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cactus's library [311 articles]

Recent papers added to cactus's library ordered by importance.
  • Minimalist Protein Model as a Diagnostic Tool for Misfolding and Aggregation
    Journal of Molecular Biology, Vol. 363, No. 1. (13 October 2006), pp. 297-308.
    by Silvina Matysiak, Cecilia Clementi
    posted to folding md model protein by cactus on 2008-04-18 12:26:33 as ****
  • Nucleation of an Allosteric Response via Ligand-induced Loop Folding
    Journal of Molecular Biology, Vol. 373, No. 1. (12 October 2007), pp. 96-111.
    by Saranga Naganathan, Dorothy Beckett
    posted to allostery dimerization experiment folding by cactus on 2008-04-18 10:06:03 as ****
  • Protein folding under confinement: A role for solvent
    PNAS (11 June 2007), 0608256104.
    by Del Lucent, V Vishal, Vijay S Pande
    posted to simulation md fullatom for_ref confinement by cactus on 2008-09-29 11:12:32 as *** along with 4 people melting choonpeng cjeans rph
  • Protein folding in confined and crowded environments
    Archives of Biochemistry and Biophysics, Vol. 469, No. 1. (1 January 2008), pp. 76-82.
    by Huan-Xiang Zhou
    posted to review crowding confinement by cactus on 2008-10-07 10:22:35 as ** along with 1 person Jporci
  • Properties of contact matrices induced by pairwise interactions in proteins
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 77, No. 5. (2008)
    by Sanzo Miyazawa, Akira R Kinjo
    posted to statistical protein potential interaction by cactus on 2008-10-07 09:08:44 as **
  • Nanopore–Protein Interactions Dramatically Alter Stability and Yield of the Native State in Restricted Spaces
    Journal of Molecular Biology, Vol. 357, No. 2. (24 March 2006), pp. 632-643.
    by M Cheung, D Thirumalai
    posted to simulation md confinement coarse-grained chaperonin by cactus on 2008-10-07 08:39:21 as **
  • Assembly and Kinetic Folding Pathways of a Tetrameric beta-Sheet Complex: Molecular Dynamics Simulations on Simplified Off-Lattice Protein Models
    Biophys. J., Vol. 86, No. 1. (1 January 2004), pp. 31-49.
    by Hyunbum Jang, Carol K Hall, Yaoqi Zhou
    posted to simulation oligomer md for_ref coarse-grained amyloid by cactus on 2008-10-07 07:28:49 as **
  • Substrate concentration dependence of the diffusion-controlled steady-state rate constant
    The Journal of Chemical Physics, Vol. 122, No. 18. (2005)
    by J Dzubiella, JA Mccammon
    posted to theory stochastic_process diffusion crowding by cactus on 2008-10-06 04:52:49 as **
  • Effect of Crowding on Protein–Protein Association Rates: Fundamental Differences between Low and High Mass Crowding Agents
    Journal of Molecular Biology, Vol. 336, No. 3. (20 February 2004), pp. 763-774.
    by N Kozer
    posted to protein-protein_interaction experiment crowding by cactus on 2008-10-03 10:38:45 as **
  • Toward realistic modeling of dynamic processes in cell signaling: Quantification of macromolecular crowding effects
    The Journal of Chemical Physics, Vol. 127, No. 15. (2007)
    by Jian Sun, Harel Weinstein
    posted to simulation reaction for_ref diffusion crowding by cactus on 2008-10-03 10:08:37 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Models for Excluded Volume Interaction between an Unfolded Protein and Rigid Macromolecular Cosolutes: Macromolecular Crowding and Protein Stability Revisited
    Biophys. J., Vol. 88, No. 2. (1 February 2005), pp. 971-985.
    by Allen P Minton
    posted to theory for_ref crowding by cactus on 2008-10-02 10:19:42 as **
  • Confinement Effects on the Thermodynamics of Protein Folding: Monte Carlo Simulations
    Biophys. J., Vol. 90, No. 5. (1 March 2006), pp. 1767-1773.
    by Nitin Rathore, Thomas A Knotts, Juan J de Pablo
    posted to simulation mc confinement by cactus on 2008-10-02 10:13:45 as ** along with 2 people choonpeng ARobson
  • Stabilization of Proteins in Confined Spaces
    Biochemistry, Vol. 40, No. 38. (25 September 2001), pp. 11289-11293.
    by HX Zhou, KA Dill
    posted to theory stability for_ref confinement by cactus on 2008-10-02 09:11:30 as ** along with 1 person softsimu
  • Molecular crowding enhances native state stability and refolding rates of globular proteins
    PNAS, Vol. 102, No. 13. (29 March 2005), pp. 4753-4758.
