CiteULike: paulschlesinger's watchlist [more than 800 articles]

	The ontology of biological sequences [My Copy] BMC Bioinformatics 2009 10:377, Vol. 10, No. 1. (Nov 2009) by Robert Hoehndorf, Janet Kelso, Heinrich Herre posted to ontology bioinformatics by sobolevnrm on 2009-11-18 13:13:01 as
	SimCT: a generic tool to visualize ontology-based relationships for biological objects [My Copy] Bioinformatics, Vol. 25, No. 23. (Dec 2009), pp. 3197-8. by Carl Herrmann, C. Bérard, Laurent Tichit posted to web software ontology by sobolevnrm on 2009-11-18 13:13:01 as
	Simulations of RNA Interactions with Monovalent Ions [My Copy] Methods in Enzymology, Vol. 469 (Nov 2009), pp. 411-432. by Alan A. Chen, M. Marucho, Nathan A. Baker, R. V. Pappu posted to review nucleic-acids electrostatics by sobolevnrm on 2009-11-18 13:13:01 as along with 1 person anuragsethi
	Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin [My Copy] Proceedings of the National Academy of Sciences (Nov 2009) by T. Wlodarski, B. Zagrovic posted to protein-protein-interactions protein-folding by sobolevnrm on 2009-11-18 13:13:01 as
	Long-range energy transfer in proteins [My Copy] Physical Biology, Vol. 6 (Dec 2009) by Francesco Piazza, Yves H. Sanejouand posted to quasiharmonic-models allostery by sobolevnrm on 2009-11-16 13:09:29 as along with 1 person anuragsethi
	Hierarchical molecular interfaces and solvation electrostatics [My Copy] 2009 SIAM/ACM Joint Conference on Geometric and Physical Modeling (2009), pp. 283-288. by C. Bajaj, Shun Chuan Albert Chen, G. Xu, Q. Zhang, W. Zhao posted to solvation multiscale geometry electrostatics by sobolevnrm on 2009-11-16 13:09:29 as
	Effect of pH on molecular constitution and distribution of hemoglobin in living erythrocyte [My Copy] Biopolymers by Y. Wu, Yao X. Huang, Li L. Kang, Zheng J. Wu, Man Luo posted to red-blood-cell nitric-oxide by sobolevnrm on 2009-11-16 13:09:29 as
	Crystal Structure of HypA, a Nickel-Binding Metallochaperone for [NiFe] Hydrogenase Maturation [My Copy] Journal of Molecular Biology (Sep 2009) by S. Watanabe, T. Arai, R. Matsumi, H. Atomi, T. Imanaka, K. Miki posted to structure nikr metalloregulation by sobolevnrm on 2009-11-16 13:09:19 as
	Performance of Nonlinear Finite-Difference Poisson−Boltzmann Solvers [My Copy] Journal of Chemical Theory and Computation by Qin Cai, Meng J. Hsieh, Jun Wang, Ray Luo posted to mathematics finite-differences electrostatics by sobolevnrm on 2009-11-16 13:09:19 as
	Computational Identification of Slow Conformational Fluctuations in Proteins [My Copy] Journal of Physical Chemistry B by Arvind Ramanathan, Pratul K. Agarwal posted to quasiharmonic-models by sobolevnrm on 2009-11-16 13:09:19 as along with 1 person anuragsethi
	Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction [My Copy] Protein Science by Yu Su, Ao Zhou, Xuefeng Xia, Wen Li, Zhirong Sun posted to solvation protein-protein-interactions protein-ligand-interactions by sobolevnrm on 2009-11-16 13:09:19 as
	Poisson-Boltzmann model in a solvent of interacting Langevin dipoles [My Copy] EPL (Europhysics Letters), Vol. 88 (Oct 2009) by D. H. Mengistu, K. Bohinc, S. May posted to solvation electrostatics beyond-mean-field by sobolevnrm on 2009-11-16 13:09:19 as
	Poisson-Boltzmann for oppositely charged bodies: an explicit derivation [My Copy] Molecular Physics, Vol. 107, No. 13. (2009), pp. 1379-1391. by Fabien Paillusson, Maria Barbi, Jean M. Victor posted to thermodynamics-kinetic-theory theoretical-physics statistical-mechanics quantum-mechanics poisson-boltzmann-theory physical-chemistry parallel-plates oppositely-charged mathematical-physics interface group-theory energy-profile electrostatics colloid-complex chemical-physics atomic-nuclear-physics by sobolevnrm on 2009-11-12 14:10:16 as
