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Tag protein_folding [199 articles]

Recent papers classified by the tag protein_folding.
  • Watching proteins fold one molecule at a time.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 6. (18 March 2003), pp. 3197-3202.
    by E Rhoades, E Gussakovsky, G Haran
    posted to protein_folding single_molecule by yusdi on 2008-04-05 15:45:13 as ****
  • Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy
    Nature, Vol. 419, No. 6908. (17 October 2002), pp. 743-747.
    by Benjamin Schuler, Everett A Lipman, William A Eaton
    posted to protein_folding single_molecule by yusdi on 2008-04-05 15:46:01 as **** along with 1 person FBerkemeier
  • Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2
    PNAS, Vol. 97, No. 10. (9 May 2000), pp. 5179-5184.
    by Ashok A Deniz, Ted A Laurence, Gangamani S Beligere, Maxime Dahan, Andrew B Martin, Daniel S Chemla, Philip E Dawson, Peter G Schultz, Shimon Weiss
    posted to fret protein_folding single_molecule by yusdi on 2008-04-05 15:44:45 as **** along with 2 people FBerkemeier seamus1089
  • Stability and peptide binding affinity of an SH3 domain from the Caenorhabditis elegans signaling protein SEM-5.
    Protein Science, Vol. 3 (1994), pp. 1261-1266.
    by WA Lim, R Fox, FM Richards
    posted to wormbase thermodynamics signal_transduction sem-5 protein_folding protein_denaturation peptides_metabolism peptides_chemistry osmolar_concentration nematode molecular_sequence_data hydrogen_ion_concentration helminth_proteins_metabolism heat guanidines_pharmacology elegans electrochemistry drug_stability disulfides_metabolism celegans caenorhabditis_elegans_chemistry caenorhabditis_elegans c_elegans c14f55 binding_sites article amino_acid_sequence by tharris on 2008-09-16 23:43:00 as *** along with 1 group C. elegans / WormBase
  • Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins
    Nature (25 May 2008)
    by Nathan H Joh, Andrew Min, Salem Faham, Julian P Whitelegge, Duan Yang, Virgil L Woods, James U Bowie
    posted to protein_engineering protein_folding structure by sobolevnrm on 2008-07-24 12:12:57 as read along with 1 person and 1 group hc5428 baker-group
  • Role of Backbone−Solvent Interactions in Determining Conformational Equilibria of Intrinsically Disordered Proteins
    J. Am. Chem. Soc. (16 May 2008)
    by Hoang T Tran, Albert Mao, Rohit V Pappu
    posted to protein_folding solvation by sobolevnrm on 2008-07-09 11:35:18 as read along with 1 person and 1 group paulschlesinger baker-group
  • Dynamic personalities of proteins
    Nature, Vol. 450, No. 7172. (12 December 2007), pp. 964-972.
    by Katherine Henzler-Wildman, Dorothee Kern
    posted to allostery experimental_methodology molecular_dynamics protein_folding protein-ligand_interactions by sobolevnrm on 2008-01-22 12:33:20 as read along with 15 people and 1 group viktor21614 ruvido barry pavanghatty chad_davis allmensch choonpeng rsantana cjeans wilbur mijam kjell phoenixzxl higueruelo GeeSharpMinor baker-group
  • Linking folding with aggregation in Alzheimer's beta-amyloid peptides
    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 molecular_dynamics pka protein_folding by sobolevnrm on 2007-11-08 13:04:01 as read along with 2 people and 1 group Diego_Prada onufriev baker-group
  • Application of principal component analysis in protein unfolding: An all-atom molecular dynamics simulation study
    The Journal of Chemical Physics, Vol. 127, No. 16. (2007)
    by Atanu Das, Chaitali Mukhopadhyay
    posted to protein_folding quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-12-20 12:38:17 as read along with 2 people and 1 group choonpeng paulschlesinger baker-group
  • notes Coarse Master Equations for Peptide Folding Dynamics
    J. Phys. Chem. B (31 January 2008)
    by NV Buchete, G Hummer
    posted to kinetics multiscale protein_folding by sobolevnrm on 2008-02-29 12:18:27 as read along with 2 people and 1 group apaydin ruvido baker-group
  • A Water-Explicit Lattice Model of Heat-, Cold-, and Pressure-Induced Protein Unfolding.
