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marck's library [150 articles]

Recent papers added to marck's library.
  • What are artificial neural networks?
    Nature Biotechnology, Vol. 26, No. 2., pp. 195-197.
    by Anders Krogh
    posted to ann by marck on 2008-08-16 02:00:47 as ** along with 12 people bertelsen mjoach ale adacier jfr Yanno jyuh dullhunk zwang cabbagezs asddd sci91078
  • Model-based prediction of sequence alignment quality
    Bioinformatics (4 August 2008), btn414.
    by Virpi Ahola, Tero Aittokallio, Mauno Vihinen, Esa Uusipaikka
    posted to msa-auto-assessing by marck on 2008-08-06 07:21:25 as **
  • Powerful fusion: PSI-BLAST and consensus sequences
    Bioinformatics (4 August 2008), btn384.
    by Dariusz Przybylski, Burkhard Rost
    posted to psiblast-variant by marck on 2008-08-06 07:16:22 as **
  • VADAR: a web server for quantitative evaluation of protein structure quality
    Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3316-3319.
    by Leigh Willard, Anuj Ranjan, Haiyan Zhang, Hassan Monzavi, Robert F Boyko, Brian D Sykes, David S Wishart
    posted to webserver structure-quality by marck on 2008-08-04 08:35:54 as **
  • Cytoprophet: A Cytoscape plug-in for protein and domain interaction networks inference
    Bioinformatics (24 July 2008), btn380.
    by Faruck Morcos, Charles Lamanna, Marcin Sikora, Jesus Izaguirre
    posted to domain-interaction by marck on 2008-07-30 09:27:31 as ** along with 1 person phoenixzxl
  • Assembly reflects evolution of protein complexes
    Nature (18 June 2008)
    by Emmanuel D Levy, Elisabetta B Erba, Carol V Robinson, Sarah A Teichmann
    posted to protein-interaction-theory evolution complex-assembly by marck on 2008-07-19 06:18:51 as ** along with 7 people phoenixzxl faion psique zwang jwm neils paulschlesinger
  • Dichotomies between computational and mathematical models
    Nature Biotechnology, Vol. 26, No. 7., pp. 737-738.
    by Anthony C Hunt, Glen EP Ropella, Sunwoo Park, Jesse Engelberg
    posted to math by marck on 2008-07-19 03:55:40 as **
  • The Origins of Specificity in Polyketide Synthase Protein Interactions
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e186.
    by Mukund Thattai, Yoram Burak, Boris I Shraiman
    posted to specificity protein-interaction-theory by marck on 2008-07-15 00:59:03 as ** along with 2 people zwang phoenixzxl
  • Design of Multi-Specificity in Protein Interfaces
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e164.
    by Elisabeth L Humphris, Tanja Kortemme
    posted to protein-protein-interface protein-engineering interaction-specificity by marck on 2008-07-11 04:00:01 as ** along with 6 people and 3 groups phoenixzxl jwm bicko Einat dpollard Scis0000002 structural_bioinformatics Bioinformatics EisenLab
  • Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network.
    Genome research (16 April 2008)
    by Ivan Iossifov, Tian Zheng, Miron Baron, T Conrad C Gilliam, Andrey Rzhetsky
    posted to integrated genetic-interaction by marck on 2008-07-11 03:59:29 as ** along with 1 person jyuh
  • Evaluating conformational changes in protein structures binding RNA.
    Proteins, Vol. 70, No. 4. (March 2008), pp. 1518-1526.
    by JJ Ellis, S Jones
    posted to rna-protein-interactions by marck on 2008-07-10 05:49:56 as **
  • Bioinformatic method for protein thermal stabilization by structural entropy optimization -- Bae et al., 10.1073/pnas.0800938105 -- Proceedings of the National Academy of Sciences
    posted to structure protein-engineering by marck on 2008-07-09 02:18:30 as **
  • Setting the standard in synthetic biology
    Nat Biotech, Vol. 26, No. 7. (July 2008), pp. 771-774.
    by Adam Arkin
    posted to synthetic-biology by marck on 2008-07-09 02:15:29 as ** along with 3 people austin grahamc dbikard
  • Refinement and standardization of synthetic biological parts and devices
    Nat Biotech, Vol. 26, No. 7. (July 2008), pp. 787-793.
    by Barry Canton, Anna Labno, Drew Endy
    posted to synthetic-biology by marck on 2008-07-09 02:15:07 as ** along with 2 people grahamc austin
  • Extracting Sequence Motifs and the Phylogenetic Features of SNARE-Dependent Membrane Traffic
    Traffic, Vol. 7, No. 8. (August 2006), pp. 1104-1118.
    by Yoshizawa, C Akiyasu, Kawashima, Shuichi, Okuda, Shujiro, Fujita, Masashi, Itoh, Masumi, Moriya, Yuki, Hattori, Masahiro, Kanehisa, Minoru
    posted to snare coiled-coil by marck on 2008-07-07 01:39:59 as **
  • Bimolecular fluorescence complementation (BiFC) analysis of protein interactions in Caenorhabditis elegans.
