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sobolevnrms Kim [47 articles]

Recent papers posted to sobolevnrms library by the author Kim. You can also see everyones Kim.
  • Release of hydrophobic molecules from polymer micelles into cell membranes revealed by Forster resonance energy transfer imaging
    Proceedings of the National Academy of Sciences, Vol. 105, No. 18. (6 May 2008), pp. 6596-6601.
    by Hongtao Chen, Sungwon Kim, Li Li, Shuyi Wang, Kinam Park, Ji-Xin Cheng
    posted to nanotech drug_design biomembranes by sobolevnrm on 2008-06-20 11:25:39 as read along with 1 group baker-group
  • PROMALS3D: a tool for multiple protein sequence and structure alignments.
    Nucleic Acids Res (20 February 2008)
    by Jimin Pei, Bong-Hyun H Kim, Nick V V Grishin
    posted to software bioinformatics by sobolevnrm on 2008-05-21 11:38:08 as read along with 2 people and 1 group newton1234 sunhwan baker-group
  • Analysis of the residue-residue coevolution network and the functionally important residues in proteins
    Proteins (in press)
    by BC Lee, K Park, D Kim
    posted to correlated_mutations bioinformatics by sobolevnrm on 2008-05-15 11:44:28 as read along with 1 group baker-group
  • PDBML: the representation of archival macromolecular structure data in XML
    Bioinformatics, Vol. 21, No. 7. (01 April 2005), pp. 988-992.
    by Westbrook John, Ito Nobutoshi, Nakamura Haruki, Henrick Kim, M Berman
    posted to structure database bioinformatics by sobolevnrm on 2008-05-05 21:23:40 as read along with 1 person and 1 group neils baker-group
  • CHARMM-GUI: A web-based graphical user interface for CHARMM
    Journal of Computational Chemistry (in press)
    by S Jo, T Kim, VG Iyer, W Im
    posted to software molecular_simulation electrostatics database by sobolevnrm on 2008-04-28 11:28:35 as read along with 1 group baker-group
  • Analysis of the residue-residue coevolution network and the functionally important residues in proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Byung-Chul Lee, Keunwan Park, Dongsup Kim
    posted to bioinformatics correlated_mutations by sobolevnrm on 2008-03-11 11:40:30 as read along with 7 people and 2 groups wilbur friendpine barry neils mingzhi penpen926 scienbox structural_bioinformatics baker-group
  • Protein Sequence- and pH-Dependent Hydration Probed by Terahertz Spectroscopy
    J. Am. Chem. Soc., Vol. 130, No. 8. (27 February 2008), pp. 2374-2375.
    by S Ebbinghaus, SJ Kim, M Heyden, X Yu, M Gruebele, DM Leitner, M Havenith
    posted to kinetics protein_folding solvation by sobolevnrm on 2008-03-03 11:46:31 as read along with 1 group baker-group
  • Multi-reservoir device for detecting a soluble cancer biomarker
    Lab Chip, Vol. 7 (2007), pp. 288-1293.
    by Karen D Daniel, Grace Y Kim, Christophoros C Vassiliou, Farzad Jalali-Yazdi, Robert Langer, Michael J Cima
    posted to cancer ccne drug_design nanotech by sobolevnrm on 2008-02-22 11:56:18 as read along with 1 person ml115
  • Magnetic Relaxation Switch Detection of Human Chorionic Gonadotrophin
    Bioconjugate Chem., Vol. 18, No. 6. (21 November 2007), pp. 2024-2028.
    by Grace Y Kim, Lee Josephson, Robert Langer, Michael J Cima
    posted to cancer ccne imaging nanotech by sobolevnrm on 2008-02-22 11:55:42 as read along with 1 person and 1 group ml115 baker-group
  • Corpus annotation for mining biomedical events from literature
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Jin D Kim, Tomoko Ohta, Jun'ichi Tsujii
    posted to bioinformatics by sobolevnrm on 2008-02-15 12:19:11 as read along with 8 people and 2 groups jyuh yas dullhunk bhaddow gmonce vlachmore wchapman mircea baker-group dbmi-nlp
  • An extended dynamical hydration shell around proteins.
