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Group: baker-group - with tag quasiharmonic-models_elastic-network_gnm_nma_pca_etc [259 articles]

Neue Artikel von Mitliedern der Gruppe baker-group Gruppe with tag quasiharmonic-models_elastic-network_gnm_nma_pca_etc
  • The signaling pathway of rhodopsin.
    Structure, Vol. 15, No. 5. (May 2007), pp. 611-623.
    by Y Kong, M Karplus
    posted to allostery quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-07-11 12:18:57 as read along with 2 people vahmurk dimka
  • Signaling pathways of PDZ2 domain: A molecular dynamics interaction correlation analysis
    Proteins, Vol. in press
    by Y Kong, M Karplus
    posted to allostery quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-07-11 12:00:09 as read
  • Analysis of correlated mutations in HIV-1 protease using spectral clustering
    Bioinformatics, Vol. 24, No. 10. (15 May 2008), pp. 1243-1250.
    by Ying Liu, Eran Eyal, Ivet Bahar
    posted to correlated_mutations quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-06-20 11:35:34 as read along with 2 people Ema bmaust
  • A Coupled Equilibrium Shift Mechanism in Calmodulin-Mediated Signal Transduction
    Structure, Vol. 16, No. 5. (7 May 2008), pp. 736-746.
    by Jörg Gsponer, John Christodoulou, Andrea Cavalli, Jennifer M Bui, Barbara Richter, Christopher M Dobson, Michele Vendruscolo
    posted to allostery quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-06-20 11:32:37 as read
  • Investigating protein dynamics in collective coordinate space.
    Curr Opin Struct Biol, Vol. 9, No. 2. (April 1999), pp. 164-169.
    by A Kitao, N Go
    posted to enhanced_sampling quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-06-06 11:37:30 as read along with 4 people ttjoseph ffranca barry choonpeng
  • HingeMaster: Normal mode hinge prediction approach and integration of complementary predictors
    Proteins (in press)
    by SC Flores, KS Keating, J Painter, F Morcos, K Nguyen, EA Merritt, LA Kuhn, MB Gerstein
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc software by sobolevnrm to the group baker-group on 2008-06-05 11:50:59 as read
  • Hessian-free low-mode conformational search for large-scale protein loop optimization: application to c-jun N-terminal kinase JNK3
    Journal of Computational Chemistry, Vol. 22, No. 1. (2000), pp. 21-30.
    by I Kolossváry, GM Keserü
    posted to enhanced_sampling quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-05-27 16:08:08 as read
  • Collective Langevin dynamics of conformational motions in proteins
    The Journal of Chemical Physics, Vol. 124, No. 21. (2006)
    by Oliver F Lange, Helmut Grubmuller
    posted to enhanced_sampling quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-05-27 16:06:12 as read along with 1 person choonpeng
  • Long time scale molecular dynamics subspace integration method applied to anharmonic crystals and glasses
    The Journal of Chemical Physics, Vol. 99, No. 11. (1993), pp. 9070-9079.
    by Brian Space, Herschel Rabitz, Attila Askar
    posted to enhanced_sampling quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-05-27 16:04:43 as read
  • Molecular dynamics simulations of peptides and proteins with amplified collective motions.
    Biophys J, Vol. 84, No. 6. (June 2003), pp. 3583-3593.
    by Z Zhang, Y Shi, H Liu
    posted to enhanced_sampling quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-05-27 16:03:07 as read along with 2 people baaden aqeel
  • Coarse-grained dynamics of the receiver domain of NtrC: Fluctuations, correlations and implications for allosteric cooperativity
    Proteins (in press)
    by MS Liu, BD Todd, S Yao, ZP Feng, RS Norton, RJ Sadus
    posted to allostery quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-05-20 11:47:39 as read
  • 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 molecular_dynamics multiscale quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-05-12 11:53:54 as read along with 2 people paulschlesinger aqeel
  • What is principal component analysis?
    Nature Biotechnology, Vol. 26, No. 3., pp. 303-304.
    by Markus Ringnér
    posted to clustering mathematics quasiharmonic-models_elastic-network_gnm_nma_pca_etc statistics by sobolevnrm to the group baker-group on 2008-04-28 11:33:49 as read along with 53 people and 2 groups Yanno jyuh operon barry baaic dullhunk Bevan_Weir zeji gareth massivemayhem zwang GustavoLacerda GeeSharpMinor bmaust zambujo mingzhi starz1010101 maralena wchannels sunhwan jennifermbui kdelavega zhouyu rsantana laharrin fryanpan kengg rvosa dekay23 adacier hpaces waghsk rchauhan pavanghatty kristgy jfr bibay2004 xingxu quianominorleo craigwilson06 ashko markusd dayjm dimka i-stevenson chrissp100 tharris ale mjoach HugoMarcelo jdiezperezj rrbarb Nici FAB-lab Bioinformatics
  • Accurate Structural Correlations from Maximum Likelihood Superpositions
    PLoS Computational Biology, Vol. 4, No. 2. (2008), e43.
