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blackbart さんのウォッチリスト [1000+ articles]

最近追加された論文の中で blackbart さんの設定条件に合うもののリストです
  • Local Function Conservation in Sequence and Structure Space
    PLoS Comput Biol, Vol. 4, No. 7. (4 July 2008), e1000105.
    by Nils Weinhold, Oliver Sander, Francisco S Domingues, Thomas Lengauer, Ingolf Sommer
    posted to protein_structure protein_sequence function_prediction by barry to the group structural_bioinformatics on 2008-09-08 17:53:09 as read along with 2 people and 2 groups cabbagesofdoom Ema McCammon Bioinformatics
  • Flexible protein alignment and hinge detection
    Proteins: Structure, Function, and Genetics, Vol. 48, No. 2. (2002), pp. 242-256.
    by Maxim Shatsky, Ruth Nussinov, Haim J Wolfson
    posted to structure protein hinge flexibility alignment by nickolay on 2008-09-07 17:31:30 as ***
  • Optimal isotope labelling for NMR protein structure determinations
    Nature, Vol. 440, No. 7080., pp. 52-57.
    by Masatsune Kainosho, Takuya Torizawa, Yuki Iwashita, Tsutomu Terauchi, Akira M Ono, Peter Gã¼ntert
    posted to assignment by lna on 2008-09-03 16:02:08 as **
  • Salt-Mediated Electrostatics in the Association of TATA Binding Proteins to DNA: A Combined Molecular Mechanics/Poisson-Boltzmann Study
    Biophys. J., Vol. 94, No. 12. (15 June 2008), pp. 4634-4645.
    by Johan H Bredenberg, Cristina Russo, Marcia O Fenley
    posted to electrostatics protein_dna solvation by barry to the group structural_bioinformatics on 2008-08-29 19:08:02 as *** along with 1 person and 2 groups sobolevnrm baker-group McCammon
  • notes Rate of Loop Formation in Peptides: A Simulation Study
    Journal of Molecular Biology, Vol. 382, No. 2. (3 October 2008), pp. 556-565.
    by Matthias J Feige, Emanuele Paci
    posted to md_simulation by barry to the group structural_bioinformatics on 2008-08-29 19:03:07 as ** along with 1 group McCammon
  • Agonist-Induced Conformational Changes in Bovine Rhodopsin: Insight into Activation of G-Protein-Coupled Receptors
    Journal of Molecular Biology, Vol. 382, No. 2. (3 October 2008), pp. 539-555.
    by Supriyo Bhattacharya, Spencer E Hall, Nagarajan Vaidehi
    posted to gpcr by barry to the group structural_bioinformatics on 2008-08-29 18:52:34 as *
  • sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank.
    J Chem Inf Model, Vol. 46, No. 2. (r 2006), pp. 717-727.
    by E Kellenberger, P Muller, C Schalon, G Bret, N Foata, D Rognan
    posted to binding database drug ligand protein site by nickolay on 2008-08-27 15:49:30 as read along with 6 people and 1 group BragilMassoud caporaso schlauchi daevans ramensky sim82 biomedical-nlp
  • A simple and fuzzy method to align and compare druggable ligand-binding sites
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Claire Schalon, Jean-Sébastien Surgand, Esther Kellenberger, Didier Rognan
    posted to binding comparison fingerprint ligand protein similarity site by nickolay on 2008-08-27 14:14:35 as read along with 3 people tjimenez bicko willpitt
  • An Enzymatic Atavist Revealed in Dual Pathways for Water Activation
    PLoS Biology, Vol. 6, No. 8. (1 August 2008), e206.
    by Donghong Min, Helen R Josephine, Hongzhi Li, Clemens Lakner, Iain S Macpherson, Gavin J Naylor, David Swofford, Lizbeth Hedstrom, Wei Yang
    posted to imp_dehydrogenase qm_mm by barry to the group structural_bioinformatics on 2008-08-26 18:45:20 as ***** along with 2 groups Bioinformatics McCammon
  • Allostery: an illustrated definition for the 'second secret of life'
    Trends in biochemical sciences (13 August 2008)
    by Aron W W Fenton
    posted to allosteric review by barry to the group structural_bioinformatics on 2008-08-23 20:39:33 as ** along with 1 person and 1 group ruvido McCammon
  • Fast embedding methods for clustering tens of thousands of sequences.
