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aqeels library [313 articles]

Nye artikler sendt til aqeels bibliotek.
  • A Unification of the Elastic Network Model and the Gaussian Network Model for Optimal Description of Protein Conformational Motions and Fluctuations
    Biophys. J., Vol. 94, No. 10. (15 May 2008), pp. 3853-3857.
    by Wenjun Zheng
    posted to enm_improvements_combination by aqeel on 2008-06-22 14:49:36 as **
  • The Intrinsic Dynamics and Function of Nickel Binding Regulatory Protein: Insights from Elastic Network Analysis
    Biophys. J. (28 January 2008), biophysj.107.115576.
    by Guanglei Cui, Kenneth Merz
    posted to enm_studies_super-mole by aqeel on 2008-06-22 14:40:46 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Large scale motions in a biosensor protein glucose oxidase: A combined approach by QENS, normal mode analysis, and molecular dynamics studies
    Biopolymers, Vol. 89, No. 7. (2008), pp. 582-594.
    by Sujit S Tatke, Chun K Loong, Nicolas D'Souza, Richard T Schoephoerster, M Prabhakaran
    posted to enm_studies_specific by aqeel on 2008-06-22 14:38:05 as **
  • Evolutionary divergence of protein structure: The linearly forced elastic network model
    Chemical Physics Letters, Vol. 457, No. 4-6. (27 May 2008), pp. 413-416.
    by Julián Echave
    posted to enm_study_evolutionary-deformations by aqeel on 2008-06-22 14:22:15 as **
  • Collective motions of rigid fragments in protein structures from smoothed electron density distributions.
    Journal of computational chemistry, Vol. 29, No. 9. (15 July 2008), pp. 1472-1489.
    by L Leherte, DP Vercauteren
    posted to enm_application_d-enm by aqeel on 2008-06-22 14:10:44 as **
  • Proteins: coexistence of stability and flexibility.
    Physical review letters, Vol. 100, No. 20. (23 May 2008)
    by S Reuveni, R Granek, J Klafter
    posted to protein_flexibility_stability by aqeel on 2008-06-22 14:05:00 as **
  • MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape.
    Nucleic acids research, Vol. 35, No. Web Server issue. (July 2007)
    by J Franklin, P Koehl, S Doniach, M Delarue
    posted to enm_application_pathways by aqeel on 2008-06-06 12:01:53 as **
  • Normal mode partitioning of Langevin dynamics for biomolecules
    The Journal of Chemical Physics, Vol. 128, No. 14. (2008)
    by Christopher R Sweet, Paula Petrone, Vijay S Pande, Jesús A Izaguirre
    posted to enm_improvements_partition by aqeel on 2008-06-06 11:55:53 as ** along with 2 people and 1 group sobolevnrm paulschlesinger baker-group
  • The MARTINI Coarse-Grained Force Field: Extension to Proteins
    J. Chem. Theory Comput. (16 April 2008)
    by Luca Monticelli, Senthil K Kandasamy, Xavier Periole, Ronald G Larson, Peter D Tieleman, Siewert-Jan Marrink
    posted to md_coarse-grained by aqeel on 2008-06-06 09:59:41 as ** along with 5 people and 1 group softsimu Ema DanielParton sobolevnrm middledomain baker-group
  • Interaction of Anesthetics with Open and Closed Conformations of a Potassium Channel Studied via Molecular Dynamics and Normal Mode Analysis
    Biophys. J., Vol. 94, No. 11. (1 June 2008), pp. 4260-4269.
    by Satyavani Vemparala, Carmen Domene, Michael L Klein
    posted to enm_application_md by aqeel on 2008-06-06 09:56:41 as ** along with 1 person mengcite
  • Stereochemical Criteria for Polypeptide and Protein Chain Conformations: II. Allowed Conformations for a Pair of Peptide Units
    Biophys. J., Vol. 5, No. 6. (1 November 1965), pp. 909-933.
    by C Ramakrishnan, GN Ramachandran
    posted to ramachandran protein_structure_validation by aqeel on 2008-05-08 16:56:34 as **
  • Intrinsic [phi],[psi] propensities of amino acids, derived from the coil regions of known structures
    Nat Struct Mol Biol, Vol. 2, No. 7. (July 1995), pp. 596-603.
