak Raveh, Angela Enosh, Ora Schueler-Furman, Dan Halperin posted to folding motion planning protein by apaydin on 2009-03-05 19:03:00 as along with 1 person anna_yershova
	Generation, Comparison, and Merging of Pathways between Protein Conformations: Gating in K-Channels☆ [My Copy] Biophysical Journal, Vol. 95, No. 8. (15 October 2008), pp. 3850-3860. by A. Enosh, B. Raveh, O. Furmanschueler, D. Halperin, N. Bental posted to folding motion planning protein by apaydin on 2009-03-05 19:00:08 as
	CPSP-web-tools: a server for 3D lattice protein studies [My Copy] Bioinformatics, Vol. 25, No. 5. (1 March 2009), pp. 676-677. by Martin Mann, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, Rolf Backofen posted to folding lattice model protein by apaydin on 2009-02-25 19:35:46 as along with 2 people yshmte carlosjavierna
	An Improved Ant Colony Optimisation Algorithm for the 2D HP Protein Folding Problem [My Copy] Advances in Artificial Intelligence (2003), pp. 993-993. by Alena Shmygelska, Holger Hoos posted to ant colony folding hp model optimization protein by apaydin on 2009-01-21 09:52:15 as
	A new algorithm for protein folding in the HP model [My Copy] In SODA '02: Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms (2002), pp. 876-884. by Alantha Newman posted to folding hp model protein by apaydin on 2009-01-21 09:43:01 as
	Predicting Protein Folding Kinetics Via Temporal Logic Model Checking [My Copy] Algorithms in Bioinformatics (2007), pp. 252-264. by Christopher Langmead, Sumit Jha posted to folding kinetics prediction protein rate by apaydin on 2009-01-07 14:36:23 as
	Understanding the Folding Rates and Folding Nuclei of Globular Proteins [My Copy] Current Protein and Peptide Science, Vol. 8, No. 6. (December 2007), pp. 521-536. by Finkelstein, V. Alexei, Ivankov, et al.N. Dmitry, Garbuzynskiy, O. Sergiy, Galzitskaya, V. Oxana posted to folding protein rate by apaydin on 2009-01-07 09:27:50 as
	Protein Structure and Its Folding Rate [My Copy] Mathematical Modelling of Biosystems (2008), pp. 273-301. by Alexei V. Finkelstein, Dmitry N. Ivankov, Sergiy O. Garbuzynskiy, Oxana V. Galzitskaya posted to folding protein rate by apaydin on 2009-01-07 09:27:32 as
	KineticDB: a database of protein folding kinetics [My Copy] Nucl. Acids Res. (8 October 2008), gkn696. by Natalya S. Bogatyreva, Alexander A. Osypov, Dmitry N. Ivankov posted to database folding kinetics protein rate by apaydin on 2009-01-07 09:25:05 as
	Direct molecular dynamics observation of protein folding transition state ensemble. [My Copy] Biophys J, Vol. 83, No. 6. (December 2002), pp. 3525-3532. by F. Ding, N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, E. I. Shakhnovich posted to folding pfold protein transition_state_ensemble by apaydin on 2009-01-05 10:19:50 as along with 1 person choonpeng
	Protein folding: Independent unrelated pathways or predetermined pathway with optional errors [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 20. (20 May 2008), pp. 7182-7187. by Sabrina Bedard, Mallela M. Krishna, Leland Mayne, Walter S. Englander posted to folding pathways protein by apaydin on 2008-05-21 21:49:48 as along with 1 person cactus
	Protein conformational transitions explored by mixed elastic network models. [My Copy] Proteins (27 June 2007) by Wenjun Zheng, Bernard R R. Brooks, Gerhard Hummer posted to conformational elastic folding model network protein transition by apaydin on 2008-04-17 13:45:43 as along with 2 people aqeel choonpeng
	Coarse Master Equations for Peptide Folding Dynamics [My Copy] J. Phys. Chem. B (31 January 2008) by N. V. Buchete, G. Hummer posted to dynamics equation folding master molecular protein by apaydin on 2008-04-17 13:16:30 as along with 3 people and 1 group Diego_Prada ruvido sobolevnrm baker-group
	Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule. [My Copy] J Mol Biol, Vol. 358, No. 4. (12 May 2006), pp. 1179-1190. by A. Laederach, I. Shcherbakova, M. P. Liang, M. Brenowitz, R. B. Altman posted to folding rna srs by apaydin on 2007-06-06 00:59:30 as
