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sobolevnrms Yang [76 articles]

Recent papers posted to sobolevnrms library by the author Yang. You can also see everyones Yang.
  • notes Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins
    Nature, Vol. 453, No. 7199. (2008)
    by Nathan H Joh, Andrew Min, Salem Faham, Julian P Whitelegge, Duan Yang, Virgil L Woods, James U Bowie
    posted to structure misc by sobolevnrm on 2008-08-20 12:16:36 as read
  • A general statistical test for correlations in a finite-length time series
    The Journal of Chemical Physics, Vol. 128, No. 21. (2008)
    by Jeffery A Hanson, Haw Yang
    posted to statistics moleculardynamics mathematics by sobolevnrm on 2008-08-10 21:39:12 as read
  • A hybrid recursion method to robustly ensure convergence efficiencies in the simulated scaling based free energy simulations
    The Journal of Chemical Physics, Vol. 129, No. 3. (2008)
    by Lianqing Zheng, Irina O Carbone, Alexey Lugovskoy, Bernd A Berg, Wei Yang
    posted to molecularsimulation freeenergy enhancedsampling by sobolevnrm on 2008-08-02 17:53:53 as read
  • Factor Va Alters the Conformation of the Na+-Binding Loop of Factor Xa in the Prothrombinase Complex
    Biochemistry, Vol. 47, No. 22. (3 June 2008), pp. 5976-5985.
    by Likui Yang, Chandrashekhara Manithody, Shabir H Qureshi, Alireza R Rezaie
    posted to thrombin by sobolevnrm on 2008-07-24 12:13:59 as read along with 1 group baker-group
  • Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins
    Nature (25 May 2008)
    by Nathan H Joh, Andrew Min, Salem Faham, Julian P Whitelegge, Duan Yang, Virgil L Woods, James U Bowie
    posted to structure protein_folding protein_engineering by sobolevnrm on 2008-07-24 12:12:57 as read along with 1 group baker-group
  • Linear-scaling semiempirical quantum calculations for macromolecules
    The Journal of Chemical Physics, Vol. 105, No. 7. (1996), pp. 2744-2750.
    by Tai S Lee, Darrin M York, Weitao Yang
    posted to solvation quantum_mechanics by sobolevnrm on 2008-06-30 12:13:03 as read along with 1 group baker-group
  • A QM/MM study combined with the theory of energy representation: Solvation free energies for anti/syn acetic acids in aqueous solution
    Chemical Physics Letters, Vol. 419, No. 1-3. (15 February 2006), pp. 240-244.
    by Takumi Hori, Hideaki Takahashi, Masayoshi Nakano, Tomoshige Nitta, Weitao Yang
    posted to solvation quantum_mechanics by sobolevnrm on 2008-06-30 12:05:32 as read along with 1 group baker-group
  • Synthetic Antimicrobial Oligomers Induce a Composition-Dependent Topological Transition in Membranes
    J. Am. Chem. Soc., Vol. 129, No. 40. (10 October 2007), pp. 12141-12147.
    by L Yang, VD Gordon, A Mishra, A Som, KR Purdy, MA Davis, GN Tew, GCL Wong
    posted to protein-membrane_interactions biomembranes by sobolevnrm on 2008-06-13 13:18:10 as read along with 1 person and 1 group samjlord baker-group
  • HIV TAT Forms Pores in Membranes by Inducing Saddle-Splay Curvature: Potential Role of Bidentate Hydrogen Bonding13
    Angewandte Chemie International Edition, Vol. 47, No. 16. (2008), pp. 2986-2989.
    by Abhijit Mishra, Vernita d, Lihua Yang, Robert Coridan, Gerard c
    posted to protein-membrane_interactions biomembranes by sobolevnrm on 2008-06-13 13:16:41 as read along with 1 group baker-group
  • Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonian replica exchange method
    Chemical Physics Letters, Vol. 454, No. 4-6. (20 March 2008), pp. 391-395.
    by Donghong Min, Hongzhi Li, Guohui Li, Bernd A Berg, Marcia O Fenley, Wei Yang
    posted to statistical_mechanics nucleic_acids molecular_simulation electrostatics by sobolevnrm on 2008-05-08 11:41:20 as read along with 1 group baker-group
  • Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms
    PLoS Computational Biology, Vol. 4, No. 3. (2008), e1000047.
    by S Yang, B Roux
    posted to molecular_simulation allostery by sobolevnrm on 2008-05-06 11:21:23 as read along with 1 group baker-group
  • How Well Does Poisson-Boltzmann Implicit Solvent Agree with Explicit Solvent? A Quantitative Analysis
    J. Phys. Chem. B, Vol. 110, No. 37. (21 September 2006), pp. 18680-18687.
    by C Tan, L Yang, R Luo
    posted to electrostatics molecular_simulation solvation by sobolevnrm on 2008-04-18 11:27:21 as ** along with 1 group baker-group
  • In vivo tumor targeting and spectroscopic detection with surface-enhanced Raman nanoparticle tags
    Nature Biotechnology, Vol. 26, No. 1. (23 December 2007), pp. 83-90.
