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Tag quasiharmonic-models_elastic-network_gnm_nma_pca_etc [56 articles]

Recent papers classified by the tag quasiharmonic-models_elastic-network_gnm_nma_pca_etc.
  • HingeProt: Automated prediction of hinges in protein structures
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Ugur Emekli, Dina Schneidman-Duhovny, Haim J Wolfson, Ruth Nussinov, Turkan Haliloglu
    posted to bioinformatics quasiharmonic-models_elastic-network_gnm_nma_pca_etc software structure by sobolevnrm on 2007-09-13 13:14:14 as read along with 3 people and 1 group barry willpitt higueruelo baker-group
  • Harmonicity in slow protein dynamics
    Chemical Physics, Vol. 261, No. 1-2. (1 November 2000), pp. 25-37.
    by Konrad Hinsen, Andrei-Jose Petrescu, Serge Dellerue, Marie-Claire Bellissent-Funel, Gerald R Kneller
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-08-30 14:58:26 as read along with 2 people and 1 group apaydin saravan baker-group
  • 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 on 2008-04-28 11:33:49 as read along with 53 people and 3 groups Yanno guhjy 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 baker-group FAB-lab Bioinformatics
  • 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 on 2008-01-15 13:03:25 as read along with 1 group baker-group
  • 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 molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc correlatedmutations by sobolevnrm on 2007-11-08 12:54:28 as read along with 1 group baker-group
  • 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 on 2008-05-27 16:04:43 as read along with 1 group baker-group
  • 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 on 2008-01-25 12:52:15 as read along with 2 people and 1 group choonpeng Diego_Prada baker-group
  • 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 on 2008-05-12 11:53:54 as read along with 2 people and 1 group paulschlesinger aqeel baker-group
  • 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 on 2008-05-27 16:03:06 as read along with 2 people and 1 group baaden aqeel baker-group
  • 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 on 2008-02-01 15:54:48 as read along with 1 person and 1 group kb baker-group
  • 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 on 2008-07-11 12:18:57 as read along with 2 people and 1 group vahmurk dimka baker-group
  • Full correlation analysis of conformational protein dynamics
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Oliver F Lange, Helmut Grubmüller
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-09-24 13:19:05 as read along with 4 people and 1 group softsimu barry choonpeng LamBras baker-group
  • 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 on 2008-02-15 12:41:45 as read along with 1 person and 1 group nurban baker-group
  • Local feature analysis: A statistical theory for reproducible essential dynamics of large macromolecules
    Proteins: Structure, Function, and Bioinformatics, Vol. 64, No. 2. (2006), pp. 391-403.
    by Zhiyong Zhang, Willy Wriggers
    posted to molecular_dynamics molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-08-22 20:24:51 as read along with 1 group baker-group
  • 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 on 2008-02-19 12:41:24 as read along with 1 group baker-group
  • 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 on 2008-03-14 11:18:27 as read along with 1 person and 1 group barry baker-group
  • 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 on 2008-02-01 16:15:44 as read along with 1 person and 1 group tg1w baker-group
  • 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 on 2008-02-04 14:29:37 as read along with 1 person and 1 group aqeel baker-group
  • 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 on 2008-03-06 12:20:47 as read along with 1 person and 1 group choonpeng baker-group
  • 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 on 2008-02-01 16:09:51 as read along with 1 person and 1 group baueru baker-group
  • 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 on 2008-03-10 11:19:25 as read along with 2 people and 1 group jlh64 jennifermbui baker-group
  • 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 on 2008-03-06 12:21:51 as read along with 4 people and 2 groups mijogiffin barry jlh64 scienbox baker-group McCammon
  • 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 on 2007-12-20 12:39:26 as read along with 8 people and 1 group ruvido tmmurali allmensch cactus jlh64 RamuAnandakrishnan dmobley chenway baker-group
  • 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 on 2008-05-27 16:06:12 as read along with 1 person and 1 group choonpeng baker-group
  • 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 on 2008-01-10 12:46:56 as read along with 6 people and 1 group hmk zwang cactus Diego_Prada arnaudriegert hsekiguc baker-group
  • 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 on 2008-06-06 11:37:30 as read along with 4 people and 1 group ttjoseph ffranca barry choonpeng baker-group
  • 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 on 2008-06-20 11:32:37 as read along with 1 group baker-group
  • 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 on 2008-02-01 21:23:15 as ***** along with 2 people and 1 group kb j_vinals baker-group
  • 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 on 2007-10-04 12:39:43 as read along with 1 group baker-group
  • 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 on 2008-02-18 12:25:46 as read along with 1 group baker-group
  • 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 quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-08-24 12:58:43 as read along with 5 people and 3 groups ubcg08l barry aqeel choonpeng LamBras structural_bioinformatics Bioinformatics baker-group
  • 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 protein-ligand_interactions quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-08-26 19:42:23 as read along with 1 person and 1 group aqeel baker-group
  • How Directional Translocation is Regulated in a DNA Helicase Motor
    Biophys. J. (17 August 2007), biophysj.107.109546.