    by Mark B Swindells, Malcolm W Macarthur, Janet M Thornton
    posted to protein_structure_validation by aqeel on 2008-05-08 14:40:58 as **
  • An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins
    Proteins (in press)
    by S Kirillova, J Cortés, A Stefaniu, T Siméon
    posted to enm_application_pathways by aqeel on 2008-02-04 15:19:42 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
    Current Opinion in Structural Biology, Vol. 17, No. 6. (December 2007), pp. 633-640.
    by Ivet Bahar, Chakra Chennubhotla, Dror Tobi
    posted to review_allostery by aqeel on 2008-02-04 15:14:55 as ** along with 7 people and 3 groups higueruelo LamBras barry ruvido cactus sobolevnrm jennifermbui structural_bioinformatics Bioinformatics baker-group
  • Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian
    Biophys. J., Vol. 93, No. 10. (15 November 2007), pp. 3460-3469.
    by Kei Moritsugu, Jeremy C Smith
    posted to enm_improvements_hessian by aqeel on 2008-01-11 10:22:01 as ** along with 2 people and 1 group hmk sobolevnrm baker-group
  • Essential Dynamics of Helices Provide a Functional Classification of EF-Hand Proteins
    J. Proteome Res., Vol. 6, No. 11. (2 November 2007), pp. 4245-4255.
    by F Capozzi, C Luchinat, C Micheletti, F Pontiggia
    posted to nm_ed by aqeel on 2008-01-11 10:14:32 as **
  • Simulating Protein Motions with Rigidity Analysis
    Journal of Computational Biology, Vol. 14, No. 6. (2007), pp. 839-855.
    by Shawna Thomas, Xinyu Tang, Lydia Tapia, Nancy M Amato
    posted to dynamics_ensembles_robotic by aqeel on 2008-01-11 10:09:42 as **
  • Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility
    Proteins: Structure, Function, and Bioinformatics, Vol. 69, No. 4. (2007), pp. 774-780.
    by Andreas May, Martin Zacharias
    posted to enm_application_docking by aqeel on 2008-01-09 12:03:06 as **
  • High-throughput modeling and analysis of protein structural dynamics
    Brief Bioinform, Vol. 8, No. 6. (1 November 2007), pp. 432-445.
    by Xiong Liu, Hassan A Karimi
    posted to review_enm by aqeel on 2008-01-09 12:01:52 as ** along with 1 person hmk
  • Global Conformational Rearrangements in Integrin Extracellular Domains in Outside-In and Inside-Out Signaling
    Cell, Vol. 110, No. 5. (6 September 2002), pp. 599-611.
    by Junichi Takagi, Benjamin M Petre, Thomas Walz, Timothy A Springer
    posted to integrin by aqeel on 2007-11-20 12:48:56 as **
  • Integrin activation
    J Cell Sci, Vol. 117, No. 5. (15 February 2004), pp. 657-666.
    by David A Calderwood
    posted to integrin by aqeel on 2007-11-20 12:08:09 as **
  • Crystal Structure of the Extracellular Segment of Integrin alpha Vbeta 3
    Science, Vol. 294, No. 5541. (12 October 2001), pp. 339-345.
    by Jian-Ping Xiong, Thilo Stehle, Beate Diefenbach, Rongguang Zhang, Reinhardt Dunker, David L Scott, Andrzej Joachimiak, Simon L Goodman, Amin M Arnaout
    posted to integrin by aqeel on 2007-11-20 10:29:41 as **
  • Crystal structure of the extracellular segment of integrin alpha Vbeta3 in complex with an Arg-Gly-Asp ligand.
    Science, Vol. 296, No. 5565. (5 April 2002), pp. 151-155.
    by JP Xiong, T Stehle, R Zhang, A Joachimiak, M Frech, SL Goodman, MA Arnaout
    posted to integrin by aqeel on 2007-11-06 16:24:58 as **
  • Characterization of Protein Conformational States by Normal-Mode Frequencies
    J. Am. Chem. Soc. (23 August 2007)
    by BA Hall, SL Kaye, A Pang, R Perera, PC Biggin
    posted to gnm_application by aqeel on 2007-10-30 08:29:30 as ** along with 4 people and 3 groups LamBras barry choonpeng sobolevnrm structural_bioinformatics Bioinformatics baker-group
  • Protein conformational transitions explored by mixed elastic network models.