    by Ximei Qian, Xiang-Hong Peng, Dominic O Ansari, Qiqin Yin-Goen, Georgia Z Chen, Dong M Shin, Lily Yang, Andrew N Young, May D Wang, Shuming Nie
    posted to ccne imaging nanotech by sobolevnrm on 2008-04-10 12:09:11 as read along with 1 person and 1 group ml115 baker-group
  • 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 on 2008-03-28 10:58:09 as read along with 1 group baker-group
  • Quantum dot imaging for embryonic stem cells
    BMC Biotechnology, Vol. 7 (09 October 2007), 67.
    by Shuan Lin, Xiaoyan Xie, Manishkumar R Patel, Yao H Yang, Zongjin Li, Feng Cao, Olivier Gheysens, Yan Zhang, Sanjiv S Gambhir, Jiang H Rao, Joseph C Wu
    posted to ccne imaging nanotech by sobolevnrm on 2008-03-06 12:23:16 as read along with 2 people and 1 group SteveTheRed ml115 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
  • Ion Size and Image Effect on Electrokinetic Flows
    Langmuir (1 February 2008)
    by Y Liu, M Liu, WM Lau, J Yang
    posted to diffusion electrostatics statistical_mechanics by sobolevnrm on 2008-02-28 12:34:59 as read along with 1 person and 1 group mikaellund baker-group
  • 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 hsekiguc ruvido biehl baker-group
  • Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA.
    by Ninad V Prabhu, Manoranjan Panda, Qingyi Yang, Kim A Sharp
    posted to electrostatics nucleic_acids solvation by sobolevnrm on 2008-01-21 12:55:09 as read along with 3 people and 1 group dimka RamuAnandakrishnan onufriev baker-group
  • From the Cover: Mapping hydration dynamics around a protein surface.
    Proc Natl Acad Sci U S A, Vol. 104, No. 47. (20 November 2007), pp. 18461-18466.
    by L Zhang, L Wang, YT Kao, W Qiu, Y Yang, O Okobiah, D Zhong
    posted to kinetics solvation by sobolevnrm on 2007-12-21 12:27:58 as read along with 2 people and 2 groups skoch3 kjell Koch_Lab baker-group
  • Illuminating the mechanistic roles of enzyme conformational dynamics
    Proceedings of the National Academy of Sciences, Vol. 104, No. 46. (13 November 2007), pp. 18055-18060.
    by Jeffrey A Hanson, Karl Duderstadt, Lucas P Watkins, Sucharita Bhattacharyya, Jason Brokaw, Jhih-Wei Chu, Haw Yang
    posted to allostery by sobolevnrm on 2007-12-10 12:36:26 as read along with 1 person and 1 group biehl baker-group
  • Specific Ion Effects on Interfacial Water Structure near Macromolecules
    J. Am. Chem. Soc., Vol. 129, No. 40. (10 October 2007), pp. 12272-12279.
    by X Chen, T Yang, S Kataoka, PS Cremer
    posted to electrostatics solvation by sobolevnrm on 2007-10-08 12:42:30 as read along with 1 group baker-group
  • Hybrid Hamiltonian replica exchange molecular dynamics simulation method employing the Poisson--Boltzmann model
    The Journal of Chemical Physics, Vol. 127, No. 8. (2007)
    by Yuguang Mu, Ye Yang, Weixin Xu
    posted to electrostatics multiscale solvation by sobolevnrm on 2007-09-04 12:38:17 as read along with 1 group baker-group
  • Computer Modeling of Mitochondrial Tricarboxylic Acid Cycle, Oxidative Phosphorylation, Metabolite Transport, and Electrophysiology
    J. Biol. Chem., Vol. 282, No. 34. (24 August 2007), pp. 24525-24537.
    by Fan Wu, Feng Yang, Kalyan C Vinnakota, Daniel A Beard
    posted to systems_biology by sobolevnrm on 2007-08-22 12:25:15 as read along with 1 person and 1 group paulschlesinger baker-group
  • Insights into Equilibrium Dynamics of Proteins from Comparison of NMR and X-Ray Data with Computational Predictions
    Structure, Vol. 15, No. 6. (2007), pp. 741-9.