    Computational biology and chemistry, Vol. 32, No. 4. (August 2008), pp. 282-286.
    by G Blackshields, M Larkin, IM Wallace, A Wilm, DG Higgins
    posted to bioinf_methods clustering protein_sequence by barry to the group structural_bioinformatics on 2008-08-23 20:27:35 as **** along with 1 group Bioinformatics
  • A comparison of common programming languages used in bioinformatics
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Mathieu Fourment, Michael Gillings
    posted to programming review by barry to the group structural_bioinformatics on 2008-08-21 18:01:49 as * along with 11 people and 1 group jamselem dullhunk laughcry ibuch urgi sci91078 renatomilani xili03 phoenixzxl jyuh chad_davis Bioinformatics
  • Synergistic approach to improve "alchemical" free energy calculation in rugged energy surface.
    The Journal of chemical physics, Vol. 126, No. 14. (14 April 2007)
    by D Min, H Li, G Li, R Bitetti-Putzer, W Yang
    posted to discussion_free_energy free_energy by barry to the group structural_bioinformatics on 2008-08-20 22:16:00 as ** along with 1 group McCammon
  • Protein structure alignment considering phenotypic plasticity
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i98-104.
    by Gergely Csaba, Fabian Birzele, Ralf Zimmer
    posted to algorithm alignment function prediction structure by nickolay on 2008-08-19 20:53:48 as **
  • Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i105-111.
    by Rafael Najmanovich, Natalja Kurbatova, Janet Thornton
    posted to algorithm alignment atomic binding comparison site structure by nickolay on 2008-08-19 20:51:58 as read along with 2 people neils reyez
  • Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin
    Journal of Molecular Biology, Vol. 381, No. 5. (19 September 2008), pp. 1407-1420.
    by Yang Yang, Haibo Yu, Qiang Cui
    posted to md_simulation molecular_motors motor_model myosin qm by barry to the group structural_bioinformatics on 2008-08-18 20:21:10 as ** along with 1 group Bioinformatics
  • MIPS: a database for genomes and protein sequences.
    Nucleic Acids Res, Vol. 30, No. 1. (1 January 2002), pp. 31-34.
    by HW Mewes, D Frishman, U Güldener, G Mannhaupt, K Mayer, M Mokrejs, B Morgenstern, M Münsterkötter, S Rudd, B Weil
    posted to no-tag by dgruiz on 2008-08-08 14:07:42 as ** along with 3 people and 1 group irenas chad_davis dylanwalker dbk-lab
  • ChemmineR: A Compound Mining Framework for R.
    Bioinformatics (Oxford, England) (2 July 2008)
    by Yiqun Cao, Anna Charisi, Li-Chang C Cheng, Tao Jiang, Thomas Girke
    posted to cheminformatics data mining r statistics by nickolay on 2008-08-05 18:20:45 as *** along with 2 people jyuh girschick
  • The importance of stupidity in scientific research
    J Cell Sci, Vol. 121, No. 11. (1 June 2008), 1771.
    by Martin A Schwartz
    posted to advice career essay by barry to the group structural_bioinformatics on 2008-07-16 22:25:46 as **** along with 5 people and 1 group dullhunk arindrartow ibuch casutton jporternj McCammon
  • Object-oriented design patterns in Fortran 90/95: mazev1, mazev2 and mazev3
    Computer Physics Communications, Vol. 178, No. 8. (15 April 2008), pp. 611-620.
    by Viktor K Decyk, Henry J Gardner
    posted to fortran by lna on 2008-07-16 10:16:19 as ** along with 1 person peterheng
  • Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures.