	Comparing atomistic simulation data with the NMR experiment: How much can NOEs actually tell us? [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 63, No. 1. (2006), pp. 210-218. by Bojan Zagrovic, Wilfred F. van Gunsteren posted to folding nmr noe protein unfolded by apaydin on 2007-06-04 18:50:33 as along with 1 person allmensch
	Chemical Theory and Computation Special Feature: Protein folding pathways from replica exchange simulations and a kinetic network model [My Copy] PNAS, Vol. 102, No. 19. (10 May 2005), pp. 6801-6806. by Michael Andrec, Anthony K. Felts, Emilio Gallicchio, Ronald M. Levy posted to exchange folding kinetic model network protein replica simulations by apaydin on 2007-03-09 22:58:30 as along with 2 people rainse allmensch
	mastereqn-alanine-long-times.pdf (application/pdf Object) [My Copy] by Chodera, Dill posted to dynamics folding molecular protein srs by apaydin on 2007-03-08 19:01:57 as
	Folding rates and low-entropy-loss routes of two-state proteins. [My Copy] J Mol Biol, Vol. 329, No. 3. (6 June 2003), pp. 585-598. by T. R. Weikl, K. A. Dill posted to srs rate protein prediction folding entropy by apaydin on 2007-01-19 21:39:58 as
	Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation [My Copy] Proteins: Structure, Function, and Genetics, Vol. 20, No. 1. (1994), pp. 68-84. by Kon H. Lee, Dong Xie, Ernesto Freire, Mario L. Amzel posted to study sidechain folding entropy empirical configurational binding by apaydin on 2007-01-17 22:31:42 as along with 1 person gisle
	The magnitude of the backbone conformational entropy change in protein folding. [My Copy] Proteins, Vol. 25, No. 2. (June 1996), pp. 143-156. by J. A. D'Aquino, J. Gómez, V. J. Hilser, K. H. Lee, L. M. Amzel, E. Freire posted to protein folding entropy conformational backbone by apaydin on 2007-01-17 22:29:56 as along with 1 person rsantana
	Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 12. (22 March 2005), pp. 4282-4287. by S. T. Whitten, B. García-Moreno E, V. J. Hilser posted to srs protein folding corex by apaydin on 2007-01-12 23:00:30 as along with 1 person lna
	A statistical thermodynamic model of the protein ensemble. [My Copy] Chem Rev, Vol. 106, No. 5. (May 2006), pp. 1545-1558. by V. J. Hilser, B. García-Moreno E, T. G. Oas, G. Kapp, S. T. Whitten posted to simplified protein model go folding finkelstein ensemble denatured by apaydin on 2007-01-10 21:10:38 as
	Funnel sculpting for in silico assembly of secondary structure elements of proteins [My Copy] PNAS (2003) by Boris Fain, Michael Levitt posted to folding funnel protein by apaydin on 2006-11-13 13:56:49 as
	folding rate prediction [My Copy] by Finkelstein posted to analysis finkelstein folding phi prediction rate value by apaydin on 2006-10-30 21:30:31 as
	Small Proteins Fold Through Transition States With Native-like Topologies [My Copy] Journal of Molecular Biology, Vol. 361, No. 4. (25 August 2006), pp. 755-770. by Adarsh D. Pandit, Abhishek Jha, Karl F. Freed, Tobin R. Sosnick posted to folding protein protein_folding psi-value-analysis by apaydin on 2006-08-11 16:33:35 as
	Common Motifs and Topological Effects in the Protein Folding Transition State [My Copy] Journal of Molecular Biology, Vol. 359, No. 4. (16 June 2006), pp. 1075-1085. by Isaac A. Hubner, Magnus Lindberg, Ellinor Haglund, Mikael Oliveberg, Eugene I. Shakhnovich posted to folding molecular_dynamics pfold phi_value_analysis protein_dynamics protein_folding rate_determination rate_prediction transition_state_ensemble by apaydin on 2006-06-11 16:28:27 as
	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 aggregation folding markov_chains pfold prm probabilistic_roadmaps protein_folding by apaydin on 2006-05-21 19:59:06 as along with 2 people Diego_Prada mtw
	A peptide model of a protein folding intermediate. [My Copy] Nature, Vol. 336, No. 6194. (3 November 1988), pp. 42-48. by T. G. Oas, P. S. Kim posted to bpti folding intermediate protein by apaydin on 2006-05-09 22:30:10 as
	Structure and stability of monomeric lambda repressor: NMR evidence for two-state folding. [My Copy] Biochemistry, Vol. 34, No. 12. (28 March 1995), pp. 3884-3892. by G. S. Huang, T. G. Oas posted to folding protein by apaydin on 2006-05-09 22:29:55 as