    Proc Natl Acad Sci U S A, Vol. 104, No. 52. (26 December 2007), pp. 20749-20752.
    by S Ebbinghaus, SJ Kim, M Heyden, X Yu, U Heugen, M Gruebele, DM Leitner, M Havenith
    posted to diffusion experimental_methodology kinetics molecular_dynamics solvation by sobolevnrm on 2008-01-31 12:59:41 as read along with 1 person and 1 group choonpeng baker-group
  • An integrated system for studying residue coevolution in proteins
    Bioinformatics, Vol. 24, No. 2. (15 January 2008), pp. 290-292.
    by Kevin Y Yip, Prianka Patel, Philip M Kim, Donald M Engelman, Drew Mcdermott, Mark Gerstein
    posted to bioinformatics correlated_mutations by sobolevnrm on 2008-01-14 12:28:24 as read along with 3 people and 1 group ca3295 chrys friendpine baker-group
  • Coarse-grained models for simulations of multi-protein complexes: Application to ubiquitin binding
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Young C Kim, Gerhard Hummer
    posted to multiscale protein-protein_interactions by sobolevnrm on 2008-01-03 12:50:28 as read along with 3 people and 3 groups barry iantunbridge mikaellund structural_bioinformatics Bioinformatics baker-group
  • Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations
    PLoS ONE, Vol. 2, No. 9., e880.
    by S Jo, T Kim, W Im
    posted to biomembranes molecular_dynamics molecular_simulation software by sobolevnrm on 2007-12-21 12:36:10 as read along with 1 group baker-group
  • Binding similarity network of ligand
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Keunwan Park, Dongsup Kim
    posted to bioinformatics protein-ligand_interactions by sobolevnrm on 2007-12-20 12:31:21 as read along with 1 group baker-group
  • Bidirectional mapping between self-consistent field theory and molecular dynamics: Application to immiscible homopolymer blends
    The Journal of Chemical Physics, Vol. 127, No. 14. (2007)
    by Thomas D Sewell, Kim, Dmitry Bedrov, Grant D Smith, Russell B Thompson
    posted to molecular_simulation multiscale by sobolevnrm on 2007-10-22 12:50:12 as read along with 1 group baker-group
  • Nanotechnology Applications in Cancer
    Annual Review of Biomedical Engineering, Vol. 9 (2007), pp. 257-88.
    by S Nie, Y Xing, GJ Kim, JW Simons
    posted to drug_design nanotech by sobolevnrm on 2007-07-26 13:34:06 as read along with 1 group baker-group
  • Biodistribution and anti-tumor efficacy of doxorubicin loaded glycol-chitosan nanoaggregates by EPR effect
    Journal of Controlled Release, Vol. 91, No. 1-2. (2003), pp. 135-45.
    by YJ Son, JS Jang, YW Cho, H Chung, RW Park, IC Kwon, IS Kim, JY Park, SB Seo, CR Park, SY Jeong
    posted to drug_design nanotech by sobolevnrm on 2007-05-25 14:38:05 as read along with 1 group baker-group
  • Ligand binding and allostery can emerge simultaneously
    Protein Science, Vol. 16, No. 5. (2007), pp. 929-37.
    by J Liang, JR Kim, JT Boock, TJ Mansell, M Ostermeier
    posted to allostery protein_engineering by sobolevnrm on 2007-05-25 14:37:08 as read along with 1 group baker-group
  • PROMALS web server for accurate multiple protein sequence alignments
    Nucleic Acids Research (in press)
    by J Pei, BH Kim, M Tang, NV Grishin
    posted to bioinformatics software by sobolevnrm on 2007-05-25 14:37:08 as read along with 1 group baker-group
  • Peptide insertion, positioning, and stabilization in a membrane: Insight from an all-atom molecular dynamics simulation
    Biopolymers (in press)
    by A Babakhani, AA Gorfe, J Gullingsrud, JE Kim, JA Mccammon
    posted to biomembranes by sobolevnrm on 2007-05-25 14:36:28 as read along with 1 group baker-group
  • Diffusion influence on MichaelisâMenten kinetics: II. The low substrate concentration limit
    Journal of Physics: Condensed Matter, Vol. 19, No. 6. (2007)
    by H Kim, KJ Shin
    posted to diffusion kinetics by sobolevnrm on 2007-05-25 14:36:05 as read along with 1 group baker-group
  • Motifs for molecular recognition exploiting hydrophobic enclosure in proteinâligand binding
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 3. (2007), pp. 808-13.