    by LW Yang, E Eyal, C Chennubhotla, J Jee, AM Gronenborn, I Bahar
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-06-20 12:33:33 as read along with 1 group baker-group
  • Budding Dynamics of Individual Domains in Multicomponent Membranes Simulated by N-Varied Dissipative Particle Dynamics
    Journal of Physical Chemistry B (in press)
    by B Hong, F Qiu, H Zhang, Y Yang
    posted to biomembranes multiscale by sobolevnrm on 2007-05-25 14:38:05 as read along with 1 group baker-group
  • Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
    Physical Review B, Vol. 37, No. 2. (1988), pp. 785-9.
    by C Lee, W Yang, RG Parr
    posted to quantum_mechanics by sobolevnrm on 2007-05-25 14:38:05 as read along with 1 group baker-group
  • Binding Free Energy Contributions of Interfacial Waters in HIV-1 Protease/Inhibitor Complexes
    Journal of the American Chemical Society, Vol. 128, No. 36. (2006), pp. 11830-9.
    by Y Lu, CY Yang, S Wang
    posted to protein-ligand_interactions solvation by sobolevnrm on 2007-05-25 14:37:06 as read along with 1 group baker-group
  • Evidence of Cholesterol Accumulated in High Curvature Regions: Implication to the Curvature Elastic Energy for Lipid Mixtures
    Biophysical Journal, Vol. 92, No. 8. (2007), pp. 2819-30.
    by W Wang, L Yang, HW Huang
    posted to biomembranes by sobolevnrm on 2007-05-25 14:36:49 as read along with 1 group baker-group
  • Quantitative Membrane Electrostatics with the Atomic Force Microscope
    Biophysical Journal, Vol. 92, No. 6. (2007), pp. 1966-74.
    by Y Yang, KM Mayer, JH Hafner
    posted to biomembranes electrostatics by sobolevnrm on 2007-05-25 14:36:29 as read along with 1 group baker-group
  • Biomimetic amplification of nanoparticle homing to tumors
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 3. (2007), pp. 932-6.
    by D Simberg, T Duza, JH Park, M Essler, J Pilch, L Zhang, AM Derfus, M Yang, RM Hoffman, S Bhatia, MJ Sailor, E Ruoslahti
    posted to drugdesign nanotech by sobolevnrm on 2007-05-25 14:36:05 as read along with 1 group baker-group
  • UvrD Helicase Unwinds DNA One Base Pair at a Time by a Two-Part Power Stroke
    Cell, Vol. 127, No. 7. (2006), pp. 1349-60.
    by JY Lee, W Yang
    posted to helicase by sobolevnrm on 2007-05-25 14:36:04 as read along with 1 group baker-group
  • Ewald Summation for Uniformly Charged Surface
    Journal of Chemical Theory and Computation, Vol. 2, No. 6. (2006), pp. 1618-23.
    by W Yang, X Jin, Q Liao
    posted to biomembranes electrostatics molecular_simulation by sobolevnrm on 2007-05-25 14:24:57 as read along with 1 group baker-group
  • Anisotropic network model: systematic evaluation and a new web interface
    Bioinformatics, Vol. 22, No. 21. (2006), pp. 2619-27.
    by E Eyal, LW Yang, I Bahar
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-05-25 14:24:56 as read along with 1 group baker-group
  • How Well Does Poisson-Boltzmann Implicit Solvent Agree with Explicit Solvent? A Quantitative Analysis
    Journal of Physical Chemistry B, Vol. 110, No. 37. (2006), pp. 18680-7.
    by C Tan, L Yang, R Luo
    posted to electrostatics solvation by sobolevnrm on 2007-05-25 14:23:19 as read along with 1 group baker-group
  • Mathematical modeling of the nitric oxide/cGMP pathway in the vascular smooth muscle cell
    American Journal of Physiology - Heart and Circulatory Physiology, Vol. 289, No. 2. (2005), pp. H886-H897.
    by J Yang, JW Clark, RM Bryan, CS Robertson
    posted to diffusion nitric_oxide systems_biology by sobolevnrm on 2007-05-25 14:23:19 as read along with 1 group baker-group
  • Binding of Aminoglycosidic Antibiotics to the Oligonucleotide A-Site Model and 30S Ribosomal Subunit: Poisson-Boltzmann Model, Thermal Denaturation, and Fluorescence Studies
    Journal of Medicinal Chemistry, Vol. 49, No. 18. (2006), pp. 5478-90.
    by G Yang, J Trylska, Y Tor, JA Mccammon
    posted to electrostatics nucleic_acids ribosome by sobolevnrm on 2007-05-25 14:23:18 as read along with 1 group baker-group
  • Effective stochastic dynamics on a protein folding energy landscape
    Journal of Chemical Physics, Vol. 125 (2006)
    by S Yang, JN Onuchic, H Levine
    posted to diffusion multiscale protein_folding quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-05-25 14:23:17 as read along with 1 group baker-group
  • Elucidating the Conformational Dependence of Calculated pKa Values
    Journal of Chemical Theory and Computation, Vol. 2, No. 4. (2006), pp. 927-38.