    Biophys J (31 August 2007)
    by Bryan A A Patel, Pablo G G Debenedetti, Frank H H Stillinger, Peter J J Rossky
    posted to protein_folding solvation statistical_mechanics by sobolevnrm on 2007-12-27 12:19:28 as read along with 1 person and 1 group saunders baker-group
  • Vi -Value Analysis: A Pressure-Based Method for Mapping the Folding Transition State Ensemble of Proteins
    J. Am. Chem. Soc. (26 October 2007)
    by L Mitra, K Hata, R Kono, A Maeno, D Isom, JB Rouget, R Winter, K Akasaka, B Garcia-Moreno, CA Royer
    posted to protein_folding solvation by sobolevnrm on 2007-10-29 11:23:23 as read along with 1 group baker-group
  • Protein Sequence- and pH-Dependent Hydration Probed by Terahertz Spectroscopy
    J. Am. Chem. Soc., Vol. 130, No. 8. (27 February 2008), pp. 2374-2375.
    by S Ebbinghaus, SJ Kim, M Heyden, X Yu, M Gruebele, DM Leitner, M Havenith
    posted to kinetics protein_folding solvation by sobolevnrm on 2008-03-03 11:46:31 as read along with 1 group baker-group
  • A polymer physics perspective on driving forces and mechanisms for protein aggregation
    Archives of Biochemistry and Biophysics, Vol. 469, No. 1. (1 January 2008), pp. 132-141.
    by Rohit V Pappu, Xiaoling Wang, Andreas Vitalis, Scott L Crick
    posted to protein_folding by sobolevnrm on 2008-01-07 13:55:20 as read along with 1 group baker-group
  • Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations
    Protein Engineering, Design and Selection, Vol. 21, No. 6. (1 June 2008), pp. 353-368.
    by David A Beck, Amanda L Jonsson, Dustin R Schaeffer, Kathryn A Scott, Ryan Day, Rudesh D Toofanny, Darwin O Alonso, Valerie Daggett
    posted to bioinformatics database molecular_dynamics protein_folding by sobolevnrm on 2008-07-10 11:55:38 as read along with 1 group baker-group
  • Structural motifs of biomolecules
    Proceedings of the National Academy of Sciences, Vol. 104, No. 44. (30 October 2007), pp. 17283-17286.
    by Jayanth R Banavar, Trinh X Hoang, John H Maddocks, Amos Maritan, Chiara Poletto, Andrzej Stasiak, Antonio Trovato
    posted to misc protein_folding by sobolevnrm on 2007-10-31 16:36:38 as read along with 3 people and 1 group zwang afenley hpaces baker-group
  • Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation
    Proceedings of the National Academy of Sciences, Vol. 104, No. 44. (30 October 2007), pp. 17261-17265.
    by Lars Meinhold, Jeremy C Smith, Akio Kitao, Ahmed H Zewail
    posted to experimental_methodology molecular_dynamics protein_folding solvation by sobolevnrm on 2007-10-31 12:33:06 as read along with 1 group baker-group
  • Protein Stability Prediction: A Poisson-Boltzmann Approach
    J. Phys. Chem. B (23 January 2008)
    by YH Tan, R Luo
    posted to electrostatics protein_folding solvation by sobolevnrm on 2008-02-21 12:43:21 as read along with 1 person and 1 group mikaellund baker-group
  • Effects of long-range electrostatic forces on simulated protein folding kinetics
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA.
