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aqeels library [339 articles]

Neue Artikel in aqeels Bibliothek.
  • Identification of Specific Interactions that Drive Ligand-induced Closure in Five Enzymes with Classic Domain Movements
    Journal of Molecular Biology, Vol. 339, No. 4. (June 2004), pp. 1001-1021.
    by S Hayward
    posted to protein_domain by aqeel on 2008-12-02 12:53:50 as **
  • A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography.
    Proceedings of the National Academy of Sciences of the United States of America (1 October 2008)
    by Mingyang Lu, Jianpeng Ma
    posted to enm_improvements by aqeel on 2008-11-25 18:04:52 as ** along with 5 people and 4 groups apaydin ruvido agrossfield skoddet barry Nielsen group structural_bioinformatics McCammon Bioinformatics
  • Recognition-induced Conformational Changes in Protein-Protein Docking
    Current Pharmaceutical Biotechnology, Vol. 9, No. 2. (April 2008), pp. 77-86.
    by Lensink, , Mendez,
    posted to review_docking by aqeel on 2008-10-10 19:28:18 as ** along with 1 person viktor21614
  • Relating sequence evolution of HIV1-protease to its underlying molecular mechanics
    Gene, Vol. 422, No. 1-2. (01 October 2008), pp. 30-36.
    by K Hamacher
    posted to hiv1 by aqeel on 2008-10-10 19:21:09 as **
  • Evolutionary conservation of protein vibrational dynamics.
    Gene, Vol. 422, No. 1-2. (1 October 2008), pp. 7-13.
    by S Maguid, S Fernandez-Alberti, J Echave
    posted to enm_study_evolutionary-deformations by aqeel on 2008-10-10 19:14:25 as ** along with 2 people edvin gisle
  • Coarse-grained dynamics of the receiver domain of NtrC: fluctuations, correlations and implications for allosteric cooperativity.
    Proteins, Vol. 73, No. 1. (October 2008), pp. 218-227.
    by MS Liu, BD Todd, S Yao, ZP Feng, RS Norton, RJ Sadus
    posted to enm_studies_specific by aqeel on 2008-10-10 19:07:21 as **
  • CONFORMATIONAL TRANSITION PATHWAYS EXPLORED BY MONTE CARLO SIMULATION INTEGRATED WITH COLLECTIVE MODES
    Biophys. J. (1 August 2008), biophysj.107.128447.
    by Nigar Kantarci-Carsibasi, Turkan Haliloglu, Pemra Doruker
    posted to kinase enm_application_pathways by aqeel on 2008-10-02 12:10:36 as ** along with 2 people viktor21614 sunhwan
  • Intrinsic motions along an enzymatic reaction trajectory
    Nature (18 November 2007)
    by Katherine A Henzler-Wildman, Vu Thai, Ming Lei, Maria Ott, Magnus Wolf-Watz, Tim Fenn, Ed Pozharski, Mark A Wilson, Gregory A Petsko, Martin Karplus, Christian G Hübner, Dorothee Kern
    posted to kinase dynamics_trajectories by aqeel on 2008-10-02 11:53:08 as ** along with 9 people and 1 group ubcg08l ruvido barry ebeutler cactus sobolevnrm paulschlesinger jlh64 yalexeev baker-group
  • Improved sampling methods for molecular simulation.
    Curr Opin Struct Biol, Vol. 17, No. 2. (April 2007), pp. 187-191.
    by H Lei, Y Duan
    posted to review_md by aqeel on 2008-09-30 16:42:57 as ** along with 3 people viktor21614 BragilMassoud allmensch
  • Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation
    Current Opinion in Structural Biology, Vol. 17, No. 2. (April 2007), pp. 181-186.
    by Hagai Meirovitch
    posted to review_free-energy by aqeel on 2008-09-30 16:40:46 as ** along with 3 people and 1 group sunhwan dmobley cchang group
  • Transition networks for modeling the kinetics of conformational change in macromolecules
    Current Opinion in Structural Biology, Vol. 18, No. 2. (April 2008), pp. 154-162.
    by Frank Noé, Stefan Fischer
    posted to review_transition by aqeel on 2008-09-30 16:35:55 as ** along with 4 people and 3 groups barry sobolevnrm paulschlesinger toerst structural_bioinformatics baker-group McCammon
  • Combining Efficient Conformational Sampling with a Deformable Elastic Network Model Facilitates Structure Refinement at Low Resolution
    Structure, Vol. 15, No. 12. (13 December 2007), pp. 1630-1641.
    by Gunnar F Schroder, Axel T Brunger, Michael Levitt
    posted to enm_application_struct-refine by aqeel on 2008-09-30 16:23:31 as ** along with 4 people and 1 group cjeans sobolevnrm jlh64 TOchi baker-group
  • Flexible ligand docking to multiple receptor conformations: a practical alternative.