    by DL Theobald, DS Wuttke
    posted to molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-04-14 12:25:45 as read along with 1 person zwang
  • Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL
    Molecular BioSystems, Vol. 4 (2008), pp. 287-292.
    by C Chennubhotla, Z Yang, I Bahar
    posted to allostery quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-03-28 10:58:10 as read
  • Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange
    J. Chem. Theory Comput., Vol. 4, No. 3. (11 March 2008), pp. 477-487.
    by M Zacharias
    posted to molecular_dynamics molecular_simulation multiscale quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-03-14 11:18:27 as read along with 1 person barry
  • Normal Mode Flexible Fitting of High-Resolution Structure of Biological Molecules toward 1 Dimensional Low-Resolution Data
    Biophys. J. (9 November 2007), biophysj.107.122218.
    by Christian Gorba, Osamu Miyashita, Florence Tama
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc structure by sobolevnrm to the group baker-group on 2008-03-10 11:19:25 as read along with 2 people jlh64 jennifermbui
  • Structural flexibility in proteins: impact of the crystal environment
    Bioinformatics, Vol. 24, No. 4. (15 February 2008), pp. 521-528.
    by Konrad Hinsen
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc structure by sobolevnrm to the group baker-group on 2008-03-06 12:21:51 as read along with 4 people and 1 group mijogiffin barry jlh64 scienbox McCammon
  • Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes.
    Structure, Vol. 16, No. 2. (12 February 2008), pp. 321-330.
    by Lei Yang, Guang Song, Alicia Carriquiry, Robert L L Jernigan
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc structure by sobolevnrm to the group baker-group on 2008-03-06 12:20:47 as read along with 1 person choonpeng
  • Dynamics of the Acetylcholinesterase Tetramer
    Biophys. J., Vol. 94, No. 4. (15 February 2008), pp. 1144-1154.
    by Alemayehu A Gorfe, Chia-En A Chang, Ivaylo Ivanov, Andrew J Mccammon
    posted to acetylcholinesterase diffusion kinetics molecular_dynamics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-02-22 12:09:51 as read
  • Quantification of intra- and inter-cluster relations in nonstationary and noisy data
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 77, No. 1. (2008)
    by Christian Rummel
    posted to clustering quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-02-19 12:41:24 as read
  • Multiscale complex network of protein conformational fluctuations in single-molecule time series
    Proceedings of the National Academy of Sciences, Vol. 105, No. 2. (15 January 2008), pp. 536-541.
    by Chun-Biu Li, Haw Yang, Tamiki Komatsuzaki
    posted to experimental_methodology kinetics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-02-19 12:19:20 as read along with 3 people ruvido biehl hsekiguc
  • Dimerization Affects Collective Dynamics of Triosephosphate Isomerase
    Biochemistry, Vol. 47, No. 5. (5 February 2008), pp. 1358-1368.
    by S Cansu, P Doruker
    posted to protein-protein_interactions quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-02-18 12:25:46 as read
  • Automated Generation of Reduced Stochastic Weather Models I: Simultaneous Dimension and Model Reduction for Time Series Analysis
    Multiscale Modeling & Simulation, Vol. 6, No. 4. (2008), pp. 1125-1145.
    by Illia Horenko, Rupert Klein, Stamen Dolaptchiev, Christof Schütte
    posted to kinetics multiscale quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-02-15 12:41:46 as read along with 1 person nurban
  • Normality Tests for Spatially Correlated Data
    Mathematical Geology, Vol. 36, No. 6. (2004), pp. 659-681.
    by Eulogio Pardo-Igúzquiza, Peter A Dowd
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc statistical_mechanics by sobolevnrm to the group baker-group on 2008-02-13 14:18:58 as read
  • 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 metalloregulation molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-02-04 14:29:37 as read along with 1 person aqeel
  • Diffusion maps, spectral clustering and reaction coordinates of dynamical systems
    ArXiv Mathematics e-prints (March 2005)
    by B Nadler, S Lafon, RR Coifman, IG Kevrekidis
    posted to clustering mathematics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-02-01 21:23:15 as ***** along with 2 people kb j_vinals
  • Diffusion Maps, Spectral Clustering and Eigenfunctions of Fokker-Planck operators
    (6 Jun 2005)
    by Boaz Nadler, Stephane Lafon, Ronald R Coifman, Ioannis G Kevrekidis
    posted to clustering mathematics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-02-01 21:22:37 as *****
  • Diffusion maps, spectral clustering and reaction coordinates of dynamical systems
    Applied and Computational Harmonic Analysis, Vol. 21, No. 1. (July 2006), pp. 113-127.
    by Boaz Nadler, Stephane Lafon, Ronald R Coifman, Ioannis G Kevrekidis
    posted to clustering mathematics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-02-01 16:15:44 as read along with 1 person tg1w
  • Diffusion maps
    Applied and Computational Harmonic Analysis, Vol. 21, No. 1. (July 2006), pp. 5-30.