    by Jin Yu, Taekjip Ha, Klaus Schulten
    posted to allostery helicase quasiharmonic-models_elastic-network_gnm_nma_pca_etc correlatedmutations by sobolevnrm on 2007-08-26 19:58:10 as read along with 1 group baker-group
  • 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 on 2008-01-17 12:32:48 as read along with 2 people and 1 group neils paulschlesinger baker-group
  • 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 on 2008-02-01 21:22:37 as ***** along with 1 group baker-group
  • 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 on 2008-02-01 16:06:54 as read along with 1 group baker-group
  • 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 on 2007-11-16 00:47:06 as read along with 1 person and 1 group jlh64 baker-group
  • Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Andrew W Stumpff-Kane, Katarzyna Maksimiak, Michael S Lee, Michael Feig
    posted to multiscale quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-09-24 13:17:24 as read along with 1 person and 2 groups barry structural_bioinformatics baker-group
  • 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 on 2007-12-20 12:38:17 as read along with 2 people and 1 group choonpeng paulschlesinger baker-group
  • Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Andreas May, Martin Zacharias
    posted to protein-protein_interactions quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-08-30 12:42:59 as read along with 1 group baker-group
  • 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 on 2007-12-20 12:39:49 as read along with 9 people and 1 group ubcg08l ruvido barry aqeel ebeutler cactus paulschlesinger jlh64 yalexeev baker-group
  • 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 on 2008-02-13 14:18:57 as read along with 1 group baker-group
  • 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 on 2007-11-02 11:12:27 as read along with 1 group 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 allostery quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-12-04 16:45:11 as read along with 8 people and 4 groups barry aqeel ruvido cactus jennifermbui higueruelo LamBras jmccammon structural_bioinformatics Bioinformatics baker-group McCammon
  • 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 on 2008-02-19 12:19:19 as read along with 3 people and 1 group ruvido biehl hsekiguc baker-group
  • Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis.
    Proteins, Vol. 23, No. 2. (October 1995), pp. 177-186.
    by S Hayward, A Kitao, N Go
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-09-24 13:25:50 as read along with 4 people and 1 group lna aqeel gane5h saravan baker-group
  • 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 on 2008-01-24 12:53:27 as read along with 1 person and 1 group bigbossman baker-group
  • 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 on 2007-10-08 12:57:46 as read along with 3 people and 1 group zwang cactus phoenixzxl baker-group
  • Evaluation of Configurational Entropy Methods from Peptide Folding-Unfolding Simulation
    J. Phys. Chem. B, Vol. 111, No. 49. (13 December 2007), pp. 13807-13813.
    by DW Li, M Khanlarzadeh, J Wang, S Huo, R Bruschweiler
    posted to molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2008-01-22 12:59:16 as read
  • 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 on 2008-01-30 12:47:02 as read along with 2 people and 2 groups samjlord hmk moernerlab baker-group
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