    by Margaret S Cheung, Dmitri Klimov, D Thirumalai
    posted to simulation md for_ref crowding coarse-grained by cactus on 2008-10-02 07:00:45 as ** along with 1 person sikorski
  • notes 15N NMR Spin Relaxation Dispersion Study of the Molecular Crowding Effects on Protein Folding under Native Conditions
    J. Am. Chem. Soc., Vol. 128, No. 12. (29 March 2006), pp. 3916-3917.
    by X Ai, Z Zhou, Y Bai, WY Choy
    posted to nmr experiment crowding by cactus on 2008-10-01 09:15:21 as **
  • Fast Local Backbone Dynamics of Encapsulated Ubiquitin
    J. Am. Chem. Soc., Vol. 128, No. 30. (2 August 2006), pp. 9580-9581.
    by AK Simorellis, PF Flynn
    posted to nmr experiment crowding by cactus on 2008-10-01 08:07:38 as **
  • The influence of macromolecular crowding on HIV-1 protease internal dynamics.
    Journal of the American Chemical Society, Vol. 128, No. 18. (10 May 2006), pp. 6006-6007.
    by DD Minh, CE Chang, J Trylska, V Tozzini, JA McCammon
    posted to simulation md for_ref crowding coarse-grained by cactus on 2008-10-01 07:56:42 as **
  • Structural transitions of confined model proteins: molecular dynamics simulation and experimental validation.
    Biophys J, Vol. 90, No. 9. (1 May 2006), pp. 3224-3238.
    by D Lu, Z Liu, J Wu
    posted to simulation md experiment confinement coarse-grained by cactus on 2008-09-29 09:07:42 as ** along with 2 people allmensch choonpeng
  • Optimal Finite-Time Processes In Stochastic Thermodynamics
    Physical Review Letters, Vol. 98, No. 10. (2007)
    by Tim Schmiedl, Udo Seifert
    posted to thermodynamics stochastic physics for_rev by cactus on 2008-09-25 04:06:16 as ** along with 1 person softsimu
  • Protein topology determines binding mechanism.
    Proc Natl Acad Sci U S A, Vol. 101, No. 2. (13 January 2004), pp. 511-516.
    by Y Levy, PG Wolynes, JN Onuchic
    posted to binding folding protein ref-pc simulation theory by cactus on 2008-08-05 05:20:13 as ** along with 1 person and 1 group pdelosri EPFL_SB_ITP_LBS
  • Energetics of a Forced Thermal Ratchet
    Physical Review Letters, Vol. 80, No. 24. (15 June 1998), 5251.
    by Hideki Kamegawa, Tsuyoshi Hondou, Fumiko Takagi
    posted to mine by cactus on 2008-07-29 08:55:27 as ** along with 1 person melting
  • Amino acid runs in eukaryotic proteomes and disease associations.
    Proc Natl Acad Sci U S A, Vol. 99, No. 1. (8 January 2002), pp. 333-338.
    by S Karlin, L Brocchieri, A Bergman, J Mrazek, AJ Gentles
    posted to analysis folding intrinsic_disorder protein proteome by cactus on 2008-07-27 09:37:08 as ** along with 2 people and 1 group tharris chrn C. elegans / WormBase
  • Coupling of folding and binding for unstructured proteins.
    Curr Opin Struct Biol, Vol. 12, No. 1. (February 2002), pp. 54-60.
    by HJ Dyson, PE Wright
    posted to intrinsic_disorder protein ref-pc review by cactus on 2008-07-27 09:26:08 as ** along with 2 people chad_davis allmensch
  • Natively unfolded proteins: A point where biology waits for physics
    Protein Sci, Vol. 11, No. 4. (1 April 2002), pp. 739-756.
    by Vladimir N Uversky
    posted to intrinsic_disorder protein ref-pc review by cactus on 2008-07-27 09:24:06 as ** along with 4 people allmensch ruvido Evangelia ARobson
  • Mechanism of coupled folding and binding of an intrinsically disordered protein
    Nature (23 May 2007)
    by Kenji Sugase, Jane H Dyson, Peter E Wright
    posted to experiment intrinsic_disorder nmr protein by cactus on 2008-07-27 09:20:16 as ** along with 4 people cjeans allmensch amwands hsekiguc
  • Speeding molecular recognition by using the folding funnel: the fly-casting mechanism.