    by Ronald R Coifman, Stephane Lafon
    posted to clustering mathematics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-02-01 16:09:52 as read along with 1 person baueru
  • Non-linear independent component analysis with diffusion maps
    Applied and Computational Harmonic Analysis, Vol. In Press, Corrected Proof
    by Amit Singer, Ronald R Coifman
    posted to clustering mathematics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-02-01 16:06:54 as read
  • Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps
    Proceedings of the National Academy of Sciences, Vol. 102, No. 21. (24 May 2005), pp. 7426-7431.
    by RR Coifman, S Lafon, AB Lee, M Maggioni, B Nadler, F Warner, SW Zucker
    posted to bioinformatics clustering mathematics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-02-01 15:54:49 as read along with 1 person kb
  • 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
  • Stress tensor analysis of the protein quake of photoactive yellow protein
    Physical Chemistry Chemical Physics (2008), 10.1039/b714618c.
    by K Koike, K Kawaguchi, T Yamato
    posted to allostery molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-01-29 12:32:40 as read
  • Dynamics of essential collective motions in proteins: Theory
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 5. (2007)
    by Maria Stepanova
    posted to kinetics quasiharmonic-models_elastic-network_gnm_nma_pca_etc statistical_mechanics by sobolevnrm to the group baker-group on 2008-01-25 12:52:15 as read along with 2 people choonpeng Diego_Prada
  • Pattern vectors from algebraic graph theory
    Pattern Analysis and Machine Intelligence, IEEE Transactions on, Vol. 27, No. 7. (2005), pp. 1112-1124.
    by RC Wilson, ER Hancock, Bin Luo
    posted to bioinformatics graph_theory mathematics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-01-24 12:53:27 as read along with 1 person bigbossman
  • 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 experimental_methodology quasiharmonic-models_elastic-network_gnm_nma_pca_etc structure by sobolevnrm to the group baker-group on 2008-01-22 12:53:33 as read along with 4 people aqeel cjeans jlh64 TOchi
  • Conformational Switching upon Phosphorylation: A Predictive Framework Based on Energy Landscape Principles
    Biochemistry (17 January 2008)
    by J Latzer, T Shen, PG Wolynes
    posted to allostery molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-01-17 12:32:48 as read along with 2 people neils paulschlesinger
  • Backbone and side-chain ordering in a small protein
    The Journal of Chemical Physics, Vol. 128, No. 2. (2008)
    by Yanjie Wei, Walter Nadler, Ulrich HE Hansmann
    posted to molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-01-15 13:03:25 as read
  • Construction of effective free energy landscape from single-molecule time series
    Proceedings of the National Academy of Sciences, Vol. 104, No. 49. (4 December 2007), pp. 19297-19302.
    by Akinori Baba, Tamiki Komatsuzaki
    posted to mathematics molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-01-10 12:46:56 as read along with 6 people hmk zwang cactus Diego_Prada arnaudriegert hsekiguc
  • 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 allostery molecular_dynamics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2007-12-20 12:39:49 as read along with 8 people ruvido barry aqeel ebeutler cactus paulschlesinger jlh64 yalexeev
  • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    Nature (18 November 2007)
    by Katherine A Henzler-Wildman, Ming Lei, Vu Thai, Jordan S Kerns, Martin Karplus, Dorothee Kern
    posted to allostery molecular_dynamics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2007-12-20 12:39:27 as read along with 8 people ruvido tmmurali allmensch cactus jlh64 RamuAnandakrishnan dmobley chenway
  • 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
  • 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 allostery quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2007-12-04 16:45:11 as read along with 8 people and 3 groups barry aqeel ruvido cactus jennifermbui higueruelo LamBras jmccammon structural_bioinformatics Bioinformatics McCammon
  • Coarse-Grained Free Energy Functions for Studying Protein Conformational Changes: A Double-Well Network Model
    Biophys. J., Vol. 93, No. 11. (1 December 2007), pp. 3860-3871.
    by Jhih-Wei Chu, Gregory A Voth
    posted to allostery molecular_simulation multiscale quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2007-11-16 00:47:06 as read along with 1 person jlh64
  • Contact rearrangements form coupled networks from local motions in allosteric proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Michael D Daily, Tarak J Upadhyaya, Jeffrey J Gray
    posted to allostery correlated_mutations molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2007-11-08 12:54:28 as read
  • Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone
    The Journal of Chemical Physics, Vol. 127, No. 15. (2007)
    by Rajesh K Murarka, Adam Liwo, Harold A Scheraga
    posted to multiscale quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2007-11-02 11:12:28 as read
  • 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 enhanced_sampling molecular_simulation multiscale quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2007-11-01 11:59:51 as read along with 3 people aqeel hmk choonpeng
  • A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis
    Proceedings of the National Academy of Sciences, Vol. 104, No. 40. (2 October 2007), pp. 15711-15716.
    by Amit Ghosh, Saraswathi Vishveshwara
    posted to allostery quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2007-10-08 12:57:46 as read along with 3 people zwang cactus phoenixzxl
  • Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e172.
    by Chakra Chennubhotla, Ivet Bahar
    posted to allostery quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2007-10-04 12:39:43 as read
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