    by DR Livesay, DJ Jacobs, J Kanjanapangka, E Chea, H Cortez, J Garcia, P Kidd, MP Marquez, S Pande, D Yang
    posted to electrostatics pka solvation by sobolevnrm on 2007-05-25 14:23:17 as read along with 1 group baker-group
  • Predicting calcium-binding sites in proteins - A graph theory and geometry approach
    Proteins, Vol. 64, No. 1. (2006), pp. 34-42.
    by H Deng, G Chen, W Yang, JJ Yang
    posted to bioinformatics protein-ligand_interactions by sobolevnrm on 2007-05-25 14:22:46 as read along with 1 group baker-group
  • Birefringence and computational studies of a polystyrene Boger fluid in axisymmetric stagnation flow
    Journal of Non-Newtonian Fluid Mechanics, Vol. 91, No. 2-3. (2000), pp. 189-220.
    by JM Li, WR Burghardt, B Yang, B Khomami
    posted to fluid_mechanics by sobolevnrm on 2007-05-25 14:22:45 as read along with 1 group baker-group
  • Simulations of sedimentation of a sphere in a viscoelastic fluid using molecular based constitutive models
    Journal of Non-Newtonian Fluid Mechanics, Vol. 82, No. 2-3. (1999), pp. 429-52.
    by B Yang, B Khomami
    posted to fluid_mechanics by sobolevnrm on 2007-05-25 14:22:45 as read along with 1 group baker-group
  • Structural Basis of Affinity Maturation and Intramolecular Cooperativity in a Protein-Protein Interaction
    Structure, Vol. 13, No. 12. (2005), pp. 1775-87.
    by S Cho, CP Swaminathan, J Yang, MC Kerzic, R Guan, MC Kieke, DM Kranz, RA Mariuzza, EJ Sundberg
    posted to protein-protein_interactions by sobolevnrm on 2007-05-25 14:19:26 as read along with 1 group baker-group
  • Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies
    Physical Biology, Vol. 2, No. 4. (2005), pp. S173-S180.
    by C Chennubhotla, AJ Rader, LW Yang, I Bahar
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-05-25 14:19:04 as read along with 1 group baker-group
  • Incomplete Ion Dissociation Underlies the Weakened Attraction between DNA Helices at High Spermidine Concentrations
    Biophysical Journal, Vol. 89, No. 3. (2005), pp. 1932-40.
    by J Yang, DC Rau
    posted to electrostatics nucleic_acids statistical_mechanics by sobolevnrm on 2007-05-25 14:18:25 as read along with 1 group baker-group
  • Comparison between Generalized-Born and PoissonâBoltzmann methods in physics-based scoring functions for protein structure prediction
    Journal of Molecular Modeling, Vol. 12, No. 1. (2005), pp. 101-10.
    by MC Lee, R Yang, Y Duan
    posted to electrostatics by sobolevnrm on 2007-05-25 14:18:25 as read along with 1 group baker-group
  • iGNM: a database of protein functional motions based on Gaussian Network Model
    Bioinformatics, Vol. 21, No. 13. (2005), pp. 2978-87.
    by LW Yang, X Liu, CJ Jursa, M Holliman, AJ Rader, HA Karimi, I Bahar
    posted to bioinformatics database quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-05-25 14:18:04 as read along with 1 group baker-group
  • Eliminating Positively Charged Lysine epsilon-NH3+ Groups on the Surface of Carbonic Anhydrase Has No Significant Influence on Its Folding from Sodium Dodecyl Sulfate
    Journal of the American Chemical Society, Vol. 127, No. 13. (2005), pp. 4707-14.
    by KL Gudiksen, I Gitlin, J Yang, AR Urbach, DT Moustakas, GM Whitesides
    posted to electrostatics protein_folding by sobolevnrm on 2007-05-25 14:16:05 as read along with 1 group baker-group
  • Morphological Characterization of Molecular Complexes Present in the Synaptic Cleft
    Structure, Vol. 13, No. 3. (2005), pp. 423-34.
    by V Lucic, T Yang, G Schweikert, F Fã¶rster, W Baumeister
    posted to neuromuscular_junctions structure by sobolevnrm on 2007-05-25 14:15:43 as read along with 1 group baker-group
  • Manning-Oosawa Counterion Condensation
    Physical Review Letters, Vol. 94 (2005)
    by B O'Shaughnessy, Q Yang
    posted to electrostatics by sobolevnrm on 2007-05-25 14:15:43 as read along with 1 group baker-group
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