    Proc Natl Acad Sci U S A, Vol. 97, No. 16. (1 August 2000), pp. 8868-8873.
    by BA Shoemaker, JJ Portman, PG Wolynes
    posted to binding fly-casting folding protein ref-pc theory by cactus on 2008-07-27 09:14:12 as ** along with 2 people and 1 group pdelosri allmensch EPFL_SB_ITP_LBS
  • Unified perspective on proteins: A physics approach
    Physical Review E, Vol. 70, No. 4. (27 October 2004), 041905.
    by Jayanth R Banavar, Trinh X Hoang, Amos Maritan, Flavio Seno, Antonio Trovato
    posted to model protein by cactus on 2008-07-22 10:49:47 as **
  • Protein Folding and Disease: a view from the first Horizon Symposium
    Nat Rev Drug Discov, Vol. 2, No. 2. (February 2003), pp. 154-160.
    by Christopher M Dobson
    posted to amyloid folding protein review by cactus on 2008-07-22 10:40:56 as **
  • Influence of excluded volume upon macromolecular structure and associations in [`]crowded" media
    Current Opinion in Biotechnology, Vol. 8, No. 1. (February 1997), pp. 65-69.
    by Allen P Minton
    posted to crowding theory by cactus on 2008-07-18 11:51:25 as **
  • Structural stability of amyloid fibrils of [beta]2-microglobulin in comparison with its native fold
    Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, Vol. 1753, No. 1. (10 November 2005), pp. 64-75.
    by Eri Chatani, Yuji Goto
    posted to amyloid experiment microglobulin stability by cactus on 2008-07-18 11:43:15 as **
  • Progress towards a molecular-level structural understanding of amyloid fibrils
    Current Opinion in Structural Biology, Vol. 14, No. 1. (February 2004), pp. 96-103.
    by Robert Tycko
    posted to amyloid review structure by cactus on 2008-07-18 11:37:06 as **
  • Long single [alpha]-helical tail domains bridge the gap between structure and function of myosin VI
    Nat Struct Mol Biol, Vol. 15, No. 6. (June 2008), pp. 591-597.
    by Benjamin J Spink, Sivaraj Sivaramakrishnan, Jan Lipfert, Sebastian Doniach, James A Spudich
    posted to experiment motor mutation myosin by cactus on 2008-06-20 09:37:44 as ** along with 1 person and 1 group melting moernerlab
  • Protein disaggregation by the AAA+ chaperone ClpB involves partial threading of looped polypeptide segments
    Nat Struct Mol Biol, Vol. 15, No. 6. (June 2008), pp. 641-650.
    by Tobias Haslberger, Agnieszka Zdanowicz, Ingo Brand, Janine Kirstein, Kursad Turgay, Axel Mogk, Bernd Bukau
    posted to chaperone clpb dnak experiment by cactus on 2008-06-20 08:15:31 as **
  • Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association
    Proceedings of the National Academy of Sciences, Vol. 105, No. 21. (27 May 2008), pp. 7456-7461.
    by Chia-En A Chang, William A Mclaughlin, Riccardo Baron, Wei Wang, Andrew J Mccammon
    posted to binding fullatom protein simulation by cactus on 2008-06-19 09:10:36 as ** along with 1 person higueruelo
  • Paired beta-sheet structure of an Abeta(1-40) amyloid fibril revealed by electron microscopy
    Proceedings of the National Academy of Sciences, Vol. 105, No. 21. (27 May 2008), pp. 7462-7466.
    by Carsten Sachse, Marcus Fandrich, Nikolaus Grigorieff
    posted to amyloid em experiment structure by cactus on 2008-06-19 08:57:17 as **
  • Protein folding: Independent unrelated pathways or predetermined pathway with optional errors
    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 experiment folding pathway protein by cactus on 2008-06-19 06:51:57 as ** along with 1 person apaydin
  • Chaperone-dependent amyloid assembly protects cells from prion toxicity
    Proceedings of the National Academy of Sciences, Vol. 105, No. 20. (20 May 2008), pp. 7206-7211.
    by Peter M Douglas, Sebastian Treusch, Hong-Yu Ren, Randal Halfmann, Martin L Duennwald, Susan Lindquist, Douglas M Cyr
    posted to amyloid chaperone clip by cactus on 2008-06-19 06:38:58 as ** along with 1 person applebyb
  • A phase diagram for jammed matter
    Nature, Vol. 453, No. 7195., pp. 629-632.
    by Chaoming Song, Ping Wang, Hernán A Makse
    posted to clip2 granular-material packing physics by cactus on 2008-06-19 06:05:46 as ** along with 4 people soramame_0518 sen_cheng wmppaul jenda_z
  • Rattling the cage: computational models of chaperonin-mediated protein folding
    Current Opinion in Structural Biology, Vol. 18, No. 2. (April 2008), pp. 163-169.