    by Alex Robertson, Edgar Luttmann, Vijay S Pande
    posted to electrostatics molecular_simulation protein_folding by sobolevnrm on 2007-09-14 12:41:24 as read along with 1 person and 1 group RamuAnandakrishnan baker-group
  • Metal-Coupled Folding of Cys2His2 Zinc-Finger
    J. Am. Chem. Soc., Vol. 130, No. 3. (23 January 2008), pp. 892-900.
    by W Li, J Zhang, J Wang, W Wang
    posted to metalloregulation molecular_simulation protein_folding by sobolevnrm on 2008-02-20 12:47:57 as read along with 1 group baker-group
  • Coarse-Grained Protein Model Coupled with a Coarse-Grained Water Model: Molecular Dynamics Study of Polyalanine-Based Peptides
    J. Chem. Theory Comput. (2 October 2007)
    by W Han, YD Wu
    posted to molecular_simulation multiscale protein_folding by sobolevnrm on 2007-10-08 12:22:48 as read along with 1 group baker-group
  • Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction
    PNAS, Vol. 103, No. 26. (27 June 2006), pp. 9885-9890.
    by Payel Das, Mark Moll, Hernan Stamati, Lydia E Kavraki, Cecilia Clementi
    posted to molecular_simulation protein_folding quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2008-01-30 12:47:02 as read along with 2 people and 2 groups samjlord hmk moernerlab baker-group
  • Solvent Viscosity Dependence of the Protein Folding Dynamics
    J. Phys. Chem. B (30 January 2008)
    by YM Rhee, VS Pande
    posted to kinetics molecular_simulation protein_folding solvation by sobolevnrm on 2008-02-27 12:33:44 as read along with 1 group baker-group
  • Electrostatic effects in unfolded staphylococcal nuclease
    Protein Sci, Vol. 17, No. 2. (1 February 2008), pp. 216-227.
    by Nicholas C Fitzkee, Garcia-Moreno
    posted to electrostatics pka protein_folding solvation by sobolevnrm on 2008-02-26 12:16:44 as read along with 1 group baker-group
  • High-resolution structure prediction and the crystallographic phase problem
    Nature (14 October 2007)
    by Bin Qian, Srivatsan Raman, Rhiju Das, Philip Bradley, Airlie J Mccoy, Randy J Read, David Baker
    posted to protein_folding structure_prediction by sobolevnrm on 2007-12-17 12:41:20 as read along with 14 people and 2 groups apaydin aheilbut jwm eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus boris_aguilar Ema chenway ardalby baker-group OPIG
  • Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin
    Nucl. Acids Res., Vol. 35, No. 20. (29 November 2007), pp. 6995-7002.
    by Zhuoyun Zhuang, Luc Jaeger, Joan-Emma Shea
    posted to molecular_simulation nucleic_acids protein_folding by sobolevnrm on 2008-01-02 12:32:22 as read along with 1 group baker-group
  • Supercharging Proteins Can Impart Unusual Resilience
    J. Am. Chem. Soc., Vol. 129, No. 33. (22 August 2007), pp. 10110-10112.
    by MS Lawrence, KJ Phillips, DR Liu
    posted to electrostatics protein_folding by sobolevnrm on 2007-10-11 12:23:00 as read along with 2 people and 3 groups barry samjlord structural_bioinformatics moernerlab baker-group
  • The Design and Evaluation of Heparin-Binding Foldamers
    Angewandte Chemie International Edition, Vol. 44, No. 41. (2005), pp. 6685-6689.
    by Sungwook Choi, Dylan J Clements, Vojislava Pophristic, Ivaylo Ivanov, Satyavani Vemparala, Joel S Bennett, Michael L Klein, Jeffrey D Winkler, William F Degrado
    posted to electrostatics protein_engineering protein_folding protein-ligand_interactions by sobolevnrm on 2008-04-16 21:11:55 as read along with 1 group baker-group
  • Protein aggregation processes: In search of the mechanism
    Protein Sci, Vol. 16, No. 11. (1 November 2007), pp. 2334-2344.