    Proteins (1 May 2008)
    by Mizuki Morita, Shugo Nakamura, Kentaro Shimizu
    posted to apo energy-based ligand prediction protein strcuture by nickolay on 2008-07-14 20:02:25 as **
  • From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase
    Journal of Molecular Biology, Vol. 359, No. 4. (16 June 2006), pp. 1023-1044.
    by Daniel Kuhn, Nils Weskamp, Stefan Schmitt, Eyke Hullermeier, Gerhard Klebe
    posted to algorithm binding classifier comparison site by nickolay on 2008-07-08 15:03:05 as ** along with 2 people apaydin stege
  • Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family.
    Bioinformatics, Vol. 23, No. 2. (15 January 2007)
    by RJ Najmanovich, A Allali-Hassani, RJ Morris, L Dombrovsky, PW Pan, M Vedadi, AN Plotnikov, A Edwards, C Arrowsmith, JM Thornton
    posted to to-be-tagged by nickolay on 2008-07-08 14:47:52 as ** along with 1 person grottenolm
  • LigProf: A simple tool for in silico prediction of ligand-binding sites
    Journal of Molecular Modeling, Vol. 13, No. 3. (March 2007), pp. 445-455.
    by Koczyk, Grzegorz, Wyrwicz, Lucjan, Rychlewski, Leszek
    posted to binding comparison motif server site software by nickolay on 2008-07-08 14:38:30 as **
  • Do Structurally Similar Ligands Bind in a Similar Fashion?
    J. Med. Chem., Vol. 49, No. 23. (16 November 2006), pp. 6716-6725.
    by J Bostrom, A Hogner, S Schmitt
    posted to binding comparison ligand-based site by nickolay on 2008-07-08 14:24:45 as read along with 3 people schlauchi daevans superpyrin
  • Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors.
    Proteins, Vol. 51, No. 3. (15 May 2003), pp. 423-433.
    by CN Cavasotto, AJ Orry, RA Abagyan
    posted to algorithm binding gpcr identification site small by nickolay on 2008-07-08 14:04:41 as **
  • Comprehensive identification of "druggable" protein ligand binding sites.
    Genome Inform Ser Workshop Genome Inform, Vol. 15, No. 2. (2004), pp. 31-41.
    by J An, M Totrov, R Abagyan
    posted to algorithm binding identification site software by nickolay on 2008-07-08 13:56:28 as ** along with 1 person sriram_s
  • Protein-protein binding is often associated with changes in protonation state
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Aaron C Mason, Jan H Jensen
    posted to binding protein-protein titration by barry to the group structural_bioinformatics on 2008-07-08 01:26:01 as ** along with 4 people and 2 groups bicko chad_davis sobolevnrm RamuAnandakrishnan baker-group McCammon
  • X-ray structure of a prokaryotic pentameric ligand-gated ion channel
    Nature (05 March 2008)
    by Ricarda JC Hilf, Raimund Dutzler
    posted to achr ion_channel by barry to the group structural_bioinformatics on 2008-07-08 01:24:17 as ** along with 2 people and 1 group neils jmccammon McCammon
  • How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach
    J. Chem. Theory Comput., Vol. 4, No. 4. (8 April 2008), pp. 626-636.
    by Hugh Nymeyer
    posted to md_simulation replica_exchange by barry to the group structural_bioinformatics on 2008-07-08 01:17:17 as ** along with 3 people and 2 groups agrossfield sobolevnrm loison baker-group McCammon
  • Novel Method for Probing the Specificity Binding Profile of Ligands: Applications to HIV Protease
    Chemical Biology & Drug Design, Vol. 71, No. 5. (2008), pp. 387-407.