    Proteins (27 June 2007)
    by Wenjun Zheng, Bernard R R Brooks, Gerhard Hummer
    posted to enm_improvements_morphing by aqeel on 2007-10-02 10:59:45 as ** along with 2 people apaydin choonpeng
  • Dynamics of Firefly Luciferase Inhibition by General Anesthetics: Gaussian and Anisotropic Network Analyses
    Biophys. J., Vol. 93, No. 6. (15 September 2007), pp. 1895-1905.
    by Agnieszka Szarecka, Yan Xu, Pei Tang
    posted to enm_studies_specific by aqeel on 2007-10-02 10:14:51 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Phi/psi-chology: Ramachandran revisited.
    Structure, Vol. 4, No. 12. (15 December 1996), pp. 1395-1400.
    by GJ Kleywegt, TA Jones
    posted to protein_structure_validation by aqeel on 2007-10-01 17:14:14 as ** along with 1 person xiaobeizhao
  • Normal-Mode Analysis of the Glycine Alpha1 Receptor by Three Separate Methods
    J. Chem. Inf. Model., Vol. 47, No. 4. (23 July 2007), pp. 1572-1579.
    by EJ Bertaccini, JR Trudell, E Lindahl
    posted to enm_studies_specific by aqeel on 2007-10-01 12:14:33 as **
  • Protein folding by zipping and assembly.
    Proc Natl Acad Sci U S A, Vol. 104, No. 29. (17 July 2007), pp. 11987-11992.
    by SB Ozkan, GA Wu, JD Chodera, KA Dill
    posted to dynamics_folding by aqeel on 2007-10-01 11:18:27 as ** along with 2 people wouterboomsma cdeane
  • Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i175-184.
    by Eran Eyal, Chakra Chennubhotla, Lee-Wei Yang, Ivet Bahar
    posted to enm_application_struct-refine by aqeel on 2007-10-01 10:28:14 as ** along with 1 person jlh64
  • Structural and dynamical alignment of enzymes with partial structural similarity
    Journal of Physics: Condensed Matter, Vol. 19, No. 28. (2007), 285206.
    by Vincenzo Carnevale, Francesco Pontiggia, Cristian Micheletti
    posted to dynamics_homologous by aqeel on 2007-10-01 10:13:42 as **
  • Detecting similarities among distant homologous proteins by comparison of domain flexibilities
    Protein Engineering, Design and Selection (30 June 2007), gzm021.
    by Alessandro Pandini, Giancarlo Mauri, Annalisa Bordogna, Laura Bonati
    posted to dynamics_homologous by aqeel on 2007-10-01 10:09:08 as ** along with 2 people and 2 groups edvin barry structural_bioinformatics Bioinformatics
  • From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes
    Proteins: Structure, Function, and Bioinformatics, Vol. 68, No. 3. (2007), pp. 646-661.
    by Allison P Heath, Lydia E Kavraki, Cecilia Clementi
    posted to toread by aqeel on 2007-09-17 10:40:03 as ** along with 1 person mijam
  • How Well Can We Understand Large-Scale Protein Motions Using Normal Modes of Elastic Network Models?
    Biophys J (4 May 2007)
    by Lei Yang, Guang Song, Robert L L Jernigan
    posted to enm_studies_comparison by aqeel on 2007-09-13 10:17:31 as ** along with 3 people and 2 groups barry choonpeng willpitt structural_bioinformatics Bioinformatics
  • Integrin structures and conformational signaling.
    Curr Opin Cell Biol, Vol. 18, No. 5. (October 2006), pp. 579-586.
    by BH Luo, TA Springer
    posted to integrin by aqeel on 2007-09-07 11:11:37 as ** along with 1 person choonpeng
  • Integrin structure, allostery, and bidirectional signaling.
    Annu Rev Cell Dev Biol, Vol. 21 (2005), pp. 381-410.
    by MA Arnaout, B Mahalingam, JP Xiong
    posted to integrin by aqeel on 2007-09-07 11:09:56 as ** along with 2 people tsjipko Verena
  • New insights into the structural basis of integrin activation.
    Blood, Vol. 102, No. 4. (15 August 2003), pp. 1155-1159.
    by JP Xiong, T Stehle, SL Goodman, MA Arnaout
    posted to integrin by aqeel on 2007-09-07 10:53:52 as **
  • Structures of integrin domains and concerted conformational changes in the bidirectional signaling mechanism of alphaIIbbeta3.