	Submillisecond folding of monomeric lambda repressor. [My Copy] Proc Natl Acad Sci U S A, Vol. 92, No. 15. (18 July 1995), pp. 6878-6882. by G. S. Huang, T. G. Oas posted to folding protein by apaydin on 2006-05-09 22:29:41 as along with 1 person dsmueller
	Microsecond protein folding through a compact transition state. [My Copy] J Mol Biol, Vol. 263, No. 2. (25 October 1996), pp. 311-322. by R. E. Burton, G. S. Huang, M. A. Daugherty, P. W. Fullbright, T. G. Oas posted to folding protein by apaydin on 2006-05-09 22:29:27 as
	The energy landscape of a fast-folding protein mapped by Ala-->Gly substitutions. [My Copy] Nat Struct Biol, Vol. 4, No. 4. (April 1997), pp. 305-310. by R. E. Burton, G. S. Huang, M. A. Daugherty, T. L. Calderone, T. G. Oas posted to folding protein by apaydin on 2006-05-09 22:29:14 as
	The structural distribution of cooperative interactions in proteins: analysis of the native state ensemble. [My Copy] Proc Natl Acad Sci U S A, Vol. 95, No. 17. (18 August 1998), pp. 9903-9908. by V. J. Hilser, D. Dowdy, T. G. Oas, E. Freire posted to allostery folding protein by apaydin on 2006-05-09 22:27:03 as along with 4 people lna aqeel shuns choonpeng
	A quantitative, high-throughput screen for protein stability. [My Copy] Proc Natl Acad Sci U S A, Vol. 97, No. 15. (18 July 2000), pp. 8296-8301. by S. Ghaemmaghami, M. C. Fitzgerald, T. G. Oas posted to folding protein by apaydin on 2006-05-09 22:26:49 as
	Mechanism of fast protein folding. [My Copy] Annu Rev Biochem, Vol. 71 (2002), pp. 783-815. by J. K. Myers, T. G. Oas posted to collision diffusion experiments folding model protein rate review by apaydin on 2006-05-09 22:26:15 as
	Microsecond folding dynamics of the F13W G29A mutant of the B domain of staphylococcal protein A by laser-induced temperature jump. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 11. (16 March 2004), pp. 3809-3814. by G. Dimitriadis, A. Drysdale, J. K. Myers, et al.P. Arora, S. E. Radford, T. G. Oas, D. A. Smith posted to folding protein by apaydin on 2006-05-09 22:26:00 as
	Probing the folding and unfolding dynamics of secondary and tertiary structures in a three-helix bundle protein. [My Copy] Biochemistry, Vol. 43, No. 12. (30 March 2004), pp. 3582-3589. by D. M. Vu, J. K. Myers, T. G. Oas, R. B. Dyer posted to folding protein by apaydin on 2006-05-09 22:25:45 as
	Fast and faster: A designed variant of the B-domain of protein A folds in 3 musec [My Copy] Protein Science, Vol. 13, No. 4. (April 2004), pp. 847-853. by Pooja Arora, Terrence G. Oas, Jeffrey K. Myers posted to folding protein by apaydin on 2006-05-09 22:25:32 as along with 1 person RamuAnandakrishnan
	Methionine oxidation of monomeric lambda repressor: the denatured state ensemble under nondenaturing conditions. [My Copy] Protein Sci, Vol. 15, No. 3. (March 2006), pp. 533-542. by P. Chugha, H. J. Sage, T. G. Oas posted to folding protein by apaydin on 2006-05-09 22:25:16 as

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nmr	188
protein	108
protein_dynamics	106
protein_folding	66
review	52
folding	51
protein_structure_determination	43
assignments	39
structure	39
protein_ligand_binding	34
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rdc	26
prediction	19
protein_protein_binding	18
resonance_assignment	18
tutorial	18
dynamics	16
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allostery	14
chemical	14
rate_determination	14
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backbone	13
determination	13
phi_value_analysis	13
prm	13
model	12
pfold	12
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noe	11
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rate	10
shift	10
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design	8
docking	8
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function	7
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rotamer	6
srs	6
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based	5
binding	5
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enm	5
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apaydin's folding [51 articles] Export

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