    by Woody Sherman, Bruce Tidor
    posted to drug_discovery protein_ligand by barry to the group structural_bioinformatics on 2008-07-08 01:14:49 as ** along with 1 person and 1 group jmccammon McCammon
  • Calculation of protein-ligand binding free energy by using a polarizable potential
    Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6290-6295.
    by Dian Jiao, Pavel A Golubkov, Thomas A Darden, Pengyu Ren
    posted to binding free_energy md_simulation protein-ligand by barry to the group structural_bioinformatics on 2008-07-08 01:12:03 as ** along with 3 people and 2 groups jmccammon biehl sobolevnrm baker-group McCammon
  • From the Cover: A dry ligand-binding cavity in a solvated protein
    Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6296-6301.
    by Johan Qvist, Monika Davidovic, Donald Hamelberg, Bertil Halle
    posted to free_energy md_simulation protein-ligand solvation by barry to the group structural_bioinformatics on 2008-07-08 01:11:30 as ** along with 2 people and 2 groups jmccammon sobolevnrm McCammon baker-group
  • Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution
    Science, Vol. 320, No. 5882. (13 June 2008), pp. 1471-1475.
    by Oliver F Lange, Nils-Alexander Lakomek, Christophe Fares, Gunnar F Schroder, Korvin F Walter, Stefan Becker, Jens Meiler, Helmut Grubmuller, Christian Griesinger, Bert L de Groot
    posted to binding protein-protein by barry to the group structural_bioinformatics on 2008-07-08 00:52:29 as ** along with 4 people and 2 groups paulschlesinger higueruelo jmccammon cchang McCammon group
  • The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff
    Journal of Computational Chemistry, Vol. 29, No. 12. (2008), pp. 1970-1981.
    by Magdalena Gruziel, Pawel Grochowski, Joanna Trylska
    posted to electrostatics by barry to the group structural_bioinformatics on 2008-07-08 00:51:34 as ** along with 1 person and 1 group RamuAnandakrishnan McCammon
  • Protein model refinement using an optimized physics-based all-atom force field
    Proceedings of the National Academy of Sciences, Vol. 105, No. 24. (17 June 2008), pp. 8268-8273.
    by Anna Jagielska, Liliana Wroblewska, Jeffrey Skolnick
    posted to coarse_grain replica_exchange by barry to the group structural_bioinformatics on 2008-07-08 00:49:57 as ** along with 3 people and 1 group RamuAnandakrishnan jmccammon zwang McCammon
  • notes BIOCHEMISTRY: Metamorphic Proteins
    Science, Vol. 320, No. 5884. (27 June 2008), pp. 1725-1726.
    by Alexey G Murzin
    posted to protein_dynamics protein_structure review by barry to the group structural_bioinformatics on 2008-07-07 23:55:32 as ** along with 1 person marck
  • Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles.
    International journal of biological macromolecules (21 May 2008)
    by Petras J J Kundrotas, Marc F F Lensink, Emil Alexov
    posted to algorithm alignment binding complexes data_integration modelling proj_assembly structure by chad_davis to the group structural_bioinformatics on 2008-06-29 11:15:36 as **
  • Cell-free translation reconstituted with purified components.
    Nature biotechnology, Vol. 19, No. 8. (August 2001), pp. 751-755.
    by Y Shimizu, A Inoue, Y Tomari, T Suzuki, T Yokogawa, K Nishikawa, T Ueda
    posted to dhfr by lna on 2008-06-27 15:23:30 as **
  • Optimization of multiple-sequence alignment based on multiple-structure alignment.
    Proteins, Vol. 62, No. 1. (1 January 2006), pp. 209-217.
    by M Shatsky, R Nussinov, HJ Wolfson
    posted to alignment printed protein sequence structure wrmsd by nickolay on 2008-06-11 19:53:47 as ***
  • 3DCoffee: combining protein sequences and structures within multiple sequence alignments.