	Predicting new molecular targets for known drugs [My Copy] Nature (Nov 2009) by M. Keiser, V. Setola, J. Irwin, et al.C. Laggner, A. Abbas, S. Hufeisen, N. Jensen, M. Kuijer, R. Matos, T. Tran, R. Whaley, R. Glennon, J. Hert, K. Thomas, D. Edwards, B. Shoichet, B. Roth posted to protein-ligand-interactions informatics drug-design bioinformatics by sobolevnrm on 2009-11-12 14:10:16 as
	A sequence-compatible amount of native burial information is sufficient for determining the structure of small globular proteins [My Copy] Proc Natl Acad Sci USA, Vol. 106, No. 45. (Nov 2009), pp. 19001-19004. by A. Pereira de Araujo, J. Onuchic posted to structure-prediction by sobolevnrm on 2009-11-12 14:10:16 as
	Physical arguments for distance-weighted interactions in elastic network models for proteins [My Copy] Proc Natl Acad Sci USA, Vol. 106, No. 45. (Nov 2009) by K. Hinsen posted to quasiharmonic-models by sobolevnrm on 2009-11-12 14:10:16 as
	Electrostatic correlations at the Stern layer: Physics or chemistry? [My Copy] Journal of Chemical Physics, Vol. 131 (2009) by Alex Travesset, S. Vangaveti posted to statistical-mechanics electrostatics beyond-mean-field by sobolevnrm on 2009-11-12 14:10:16 as
	Simultaneous prediction of protein folding and docking at high resolution [My Copy] Proceedings of the National Academy Sciences, Vol. 106, No. 45. (2009), pp. 18978-18983. by R. Das, I. André, Y. Shen, et al.Y. Wu, A. Lemak, S. Bansal, C. H. Arrowsmith, T. Szyperski, D. Baker posted to protein-protein-interactions protein-folding by sobolevnrm on 2009-11-12 14:10:16 as
	Membrane Lipid Polymorphism [My Copy] Methods in Molecular Biology, Vol. 400 (Jan 2007), pp. 15-26. by Richard M. Epand posted to review biomembranes by sobolevnrm on 2009-11-12 14:10:16 as
	From the Cover: Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations [My Copy] Proc Natl Acad Sci USA, Vol. 106, No. 45. (Nov 2009), pp. 19011-19016. by F. Noé, C. Schütte, E. Vanden Eijnden, L. Reich, T. Weikl posted to protein-folding molecular-dynamics kinetics by sobolevnrm on 2009-11-12 14:10:16 as along with 1 person anuragsethi
	A first-order system least-squares finite element method for the Poisson-Boltzmann equation [My Copy] Journal of Computational Chemistry by Stephen D. Bond, J. H. Chaudhry, Eric C. Cyr, Luke N. Olson posted to solvation mathematics finite-element electrostatics by sobolevnrm on 2009-11-12 14:10:16 as
	Generalized Yvon-Born-Green Theory for Molecular Systems [My Copy] Physical Review Letters, Vol. 103 (2009) by J. W. Mullinax, W. G. Noid posted to statistical-mechanics multiscale integral-equation by sobolevnrm on 2009-11-09 23:13:46 as
	Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex [My Copy] Proteins by Nurit Haspel, Brian V. Geisbrecht, John Lambris, Lydia Kavraki posted to protein-protein-interactions multiscale energy-landscape by sobolevnrm on 2009-11-09 23:13:46 as along with 1 person anuragsethi
	Titration_DB: Storage and analysis of NMR-monitored protein pH titration curves [My Copy] Proteins by Damien Farrell, Emanuel S. Miranda, Helen Webb, et al.Nikolaj Georgi, Peter B. Crowley, Lawrence P. McIntosh, Jens E. Nielsen posted to solvation pka electrostatics database by sobolevnrm on 2009-11-09 23:13:46 as
	Apo and Nickel-bound Forms of the Pyrococcus Horikoshii Species of the Metalloregulatory Protein: NikR Characterized by Molecular Dynamics Simulations [My Copy] Biochemistry by Daniel J. Sindhikara, Adrian E. Roitberg, Kenneth M. Merz posted to quantum-mechanics nikr molecular-dynamics by sobolevnrm on 2009-11-09 23:13:46 as