    Exp Biol Med (Maywood), Vol. 229, No. 8. (September 2004), pp. 732-744.
    by JJ Calvete
    posted to integrin by aqeel on 2007-09-07 10:48:01 as **
  • Regulation of integrin function through conformational complexity: not simply a knee-jerk reaction?
    Curr Opin Cell Biol, Vol. 16, No. 5. (October 2004), pp. 544-551.
    by AP Mould, MJ Humphries
    posted to integrin by aqeel on 2007-09-07 10:43:28 as **
  • Coming to grips with integrin binding to ligands
    pp. 641-652.
    by MA Arnaout
    posted to integrin by aqeel on 2007-09-07 10:41:36 as **
  • Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model
    Proteins: Structure, Function, and Bioinformatics, Vol. 67, No. 4. (2007), pp. 886-896.
    by Wenjun Zheng, Jung-Chi Liao, Bernard R Brooks, Sebastian Doniach
    posted to enm_studies_specific by aqeel on 2007-07-23 09:31:56 as **
  • Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics
    Structure, Vol. 15, No. 5. (16 May 2007), pp. 565-575.
    by Manuel Rueda, Pablo Chacon, Modesto Orozco
    posted to nm_ed by aqeel on 2007-07-23 09:20:52 as ** along with 5 people edvin choonpeng ruvido cactus jlh64
  • Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution
    PNAS, Vol. 104, No. 19. (8 May 2007), pp. 7869-7874.
    by Billy K Poon, Xiaorui Chen, Mingyang Lu, Nand K Vyas, Florante A Quiocho, Qinghua Wang, Jianpeng Ma
    posted to enm_application_struct-refine by aqeel on 2007-07-17 09:17:49 as ** along with 1 person apaydin
  • Bridging from molecular simulation to biochemical networks.
    Curr Opin Struct Biol, Vol. 17, No. 2. (April 2007), pp. 166-172.
    by M Stein, RR Gabdoulline, RC Wade
    posted to review_coarse-grain by aqeel on 2007-07-17 08:10:34 as ** along with 5 people higueruelo Borelli cmmorel julius ras
  • Coarse-graining of protein structures for the normal mode studies
    Journal of Computational Chemistry, Vol. 28, No. 8. (2007), pp. 1400-1410.
    by Kilho Eom, Seung-Chul Baek, Jung-Hee Ahn, Sungsoo Na
    posted to enm_improvements_coarse-grain by aqeel on 2007-07-11 08:23:12 as ** along with 1 person choonpeng
  • Nonlinear relaxation dynamics in elastic networks and design principles of molecular machines
    PNAS, Vol. 104, No. 21. (22 May 2007), pp. 8697-8702.
    by Yuichi Togashi, Alexander S Mikhailov
    posted to enm_application_design by aqeel on 2007-05-30 08:56:09 as ** along with 2 people joseph_x_zhou cactus
  • Comment on elastic network models and proteins
    Phys. Biol., Vol. 4, No. 1. (March 2007), 60.
    by MF Thorpe
    posted to re review_enm by aqeel on 2007-05-21 09:02:57 as **
  • Reply to 'Comment on elastic network models and proteins'.
    Phys Biol, Vol. 4, No. 1. (March 2007), pp. 64-65.
    by I Bahar, C Chennubhotla, B Erman
    posted to review_enm by aqeel on 2007-05-21 09:01:29 as **
  • Protein structural variation in computational models and crystallographic data.
    Structure, Vol. 15, No. 2. (February 2007), pp. 169-177.
    by DA Kondrashov, AW Van Wynsberghe, RM Bannen, Q Cui, GN Phillips
    posted to enm_application_struct-refine by aqeel on 2007-04-30 08:48:43 as **
  • Molecular Dynamics Simulation of Protein Folding by Essential Dynamics Sampling: Folding Landscape of Horse Heart Cytochrome c
    Biophys. J., Vol. 85, No. 5. (1 November 2003), pp. 2865-2871.
    by Isabella Daidone, Andrea Amadei, Danilo Roccatano, Alfredo D Nola
    posted to nm_ed_proteinfolding by aqeel on 2007-04-27 09:53:16 as ** along with 2 people ttjoseph choonpeng
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