    by Carl Frieden
    posted to nmr protein_folding by sobolevnrm on 2007-11-09 12:14:13 as read along with 1 group baker-group
  • Mechanistic Elements of Protein Cold Denaturation
    J. Phys. Chem. B (9 January 2008)
    by CF Lopez, RK Darst, PJ Rossky
    posted to protein_folding solvation by sobolevnrm on 2008-02-15 12:32:44 as read along with 2 people and 1 group samjlord Cristiano baker-group
  • Exploring the folding funnel of a polypeptide chain by biophysical studies on protein fragments.
    J Mol Biol, Vol. 285, No. 3. (22 January 1999), pp. 1309-1333.
    by JL Neira, AR Fersht
    posted to protein_folding by simone on 2007-11-23 08:22:17 as **
  • Molecular chaperones in the cytosol: from nascent chain to folded protein.
    Science, Vol. 295, No. 5561. (8 March 2002), pp. 1852-1858.
    by FU Hartl, M Hayer-Hartl
    posted to protein_folding by simone on 2005-08-19 09:39:11 as read along with 1 person kieran101
  • notes iFold: a platform for interactive folding simulations of proteins.
    Bioinformatics, Vol. 22, No. 21. (1 November 2006), pp. 2693-2694.
    by S Sharma, F Ding, H Nie, D Watson, A Unnithan, J Lopp, D Pozefsky, NV Dokholyan
    posted to protein_folding publications simulation by shantanu on 2007-04-26 00:50:16 as ***** along with 1 person and 8 groups plofje structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology
  • notes Protein folding: Then and now.
    Arch Biochem Biophys (8 June 2007)
    by Yiwen Chen, Feng Ding, Huifen Nie, Adrian W W Serohijos, Shantanu Sharma, Kyle C C Wilcox, Shuangye Yin, Nikolay V V Dokholyan
    posted to protein_folding publications by shantanu on 2007-07-02 01:12:30 as ***** along with 1 person and 8 groups choonpeng structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology
  • Small-world view of the amino acids that play a key role in protein folding.
    Phys Rev E Stat Nonlin Soft Matter Phys, Vol. 65, No. 6 Pt 1. (June 2002)
    by M Vendruscolo, NV Dokholyan, E Paci, M Karplus
    posted to protein_folding by shantanu on 2006-01-25 05:03:12 as ** along with 3 people and 8 groups ana barry choonpeng structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology
  • Protein stability promotes evolvability
    PNAS, Vol. 103, No. 15. (11 April 2006), pp. 5869-5874.
    by Jesse D Bloom, Sy T Labthavikul, Christopher R Otey, Frances H Arnold
    posted to evolution protein_folding protein_structure by redelings on 2006-08-30 18:38:49 as ** along with 10 people and 2 groups rklancer Retchless lna Einat penka cmm BioNica Cristiano wilbur cdeane structural_bioinformatics FAB-lab
  • Hidden Markov models in computational biology. Applications to protein modeling
    Journal of Molecular Biology, Vol. 235, No. 5. (4 February 1994), pp. 1501-1531.
    by A Krogh, M Brown, IS Mian, K Sjölander, D Haussler
    posted to protein_folding multiple_sequence_alignment hmm by rabio on 2007-02-01 17:10:48 as ** along with 2 people cjeans wenhan
  • New Monte Carlo algorithms for protein folding
    Current Opinion in Structural Biology, Vol. 9, No. 2. (April 1999), pp. 177-183.
    by UH Hansmann, Y Okamoto
    posted to structure_prediction monte_carlo protein_folding review by rabio on 2006-12-11 14:32:21 as read along with 4 people dgront insectopalo iantunbridge nigham
  • Statistical thermodynamics of protein folding: Comparison of a mean-field theory with Monte Carlo simulations
    The Journal of Chemical Physics, Vol. 102, No. 3. (1995), pp. 1334-1348.