    Methods (San Diego, Calif.) (26 June 2008)
    by Susan M M Hiatt, Y John J Shyu, Holli M M Duren, Chang-Deng D Hu
    posted to experiment-interactions bifc by marck on 2008-07-07 01:34:15 as **
  • Quantitative Measurements of Protein Interactions in a Crowded Cellular Environment
    Anal. Chem. (3 July 2008)
    by Edwin Li, Jesse Placone, Mikhail Merzlyakov, Kalina Hristova
    posted to experiment-interactions by marck on 2008-07-05 05:45:01 as ** along with 1 person brianb
  • Increasing the reliability of protein interactomes.
    Drug discovery today (30 June 2008)
    by Hon Nian N Chua, Limsoon Wong
    posted to protein-interaction-network by marck on 2008-07-05 02:46:54 as ** along with 1 person jyuh
  • Phylogenetic Signal in the Eukaryotic Tree of Life
    Science, Vol. 321, No. 5885. (4 July 2008), pp. 121-123.
    by Michael J Sanderson
    posted to phylogenetic by marck on 2008-07-04 03:52:27 as ** along with 7 people and 3 groups jlgreen aprasad stajich djkt gulsacan dchughes caseybrown iSEEM Green Lab Berkeley Mycology
  • Protein multiple sequence alignment.
    Methods in molecular biology (Clifton, N.J.), Vol. 484 (2008), pp. 379-413.
    by CB Do, K Katoh
    posted to msa by marck on 2008-07-03 10:58:56 as **
  • Ykt6p Is a Multifunctional Yeast R-SNARE That Is Required for Multiple Membrane Transport Pathways to the Vacuole
    Mol. Biol. Cell, Vol. 14, No. 5. (1 May 2003), pp. 1868-1881.
    by Youngseok Kweon, Anca Rothe, Elizabeth Conibear, Tom H Stevens
    posted to snare by marck on 2008-07-02 06:10:13 as **
  • Functions of SNAREs in intracellular membrane fusion and lipid bilayer mixing
    J Cell Sci, Vol. 118, No. 17. (1 September 2005), pp. 3819-3828.
    by Christian Ungermann, Dieter Langosch
    posted to snare by marck on 2008-07-02 06:09:44 as **
  • Yeast Golgi SNARE interactions are promiscuous
    J Cell Sci, Vol. 113, No. 1. (1 January 2000), pp. 145-152.
    by MM Tsui, DK Banfield
    posted to specificity snare by marck on 2008-07-02 06:09:21 as **
  • i-SNAREs: inhibitory SNAREs that fine-tune the specificity of membrane fusion
    J. Cell Biol., Vol. 164, No. 1. (5 January 2004), pp. 79-88.
    by Oleg Varlamov, Allen Volchuk, Vahid Rahimian, Claudia A Doege, Fabienne Paumet, William S Eng, Nancy Arango, Francesco Parlati, Mariella Ravazzola, Lelio Orci, Thomas H Sollner, James E Rothman
    posted to snare by marck on 2008-07-02 06:06:14 as **
  • What is the role of SNARE proteins in membrane fusion?
    Am J Physiol Cell Physiol, Vol. 285, No. 2. (1 August 2003), pp. C237-249.
    by Joseph G Duman, John G Forte
    posted to snare by marck on 2008-07-02 06:05:43 as **
  • SNARE Interactions Are Not Selective. IMPLICATIONS FOR MEMBRANE FUSION SPECIFICITY
    J. Biol. Chem., Vol. 274, No. 9. (26 February 1999), pp. 5649-5653.
    by Bin Yang, Lino Gonzalez, Rytis Prekeris, Martin Steegmaier, Raj J Advani, Richard H Scheller
    posted to specificity snare by marck on 2008-07-02 05:42:19 as **
  • Mixed and Non-cognate SNARE Complexes. CHARACTERIZATION OF ASSEMBLY AND BIOPHYSICAL PROPERTIES
    J. Biol. Chem., Vol. 274, No. 22. (28 May 1999), pp. 15440-15446.
    by Dirk Fasshauer, Wolfram Antonin, Martin Margittai, Stefan Pabst, Reinhard Jahn
    posted to specificity snare by marck on 2008-07-02 05:39:14 as **
  • Human disease: Joining the dots from SNPs to proteins
    Nat Rev Genet, Vol. 9, No. 7. (July 2008), pp. 496-496.
    by Louisa Flintoft
    posted to snp by marck on 2008-07-02 03:43:21 as ** along with 1 person cabbagesofdoom
  • Co-Evolving Motions at Protein−Protein Interfaces of Two-Component Signaling Systems Identified by Covariance Analysis
    Biochemistry (28 June 2008)
    by Hendrik Szurmant, Benjamin G Bobay, Robert A White, Daniel M Sullivan, Richele J Thompson, Terence Hwa, James A Hoch, John Cavanagh
    posted to cma by marck on 2008-07-02 03:42:48 as ** along with 3 people pansapiens paulschlesinger neils
  • Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences.