    by T Young, R Abel, B Kim, BJ Berne, RA Friesner
    posted to protein-ligand_interactions protein-protein_interactions solvation by sobolevnrm on 2007-05-25 14:36:05 as read along with 1 group baker-group
  • Static and dynamic correlations in a charged membrane
    Physical Review E, Vol. 74 (2006)
    by W Sung, E Choi, YW Kim
    posted to biomembranes electrostatics by sobolevnrm on 2007-05-25 14:23:20 as read along with 1 group baker-group
  • PROTEIN S-NITROSYLATION: PURVIEW AND PARAMETERS
    Nature Reviews Molecular Cell Biology, Vol. 6, No. 2. (2005), pp. 150-66.
    by DT Hess, A Matsumoto, SO Kim, HE Marshall, JS Stamler
    posted to diffusion nitric_oxide by sobolevnrm on 2007-05-25 14:23:19 as read along with 1 group baker-group
  • A Brownian dynamics-finite element method for simulating DNA electrophoresis in nonhomogeneous electric fields
    Journal of Chemical Physics, Vol. 125 (2006)
    by JM Kim, PS Doyle
    posted to diffusion mathematics multiscale by sobolevnrm on 2007-05-25 14:23:18 as read along with 1 group baker-group
  • UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models
    Nucleic Acids Research, Vol. 34 (2006), pp. W57-W62.
    by Y Jang, JI Jeong, MK Kim
    posted to 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
  • Mechanisms of viral membrane fusion and its inhibition
    Annual Review of Biochemistry, Vol. 70 (2001), pp. 777-810.
    by DM Eckert, PS Kim
    posted to biomembranes by sobolevnrm on 2007-05-25 14:23:17 as read along with 1 group baker-group
  • Inferring functional information from domain co-evolution
    Bioinformatics, Vol. 22, No. 1. (2006), pp. 40-9.
    by Y Kim, M Koyutã¼rk, U Topkara, A Grama, S Subramaniam
    posted to correlated_mutations by sobolevnrm on 2007-05-25 14:19:26 as read along with 1 group baker-group
  • Surface-tension-driven microactuation based on continuous electrowetting
    Journal of Microelectromechanical Systems, Vol. 9, No. 2. (2000), pp. 171-80.
    by J Lee, CJ Kim
    posted to biomembranes electrostatics nanotech by sobolevnrm on 2007-05-25 14:19:04 as read along with 1 group baker-group
  • On the temperature and pressure dependences of cavities in the dielectric continuum picture
    Journal of Chemical Physics, Vol. 123 (2005)
    by SR Manjari, HJ Kim
    posted to electrostatics solvation by sobolevnrm on 2007-05-25 14:19:04 as read along with 1 group baker-group
  • Ion Atmosphere of Three-Way Junction Nucleic Acid
    Journal of Physical Chemistry B, Vol. 109, No. 45. (2005), pp. 21369-74.
    by U Mohanty, A Spasic, HD Kim, S Chu
    posted to electrostatics nucleic_acids by sobolevnrm on 2007-05-25 14:19:04 as read along with 1 group baker-group
  • Interactions of Liquid Crystal-Forming Molecules with Phospholipid Bilayers Studied by Molecular Dynamics Simulations
    Biophysical Journal, Vol. 89, No. 5. (2005), pp. 3141-58.
    by EB Kim, N Lockwood, M Chopra, O Guzmã!'n, NL Abbot, JJ de Pablo
    posted to biomembranes by sobolevnrm on 2007-05-25 14:19:03 as read along with 1 group baker-group
  • Extracellular Space Diffusion in Central Nervous System: Anisotropic Diffusion Measured by Elliptical Surface Photobleaching
    Biophysical Journal, Vol. 89, No. 5. (2005), pp. 3660-8.
    by MC Papadopoulos, JK Kim, AS Verkman
    posted to diffusion by sobolevnrm on 2007-05-25 14:19:03 as read along with 1 group baker-group
  • Replica exchange with solute tempering: A method for sampling biological systems in explicit water
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 39. (2005), pp. 13749-54.