    by Ming H Hao, Harold A Scheraga
    posted to structure_prediction entropy_sampling force_field mean-field monte_carlo multicanonical_ensemble protein_folding protein_thermodynamics reduced_models review by rabio on 2006-12-11 14:36:54 as read
  • Colloquium: Geometrical approach to protein folding: a tube picture
    Reviews of Modern Physics, Vol. 75, No. 1. (6 January 2003), 23.
    by Jayanth R Banavar, Amos Maritan
    posted to protein_folding by rabio on 2007-07-28 14:39:12 as **
  • Five hierarchical levels of sequence-structure correlation in proteins.
    Applied Bioinformatics, Vol. 3, No. 2-3. (2004), pp. 97-104.
    by C Bystroff, Y Shao, X Yuan
    posted to sequence-structure_alignment protein_folding protein_assessment homology_modeling by rabio on 2007-01-30 16:46:56 as *** along with 2 people and 2 groups marcius eweaver BioinfoCIPF SGU-CIPF
  • Folding of the Villin Headpiece Subdomain from Random Structures. Analysis of the Charge Distribution as a Function of pH
    Journal of Molecular Biology, Vol. 339, No. 4. (June 2004), pp. 915-925.
    by D Ripoll
    posted to protein_folding ph implicit_solvation by onufriev on 2008-11-08 22:44:59 as **
  • Diffusional limits to the speed of protein folding: fact or friction?
    Journal of Physics: Condensed Matter, Vol. 17, No. 18. (2005), pp. S1503-S1514.
    by Stephen J Hagen, Linlin Qiu, Suzette A Pabit
    posted to protein_folding by onufriev on 2008-11-08 22:32:40 as **
  • Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins.
    Proc Natl Acad Sci U S A, Vol. 100, No. 13. (24 June 2003), pp. 7587-7592.
    by JW Pitera, W Swope
    posted to implicit_solvation protein_folding by onufriev on 2008-03-05 23:45:29 as **
  • Peptide folding simulations
    Current Opinion in Structural Biology, Vol. 13, No. 2. (April 2003), pp. 168-174.
    by S Gnanakaran, Hugh Nymeyer, John Portman, Kevin Y Sanbonmatsu, Angel E García
    posted to protein_folding by onufriev on 2008-11-08 22:30:09 as ** along with 1 person loison
  • Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field.
    J Am Chem Soc, Vol. 128, No. 11. (22 March 2006), pp. 3728-3736.
    by J Chen, W Im, CL Brooks
    posted to protein_folding gb by onufriev on 2008-09-12 00:11:56 as ** along with 1 person bilab
  • Free energy landscape of protein folding in water: Explicit vs. implicit solvent
    Proteins: Structure, Function, and Genetics, Vol. 53, No. 2. (2003), pp. 148-161.
    by Ruhong Zhou
    posted to gb implicit_solvation protein_folding by onufriev on 2008-03-06 01:49:56 as ** along with 3 people choonpeng RamuAnandakrishnan msuarezdiez
  • Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study
    Journal of Computational Chemistry, Vol. 24, No. 12. (2003), pp. 1432-1436.
    by Bojan Zagrovic, Vijay Pande
    posted to protein_folding implicit_solvation gb by onufriev on 2008-09-10 05:33:35 as **
  • A residue-pairwise generalized born scheme suitable for protein design calculations.
    The journal of physical chemistry. B, Vol. 109, No. 47. (1 December 2005), pp. 22667-22673.
    by G Archontis, T Simonson
    posted to protein_folding gb by onufriev on 2008-09-12 00:02:35 as **
  • Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: All-atom molecular dynamics in implicit solvent
    Journal of Computational Chemistry, Vol. 28, No. 6. (2007), pp. 1068-1082.
    by Anna Jagielska, Harold A Scheraga
    posted to protein_folding gb by onufriev on 2008-09-12 00:21:32 as ** along with 2 people choonpeng jwagoner
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