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Group: baker-group - with tag protein_folding [176 articles]

Недавние статьи, отправленные по почте членами baker-group группы with tag protein_folding
  • 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 to the group baker-group on 2008-07-24 12:12:58 as read
  • 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 to the group baker-group on 2008-07-10 11:55:39 as read
  • 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 to the group baker-group on 2008-07-09 11:35:18 as read along with 1 person paulschlesinger
  • 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 to the group baker-group on 2008-04-16 21:11:56 as read
  • 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 to the group baker-group on 2008-03-03 11:46:31 as read
  • 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 to the group baker-group on 2008-02-29 12:18:27 as read along with 2 people apaydin ruvido
  • 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 to the group baker-group on 2008-02-27 12:33:44 as read
  • 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 to the group baker-group on 2008-02-26 12:16:44 as read
  • 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 to the group baker-group on 2008-02-21 12:43:21 as read along with 1 person mikaellund
  • 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 to the group baker-group on 2008-02-20 12:47:57 as read
  • 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 to the group baker-group on 2008-02-15 12:32:44 as read along with 2 people samjlord Cristiano
  • 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 to the group baker-group on 2008-01-30 12:47:02 as read along with 2 people and 1 group samjlord hmk moernerlab
  • 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 to the group baker-group on 2008-01-22 12:33:20 as read along with 12 people pavanghatty chad_davis allmensch choonpeng rsantana cjeans wilbur mijam kjell phoenixzxl higueruelo GeeSharpMinor
  • 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 to the group baker-group on 2008-01-07 13:55:20 as read
  • 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 to the group baker-group on 2008-01-02 12:32:22 as read
  • 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 to the group baker-group on 2007-12-27 12:19:28 as read along with 1 person saunders
  • 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 to the group baker-group on 2007-12-20 12:38:17 as read along with 2 people choonpeng paulschlesinger
  • 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 to the group baker-group on 2007-12-17 12:41:21 as read along with 15 people and 1 group apaydin aheilbut jwm chad_davis eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus boris_aguilar Ema chenway ardalby OPIG
  • 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 to the group baker-group on 2007-11-09 12:14:14 as read
  • 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 to the group baker-group on 2007-11-08 13:04:01 as read
  • 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 to the group baker-group on 2007-10-31 16:36:38 as read along with 3 people zwang afenley hpaces
  • 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 to the group baker-group on 2007-10-31 12:33:06 as read
  • 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 to the group baker-group on 2007-10-29 11:23:23 as read
  • 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 to the group baker-group on 2007-10-11 12:23:01 as read along with 2 people and 2 groups barry samjlord structural_bioinformatics moernerlab
  • 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 to the group baker-group on 2007-10-08 12:22:49 as read
  • 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 protein_folding molecular_simulation electrostatics by sobolevnrm to the group baker-group on 2007-09-14 12:41:24 as read along with 1 person RamuAnandakrishnan
  • Physics of proteins
    Annual Review of Biophysics and Biomolecular Structure, Vol. 36 (2007), pp. 261-80.
    by JR Banavar, A Maritan
    posted to structure protein_folding by sobolevnrm to the group baker-group on 2007-08-06 14:33:02 as read
  • Observation of sequential steps in the folding of intestinal fatty acid binding protein using a slow folding mutant and 19F NMR
    Proceedings of the National Academy of Sciences of the United States of America (in press)
    by H Li, C Frieden
    posted to protein_folding nmr by sobolevnrm to the group baker-group on 2007-07-15 22:17:37 as read
  • Structural and functional behavior of biologically active monomeric melittin
    Journal of Molecular Graphics and Modelling, Vol. 25, No. 6. (2007), pp. 767-72.
    by RMS Terra, JA Guimarães, H Verli
    posted to protein_folding biomembranes by sobolevnrm to the group baker-group on 2007-06-20 12:33:33 as read
  • Protein folding under confinement: A role for solvent
    Proceedings of the National Academy of Sciences of the United States of America (in press)
    by D Lucent, V Vishal, VS Pande
    posted to solvation protein_folding by sobolevnrm to the group baker-group on 2007-06-18 13:08:48 as read
  • Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
    Journal of Chemical Physics, Vol. 126 (2007)
    by JD Chodera, N Singhal, VS Pande, KA Dill, WC Swope
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc protein_folding molecular_dynamics by sobolevnrm to the group baker-group on 2007-05-25 14:37:07 as read
  • Hydration of denatured and molten globule proteins
    Nature Structural Biology, Vol. 6, No. 3. (1999), pp. 253-60.
    by VP Denisov, BH Jonsson, B Halle
    posted to solvation protein_folding by sobolevnrm to the group baker-group on 2007-05-25 14:37:06 as read
  • An analysis of the molecular origin of osmolyte-dependent protein stability
    Protein Science, Vol. 16, No. 4. (2007), pp. 733-43.
    by J Rösgen, BM Pettitt, DW Bolen
    posted to solvation protein_folding by sobolevnrm to the group baker-group on 2007-05-25 14:36:49 as read
  • Establishing the entatic state in folding metallated Pseudomonas aeruginosa azurin
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 9. (2007), pp. 3159-64.