	Density imbalances and free energy of lipid transfer in supported lipid bilayers [My Copy] Journal of Chemical Physics, Vol. 131 (2009) by C. Xing, Roland Faller posted to molecular-simulation free-energy biomembranes by sobolevnrm on 2009-11-09 23:13:46 as
	Areas of Monounsaturated Diacylphosphatidylcholines [My Copy] Biophys J, Vol. 97, No. 7. (2009), pp. 1926-1932. by Norbert K. Cerka, Jana Gallová, Daniela Uhr'iková, et al.Pavol Balgavý, Monica Bulacu, Siewert J. Marrink, John Katsaras posted to structure biomembranes by sobolevnrm on 2009-11-09 23:13:46 as
	Understanding Nanoparticle Diffusion and Exploring Interfacial Nanorheology using Molecular Dynamics Simulations [My Copy] Langmuir by Yanmei Song, Mingxiang Luo, Lenore L. Dai posted to no-tag by sobolevnrm on 2009-11-09 23:13:46 as
	An empirical potential based quasicontinuum theory for structural prediction of water [My Copy] Journal of Chemical Physics, Vol. 131, No. 18. (2009) by A. V. Raghunathan, N. R. Aluru posted to solvation multiscale by sobolevnrm on 2009-11-09 23:13:46 as
	Inversion of radial distribution functions to pair forces by solving the Yvon--Born--Green equation iteratively [My Copy] The Journal of Chemical Physics, Vol. 131, No. 13. (Jan 2009) by H. M. Cho, J. W. Chu posted to statistical-mechanics multiscale molecular-simulation integral-equation by sobolevnrm on 2009-11-09 23:13:45 as
	Location, Tilt, and Binding: A Molecular Dynamics Study of Voltage-Sensitive Dyes in Biomembranes [My Copy] Journal of Physical Chemistry B by Marlon J. Hinner, S. J. Marrink, Alex H. de Vries posted to ligand-membrane-interactions biomembranes by sobolevnrm on 2009-11-09 23:13:44 as
	Predicting pKa [My Copy] J. Chem. Inf. Model., Vol. 49, No. 9. (Sep 2009), pp. 2013-2033. by Adam C. Lee, Gordon M. Crippen posted to solvation pka electrostatics by sobolevnrm on 2009-11-06 12:56:28 as along with 1 person anuragsethi
	Buffers May Adversely Affect Model Lipid Membranes: A Cautionary Tale [My Copy] Biochemistry by Teresa P. Salvador, Oscar Ces, Richard H. Templer, Annela M. Seddon posted to solvation ligand-membrane-interactions biomembranes by sobolevnrm on 2009-11-06 12:56:27 as
	Study on the Correlation between Lateral Diffusion Effect and Effective Charge in Neutral Liposomes [My Copy] Langmuir by Elisa G. Cortés, de Dios Solier, Joan Estelrich, Roque H. Álvarez posted to solvation electrostatics diffusion biomembranes by sobolevnrm on 2009-11-04 19:05:45 as
	Mitochondrial Membranes with Mono- and Divalent Salt: Changes Induced by Salt Ions on Structure and Dynamics [My Copy] Journal of Physical Chemistry B by Sanja Pöyry, Tomasz Róg, Mikko Karttunen, Ilpo Vattulainen posted to solvation electrostatics biomembranes by sobolevnrm on 2009-11-04 19:05:45 as
	Understanding Hydrogen-Bond Patterns in Proteins using Net-work Motifs [My Copy] Bioinformatics (Oxford, England) (Sep 2009) by O. Rahat, U. Alon, Y. Levy, G. Schreiber posted to structure graph-theory bioinformatics by sobolevnrm on 2009-11-04 19:05:45 as
	Interpretation of Molecular Dynamics on Different Time Scales in Unilamellar Vesicles Using Field-Cycling NMR Relaxometry [My Copy] Journal of Physical Chemistry B by Carla J. Meledandri, Josefina Perlo, Ezequiel Farrher, Dermot F. Brougham, Esteban Anoardo posted to nmr kinetics biomembranes by sobolevnrm on 2009-11-04 19:05:45 as
	Mixed Resolution Modeling of Interactions in Condensed-Phase Systems [My Copy] Journal of Chemical Theory and Computation by Sergei Izvekov, Gregory A. Voth posted to multiscale molecular-simulation by sobolevnrm on 2009-11-04 19:05:45 as