    J Mol Biol, Vol. 340, No. 2. (2 July 2004), pp. 385-395.
    by O O'Sullivan, K Suhre, C Abergel, DG Higgins, C Notredame
    posted to alignment printed protein sequence structure wrmsd by nickolay on 2008-06-11 19:49:44 as *** along with 4 people and 4 groups ana jwm analogAI edvin structural_bioinformatics Radiation_Damage Stressosome Bioinformatics
  • Pairwise iterative superposition of distantly related proteins and assessment of the significance of 3-D structural similarity
    Protein Eng., Vol. 9, No. 12. (1 December 1996), pp. 1093-1101.
    by Alex C May
    posted to alignment iterative printed protein structure wrmsd by nickolay on 2008-06-11 19:42:10 as ***
  • Mapping the Nucleotide and Isoform-Dependent Structural and Dynamical Features of Ras Proteins
    Structure, Vol. 16, No. 6. (11 June 2008), pp. 885-896.
    by Alemayehu A Gorfe, Barry J Grant, Andrew J Mccammon
    posted to md_simulation mine ntpases pca protein_dynamics protein_structure ras by barry to the group structural_bioinformatics on 2008-06-10 22:34:01 as read along with 1 group Bioinformatics
  • Searching for functional sites in protein structures
    Current Opinion in Chemical Biology, Vol. 8, No. 1. (February 2004), pp. 3-7.
    by Susan Jones, Janet M Thornton
    posted to function printed protein read review search site structure by nickolay on 2008-06-10 19:06:59 as *** along with 6 people and 1 group BragilMassoud LeightonP chrn Einat proteasome jwm structural_bioinformatics
  • Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy.
    Journal of structural biology, Vol. 149, No. 2. (February 2005), pp. 191-203.
    by M Topf, ML Baker, B John, W Chiu, A Sali
    posted to algorithm alignment complexes data_integration em modelling proj_assembly structure by chad_davis to the group structural_bioinformatics on 2008-05-28 10:37:06 as **
  • notes Structural modeling of protein interactions by analogy: application to PSD-95.
    PLoS Comput Biol, Vol. 2, No. 11. (10 November 2006)
    by D Korkin, FP Davis, F Alber, T Luong, MY Shen, V Lucic, MB Kennedy, A Sali
    posted to algorithm binding complexes docking modelling proj_assembly structure by chad_davis to the group structural_bioinformatics on 2008-05-28 10:32:13 as *** along with 1 person bicko
  • High-throughput analysis of protein NMR spectra
    Progress in Nuclear Magnetic Resonance Spectroscopy, Vol. 46, No. 2-3. (30 May 2005), pp. 109-129.
    by Daniel Malmodin, Martin Billeter
    posted to assignment by lna on 2008-05-09 14:31:17 as **
  • MONTE: An automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins
    Journal of Biomolecular NMR, Vol. 25, No. 1. (January 2003), pp. 1-9.
    by Kevin T Hitchens, Jonathan A Lukin, Yiping Zhan, Scott A Mccallum, Gordon S Rule
    posted to assignment by lna on 2008-05-09 12:34:40 as **
  • Automated sequence-specific NMR assignment of homologous proteins using the program GARANT
    Journal of Biomolecular NMR, Vol. 7, No. 3. (1 May 1996), pp. 207-213.
    by Christian Bartels, Martin Billeter, Peter Güntert, Kurt Wüthrich
    posted to assignment garant by lna on 2008-05-08 09:23:03 as **
  • Distribution of chemical shifts in 1H nuclear magnetic resonance spectra of proteins
    Journal of Magnetic Resonance (1969), Vol. 76, No. 1. (January 1988), pp. 87-99.
    by Karl-Heinz Groß, Hans R Kalbitzer
    posted to assignment garant by lna on 2008-05-08 09:08:02 as **
    • 注: このページを引用する時は次のURLでどうぞ: http://www.citeulike.org/user/blackbart/watchlist

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