    by C Zong, CJ Wilson, T Shen, Wittung P Stafshede, SL Mayo, PG Wolynes
    posted to protein_folding protein_engineering metalloregulation allostery by sobolevnrm to the group baker-group on 2007-05-25 14:36:48 as read
  • Complex network analysis of free-energy landscapes
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 6. (2007), pp. 1817-22.
    by D Gfeller, De Los, A Caflisch, F Rao
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc protein_folding molecular_simulation by sobolevnrm to the group baker-group on 2007-05-25 14:36:28 as read
  • Anharmonicity and Self-Similarity of the Free Energy Landscape of Protein G
    Physical Review Letters, Vol. 98 (2007)
    by F Pontiggia, G Colombo, C Micheletti, H Orland
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc protein_folding by sobolevnrm to the group baker-group on 2007-05-25 14:36:05 as read
  • Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 3. (2007), pp. 733-8.
    by MV Athawale, G Goel, T Ghosh, TM Truskett, S Garde
    posted to solvation protein_folding by sobolevnrm to the group baker-group on 2007-05-25 14:36:05 as read
  • Influence of the Hofmeister Anions on Protein Stability As Studied by Thermal Denaturation and Chemical Shift Perturbation
    Biochemistry, Vol. 46, No. 3. (2007), pp. 917-23.
    by X Tadeo, M Pons, O Millet
    posted to solvation protein_folding by sobolevnrm to the group baker-group on 2007-05-25 14:36:05 as read
  • Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations
    Multiscale Modeling and Simulation, Vol. 5, No. 4. (2006), pp. 1214-26.
    by JD Chodera, WC Swope, JW Pitera, KA Dill
    posted to protein_folding kinetics by sobolevnrm to the group baker-group on 2007-05-25 14:36:04 as read
  • Solution structure of a small protein containing a fluorinated side chain in the core
    Protein Science, Vol. 16, No. 1. (2007), pp. 14-9.
    by G Cornilescu, EB Hadley, MG Woll, JL Markley, SH Gellman, C Cornilescu
    posted to protein_folding by sobolevnrm to the group baker-group on 2007-05-25 14:36:04 as read
  • Topographical complexity of multidimensional energy landscapes
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 49. (2006), pp. 18551-5.
    by GJ Rylance, RL Johnston, Y Matsunaga, CB Li, A Baba, T Komatsuzaki
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc protein_folding by sobolevnrm to the group baker-group on 2007-05-25 14:35:46 as read
  • Force field influences in beta-hairpin folding simulations
    Protein Science, Vol. 15, No. 11. (2006), pp. 2642-55.
    by TZ Lwin, R Luo
    posted to solvation protein_folding electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:24:57 as read
  • Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 45. (2006), pp. 16764-9.
    by SL Crick, M Jayraman, C Frieden, R Wetzel, RV Pappu
    posted to protein_folding by sobolevnrm to the group baker-group on 2007-05-25 14:24:57 as read
  • Tryptophan Solvent Exposure in Folded and Unfolded States of an SH3 Domain by 19F and 1H NMR
    Biochemistry, Vol. 45, No. 47. (2006), pp. 14120-8.
    by F Evanics, I Bezsonova, J Marsh, JL Kitevski, Forman JD Kay, RS Prosser
    posted to protein_folding nmr by sobolevnrm to the group baker-group on 2007-05-25 14:24:56 as read
  • Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity and trapping in the ribosome tunnel
    PLoS Computational Biology (in press)
    by A Elcock
    posted to ribosome protein_folding by sobolevnrm to the group baker-group on 2007-05-25 14:23:19 as read
  • Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study
    Journal of Computational Chemistry, Vol. 24, No. 12. (2003), pp. 1432-6.
    by B Zagrovic, V Pande
    posted to solvation protein_folding molecular_simulation diffusion by sobolevnrm to the group baker-group on 2007-05-25 14:23:18 as read
  • 19F NMR Studies of the Native and Denatured States of Green Fluorescent Protein
    Journal of the American Chemical Society, Vol. 128, No. 33. (2006), pp. 10729-37.
    by F Khan, I Kuprov, TD Craggs, PJ Hore, SE Jackson
    posted to protein_folding nmr by sobolevnrm to the group baker-group on 2007-05-25 14:23:18 as read
  • Toward an Accurate Theoretical Framework for Describing Ensembles for Proteins under Strongly Denaturing Conditions
    Biophysical Journal, Vol. 91, No. 5. (2006), pp. 1868-86.
    by HT Tran, RV Pappu
    posted to solvation protein_folding by sobolevnrm to the group baker-group on 2007-05-25 14:23:18 as read
  • Effective stochastic dynamics on a protein folding energy landscape
    Journal of Chemical Physics, Vol. 125 (2006)
    by S Yang, JN Onuchic, H Levine
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc protein_folding multiscale diffusion by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as read
  • Evaluation of intrinsic compressibility of proteins by molecular dynamics simulation
    Journal of Chemical Physics, Vol. 125 (2006)
    by K Mori, Y Seki, Y Yamada, H Matsumoto, K Soda
    posted to protein_folding molecular_dynamics by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as read
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