	Role of band 3 in regulating metabolic flux of red blood cells [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 44. (Oct 2009), pp. 18515-18520. by Ian A. Lewis, M. Estela Campanella, John L. Markley, Philip S. Low posted to red-blood-cell nitric-oxide by sobolevnrm on 2009-11-04 19:05:45 as
	Why Direct or Reversed Hofmeister Series? Interplay of Hydration, Non-electrostatic Potentials, and Ion Size [My Copy] Langmuir by D. F. Parsons, M. Boström, T. J. Maceina, A. Salis, B. W. Ninham posted to solvation interfaces electrostatics by sobolevnrm on 2009-11-04 19:05:45 as
	Interactions of Dihydrochloride Fluphenazine with DPPC Liposomes: ATR-IR and 31P NMR Studies [My Copy] Journal of Physical Chemistry B (2009) by Katarzyna C. Boczula, Joanna Szwed, Agata Jaszczyszyn, Kazimierz Gasiorowski, Aleksander Koll posted to ligand-membrane-interactions biomembranes by sobolevnrm on 2009-11-03 12:38:26 as
	Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility [My Copy] Journal of Computational Chemistry by Kenneth W. Borrelli, Benjamin Cossins, Victor Guallar posted to protein-ligand-interactions by sobolevnrm on 2009-11-03 12:38:25 as
	3D-SURFER: software for high-throughput protein surface comparison and analysis [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 21. (Nov 2009), pp. 2843-4. by David La, Juan E. Rodr'iguez, Vishwesh Venkatraman, et al.Bin Li, Lee Sael, Stephen Ueng, Steven Ahrendt, Daisuke Kihara posted to structure software bioinformatics by sobolevnrm on 2009-11-02 12:47:50 as
	A diffusional bimolecular propensity function [My Copy] The Journal of Chemical Physics, Vol. 131, No. 16. (Jan 2009) by Daniel T. Gillespie posted to kinetics diffusion by sobolevnrm on 2009-11-02 12:47:50 as
	Charge correlation effects on ionization of weak polyelectrolytes [My Copy] J Phys-Condens Mat, Vol. 21, No. 42. (Jan 2009) by A. Z. Panagiotopoulos posted to systems statistical-mechanics potentiometric-titration phase-equilibria monte-carlo-simulations model ionic-fluids electrostatics dynamics-simulation counterion-condensation chains beyond-mean-field annealed-polyelectrolytes by sobolevnrm on 2009-11-02 12:47:50 as
	Ion-specific thermodynamics of multicomponent electrolytes: A hybrid HNC/MD approach [My Copy] The Journal of Chemical Physics, Vol. 131, No. 15. (Jan 2009) by Lubov S. Vrbka, Mikael Lund, Immanuel Kalcher, Joachim Dzubiella, Roland R. Netz, Werner Kunz posted to statistical-mechanics solvation integral-equation electrostatics beyond-mean-field by sobolevnrm on 2009-11-02 12:47:50 as
	Construction of an annotated corpus to support biomedical information extraction [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (Oct 2009) by P. Thompson, S. Iqbal, J. McNaught, S. Ananiadou posted to text-mining ontology informatics by sobolevnrm on 2009-11-02 12:47:50 as
	Using the minimum description length principle for global reconstruction of dynamic systems from noisy time series [My Copy] Phys. Rev. E, Vol. 80, No. 4. (Oct 2009) by Ya, D. N. Mukhin, E. M. Loskutov, A. M. Feigen posted to quasiharmonic-models mathematics kinetics by sobolevnrm on 2009-11-02 12:47:50 as
	Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (Oct 2009) by Canan Atilgan, Ali R. Atilgan posted to quasiharmonic-models protein-ligand-interactions molecular-simulation by sobolevnrm on 2009-11-02 12:47:50 as
	“Reverse-Schur” Approach to Optimization with Linear PDE Constraints: Application to Biomolecule Analysis and Design [My Copy] Journal of Chemical Theory and Computation (2009) by Jaydeep P. Bardhan, Michael D. Altman, B. Tidor, Jacob K. White posted to solvation optimization mathematics electrostatics drug-design by sobolevnrm on 2009-11-02 12:47:50 as

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