    by Jeremy England, Del Lucent, Vijay Pande
    posted to chaperonin groel re review simulation by cactus on 2008-05-26 05:26:12 as **
  • notes Multiple Conformations of E. coli Hsp90 in Solution: Insights into the Conformational Dynamics of Hsp90
    Structure, Vol. 16, No. 5. (7 May 2008), pp. 755-765.
    by Kristin A Krukenberg, Friedrich Förster, Luke M Rice, Andrej Sali, David A Agard
    posted to chaperone structural_change structure xray-scattering by cactus on 2008-05-21 08:05:04 as ** along with 1 person TOchi
  • Improved Structures of Full-Length p97, an AAA ATPase: Implications for Mechanisms of Nucleotide-Dependent Conformational Change
    Structure, Vol. 16, No. 5. (7 May 2008), pp. 715-726.
    by Jason M Davies, Axel T Brunger, William I Weis
    posted to aaa protease xray-crystal-structure by cactus on 2008-05-21 07:50:58 as ** along with 1 person martainn
  • The Mechanics of Translocation: A Molecular "Spring-and-Ratchet" System
    Structure, Vol. 16, No. 5. (7 May 2008), pp. 664-672.
    by Stephen J Moran, Flanagan, Olivier Namy, David I Stuart, Ian Brierley, Robert J Gilbert
    posted to review ribosome translocation by cactus on 2008-05-21 07:34:52 as **
  • Monitoring Protein Conformation along the Pathway of Chaperonin-Assisted Folding
    Cell, Vol. 133, No. 1. (4 April 2008), pp. 142-153.
    by Shruti Sharma, Kausik Chakraborty, Barbara K Muller, Nagore Astola, Yun-Chi Tang, Don C Lamb, Manajit Hayer-Hartl, Ulrich F Hartl
    posted to experiment folding fret groel protein by cactus on 2008-05-14 07:28:04 as ** along with 1 person rph
  • Kemp elimination catalysts by computational enzyme design
    Nature (19 March 2008)
    by Daniela Röthlisberger, Olga Khersonsky, Andrew M Wollacott, 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 clip2 design enzyme protein by cactus on 2008-05-08 12:06:27 as ** along with 5 people and 1 group jwm msuarezdiez austin neils sobolevnrm baker-group
  • Dynamic binding orientations direct activity of HIV reverse transcriptase
    Nature, Vol. 453, No. 7192. (May 2008), pp. 184-189.
    by Elio A Abbondanzieri, Gregory Bokinsky, Jason W Rausch, Jennifer X Zhang, Stuart F Le Grice, Xiaowei Zhuang
    posted to clip2 function protein by cactus on 2008-05-08 12:05:28 as ** along with 2 people and 1 group wsjames kieran101 Oxford Virology
  • Modeling transient collapsed states of an unfolded protein to provide insights into early folding events
    Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6278-6283.
    by Daniel J Felitsky, Michael A Lietzow, Jane H Dyson, Peter E Wright
    posted to clip2 experiment folding nmr protein spin by cactus on 2008-05-07 08:23:51 as ** along with 1 person yxue
  • Intrinsic noise, dissipation cost, and robustness of cellular networks: The underlying energy landscape of MAPK signal transduction
    Proceedings of the National Academy of Sciences (17 April 2008), 0708708105.
    by Saul Lapidus, Bo Han, Jin Wang
    posted to cell network signal by cactus on 2008-05-07 08:01:43 as ** along with 4 people jjray biehl margaritis ddcttrl
  • Conservation of the regulated structure of folded myosin 2 in species separated by at least 600 million years of independent evolution
    Proceedings of the National Academy of Sciences, Vol. 105, No. 16. (22 April 2008), pp. 6022-6026.
    by Hyun S Jung, Stan A Burgess, Neil Billington, Melanie Colegrave, Hitesh Patel, Joseph M Chalovich, Peter D Chantler, Peter J Knight
    posted to clip em myosin structure by cactus on 2008-05-07 07:29:50 as **
  • The lattice as allosteric effector: Structural studies of alphabeta- and gamma-tubulin clarify the role of GTP in microtubule assembly
    Proceedings of the National Academy of Sciences, Vol. 105, No. 14. (8 April 2008), pp. 5378-5383.
    by Luke M Rice, Elizabeth A Montabana, David A Agard
    posted to allostery kinetics polymerization simulation structural_change xray-crystal-structure by cactus on 2008-05-02 11:25:14 as ** along with 1 person skv
  • The thermal impulse response of Escherichia coli
    Proceedings of the National Academy of Sciences, Vol. 105, No. 14. (8 April 2008), pp. 5373-5377.
    by Eli Paster, William S Ryu
    posted to adaptation cell clip2 ecoli temperature by cactus on 2008-05-02 11:20:31 as **
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