    Current opinion in structural biology, Vol. 18, No. 2. (April 2008), pp. 178-184.
    by M Totrov, R Abagyan
    posted to review_docking by aqeel on 2008-09-30 16:17:36 as ** along with 2 people and 3 groups oteri barry structural_bioinformatics McCammon Bioinformatics
  • Computational techniques for efficient conformational sampling of proteins
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Adam Liwo, Cezary Czaplewski, Stanislaw Oldziej, Harold A Scheraga
    posted to review_structure by aqeel on 2008-09-30 16:01:36 as ** along with 2 people barry j3xucite
  • Topologically Based Multipolar Reconstruction of Electrostatic Interactions in Multiscale Simulations of Proteins
    J. Chem. Theory Comput., Vol. 4, No. 8. (12 August 2008), pp. 1378-1385.
    by Michele Cascella, Marilisa A Neri, Paolo Carloni, Matteo D Peraro
    posted to protein_modeling_electrostatic by aqeel on 2008-09-30 14:57:10 as **
  • Energy landscape along an enzymatic reaction trajectory: hinges or cracks?
    HFSP Journal, Vol. 2, No. 2. (2008), pp. 61-64.
    by Paul C Whitford, José N Onuchic, Peter G Wolynes
    posted to protein_cracking by aqeel on 2008-09-30 14:36:07 as ** along with 2 people barry sunhwan
  • Use of normal modes for structural modeling of proteins: the case study of rat heme oxygenase 1
    European Biophysics Journal, Vol. 37, No. 7. (2008), pp. 1157-1165.
    by Jean-Didier Marechal, David Perahia
    posted to protein_structure_modeling nma by aqeel on 2008-09-30 14:05:03 as **
  • Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection
    BMC Structural Biology, Vol. 8 (01 August 2008), 34.
    by Marc N Offman, Alex L Tournier, Paul A Bates
    posted to protein_structure_prediction by aqeel on 2008-09-30 13:50:01 as **
  • Key Interactions in Integrin Ectodomain Responsible for Global Conformational Change Detected by Elastic Network Normal-Mode Analysis
    Biophys. J., Vol. 95, No. 6. (15 September 2008), pp. 2895-2908.
    by Atsushi Matsumoto, Tetsuji Kamata, Junichi Takagi, Kenji Iwasaki, Kei Yura
    posted to integrin enm_studies_specific by aqeel on 2008-09-30 13:25:25 as ** along with 1 person choonpeng
  • Intercellular Adhesion Molecule-3 Binding of Integrin alphaLbeta2 Requires Both Extension and Opening of the Integrin Headpiece
    J Immunol, Vol. 180, No. 7. (1 April 2008), pp. 4793-4804.
    by Xiao-Yan Tang, Yan-Feng Li, Suet-Mien Tan
    posted to integrin by aqeel on 2008-08-17 17:57:15 as **
  • REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes
    Biophys. J. (9 May 2008), biophysj.108.131714.
    by Kei Moritsugu, Jeremy C Smith
    posted to md_coarse-grained by aqeel on 2008-08-17 17:51:15 as ** along with 5 people and 1 group A_Coletta_Thesis paulschlesinger choonpeng jmccammon rok McCammon
  • Transmembrane and cytoplasmic domains in integrin activation and protein-protein interactions (Review)
    Molecular Membrane Biology, Vol. 25, No. 5. (2008), pp. 376-387.
    by Kate L Wegener, Iain D Campbell
    posted to integrin by aqeel on 2008-08-17 17:39:39 as **
  • Functional and computational studies of the ligand-associated metal binding site of beta3 integrins.
    Proteins, Vol. 71, No. 4. (June 2008), pp. 1779-1791.
    by M Murcia, M Jirouskova, J Li, BS Coller, M Filizola
    posted to integrin by aqeel on 2008-07-30 10:15:47 as **
  • The Croonian lecture 2006. Structure of the living cell.
    Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Vol. 363, No. 1502. (27 July 2008), pp. 2379-2391.
    by ID Campbell
    posted to review_cellstructure by aqeel on 2008-07-25 09:41:41 as **
  • Recognition-induced conformational changes in protein-protein docking.
    Current pharmaceutical biotechnology, Vol. 9, No. 2. (April 2008), pp. 77-86.
    by MF Lensink, R Méndez
    posted to review_docking by aqeel on 2008-07-25 09:25:54 as **
  • Protein−Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking
    J. Med. Chem., Vol. 51, No. 12. (26 June 2008), pp. 3499-3506.
    by Andreas May, Martin Zacharias
    posted to enm_application_docking by aqeel on 2008-07-25 09:16:38 as ** along with 1 person higueruelo
  • 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 ** along with 1 person simone
  • 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 paulschlesinger sobolevnrm 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 6 people and 2 groups Marine middledomain sobolevnrm Ema DanielParton softsimu Molecular dynamics in MSU 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 protein_structure_validation ramachandran 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 8 people and 4 groups barry ruvido cactus sobolevnrm jennifermbui higueruelo LamBras jmccammon structural_bioinformatics Bioinformatics baker-group McCammon
  • 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 3 people and 1 group hmk sobolevnrm choonpeng 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 ** along with 1 person barry
  • 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 5 people and 3 groups ubcg08l barry choonpeng sobolevnrm LamBras structural_bioinformatics Bioinformatics baker-group
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