    by P Liu, B Kim, RA Friesner, BJ Berne
    posted to molecular_simulation solvation by sobolevnrm on 2007-05-25 14:18:43 as read along with 1 group baker-group
  • Charge inversion on membranes induced by multivalent-counterion fluctuations
    Journal of Physics: Condensed Matter, Vol. 17, No. 31. (2005), pp. S2943-9.
    by YW Kim, W Sung
    posted to biomembranes electrostatics statistical_mechanics by sobolevnrm on 2007-05-25 14:18:24 as read along with 1 group baker-group
  • Rigid-Cluster Models of Conformational Transitions in Macromolecular Machines and Assemblies
    Biophysical Journal, Vol. 89, No. 1. (2005), pp. 43-55.
    by MK Kim, RL Jernigan, GS Chirikjian
    posted to 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
  • Global mapping of the protein structure space and application in structure-based inference of protein function
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 10. (2005), pp. 3651-6.
    by J Hou, SR Jun, C Zhang, SH Kim
    posted to bioinformatics structure by sobolevnrm on 2007-05-25 14:15:43 as read along with 1 group baker-group
  • tRNA dynamics on the ribosome during translation
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 35. (2004), pp. 12893-8.
    by SC Blanchard, HD Kim, Jr, JD Puglisi, S Chu
    posted to nucleic_acids by sobolevnrm on 2007-05-25 14:13:08 as read along with 1 group baker-group
  • Long-range allosteric transitions in carbamoyl phosphate synthetase
    Protein Science, Vol. 13, No. 9. (2004), pp. 2398-2405.
    by JB Thoden, X Huang, J Kim, FM Raushel, HM Holden
    posted to allostery by sobolevnrm on 2007-05-25 14:12:48 as read along with 1 group baker-group
  • A Model of the Closed Form of the Nicotinic Acetylcholine Receptor M2 Channel Pore
    Biophysical Journal, Vol. 87, No. 2. (2004), pp. 792-9.
    by S Kim, AK Chamberlain, JU Bowie
    posted to neuromuscular_junctions by sobolevnrm on 2007-05-25 14:12:47 as read along with 1 group baker-group
  • Protein structure prediction and analysis using the Robetta server
    Nucleic Acids Research, Vol. 32, No. S2. (2004), pp. W526-W531.
    by DE Kim, D Chivian, D Baker
    posted to software structure_prediction by sobolevnrm on 2007-05-25 14:10:46 as read along with 1 group baker-group
  • RAG: RNA-As-Graphs databaseâconcepts, analysis, and features
    Bioinformatics, Vol. 20, No. 8. (2004), pp. 1285-91.
    by HH Gan, D Fera, J Zorn, N Shiffeldrim, M Tang, U Laserson, N Kim, T Schlick
    posted to bioinformatics database nucleic_acids by sobolevnrm on 2007-05-25 14:09:50 as read along with 1 group baker-group
  • Elastic models of conformational transitions in macromolecules
    Journal of Molecular Graphics and Modelling, Vol. 21, No. 2. (2004), pp. 151-160.
    by MK Kim, GS Chirikjian, RL Jernigan
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-05-25 14:07:52 as read along with 1 group baker-group
  • Elastic models of conformational transitions in macromolecules
    Journal of Molecular Graphics and Modelling, Vol. 21, No. 2. (2004), pp. 151-160.
    by MK Kim, GS Chirikjian, RL Jernigan
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-05-25 14:07:52 as read along with 1 group baker-group
  • Local feature frequency profile: A method to measure structural similarity in proteins
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 11. (2004), pp. 3797-3802.
    by IG Choi, J Kwon, SH Kim
    posted to bioinformatics by sobolevnrm on 2007-05-25 14:05:06 as read along with 1 group baker-group
  • Cloning, mutagenesis, and expression of the acetylcholinesterase gene from a strain of Musca domestica; the change from a drug-resistant to a sensitive enzyme
    Mol Cells, Vol. 15, No. 2. (2003), pp. 208-15.
    by CS Kim, WT Kim, KS Boo, SI Kim
    posted to acetylcholinesterase nerve_agents by sobolevnrm on 2007-05-25 13:56:20 as read along with 1 group baker-group
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