    Nucleic acids research (27 June 2008)
    by S Pitre, C North, M Alamgir, M Jessulat, A Chan, X Luo, J R R Green, M Dumontier, F Dehne, A Golshani
    posted to ppi-prediction by marck on 2008-07-02 03:41:15 as **
  • Identifying functional modules in protein-protein interaction networks: an integrated exact approach.
    Bioinformatics (Oxford, England), Vol. 24, No. 13. (1 July 2008)
    by MT Dittrich, GW Klau, A Rosenwald, T Dandekar, T Müller
    posted to network-module by marck on 2008-07-02 03:39:54 as ** along with 2 people jyuh bootsy
  • Selectional and Mutational Scope of Peptides Sequestering the Jun-Fos Coiled-Coil Domain.
    Journal of molecular biology (17 May 2008)
    by Urs B B Hagemann, Jody M M Mason, Kristian M M Müller, Katja M M Arndt
    posted to coiled-coil bzip by marck on 2008-07-02 03:38:03 as ** along with 1 person kevinchannon
  • Distinct SNARE complexes mediating membrane fusion in Golgi transport based on combinatorial specificity
    Proceedings of the National Academy of Sciences, Vol. 99, No. 8. (16 April 2002), pp. 5424-5429.
    by Francesco Parlati, Oleg Varlamov, Keren Paz, James A Mcnew, David Hurtado, Thomas H Sollner, James E Rothman
    posted to specificity snare by marck on 2008-07-01 12:02:45 as **
  • Signaling by Transmembrane Proteins Shifts Gears
    Cell, Vol. 126, No. 5. (8 September 2006), pp. 829-831.
    by Masayori Inouye
    posted to domain-hamp coiled-coil by marck on 2008-07-01 11:57:35 as **
  • Conserved structural features of the synaptic fusion complex: SNARE proteins reclassified as Q- and R-SNAREs
    Proceedings of the National Academy of Sciences, Vol. 95, No. 26. (22 December 1998), pp. 15781-15786.
    by Dirk Fasshauer, Bryan R Sutton, Axel T Brunger, Reinhard Jahn
    posted to snare 0layer by marck on 2008-07-01 11:55:52 as **
  • The HAMP domain structure implies helix rotation in transmembrane signaling.
    Cell, Vol. 126, No. 5. (8 September 2006), pp. 929-940.
    by M Hulko, F Berndt, M Gruber, JU Linder, V Truffault, A Schultz, J Martin, JE Schultz, AN Lupas, M Coles
    posted to domain-hamp coiled-coil by marck on 2008-07-01 10:59:59 as **
  • The specificity of SNARE-dependent fusion is encoded in the SNARE motif.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 10. (9 March 2004), pp. 3376-3380.
    by F Paumet, V Rahimian, JE Rothman
    posted to specificity snare by marck on 2008-07-01 10:58:04 as **
  • Identification of functionally interacting SNAREs by using complementary substitutions in the conserved '0' layer.
    Molecular biology of the cell, Vol. 16, No. 5. (May 2005), pp. 2263-2274.
    by CT Graf, D Riedel, HD Schmitt, R Jahn
    posted to snare 0layer by marck on 2008-07-01 10:57:32 as **
  • Cradle-loop barrels and the concept of metafolds in protein classification by natural descent
    Current Opinion in Structural Biology, Vol. 18, No. 3. (June 2008), pp. 358-365.
    by Vikram Alva, Kristin K Koretke, Murray Coles, Andrei N Lupas
    posted to structure-evolution by marck on 2008-07-01 10:56:54 as **
  • Stringent 3Q.1R composition of the SNARE 0-layer can be bypassed for fusion by compensatory SNARE mutation or by lipid bilayer modification.
    The Journal of biological chemistry, Vol. 282, No. 20. (18 May 2007), pp. 14861-14867.
    by RA Fratti, KM Collins, CM Hickey, W Wickner
    posted to snare coiled-coil by marck on 2008-07-01 10:41:12 as **
  • Exocytosis requires asymmetry in the central layer of the SNARE complex.
    EMBO J, Vol. 19, No. 22. (15 November 2000), pp. 6000-6010.
    by R Ossig, HD Schmitt, B de Groot, D Riedel, S Keränen, H Ronne, H Grubmüller, R Jahn
    posted to snare by marck on 2008-07-01 10:20:12 as ** along with 1 person baaden
  • Structural insights into the SNARE mechanism
    Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1641, No. 2-3. (18 August 2003), pp. 87-97.
    by Dirk Fasshauer
    posted to snare by marck on 2008-07-01 10:11:35 as **
  • Homotypic fusion of early endosomes: SNAREs do not determine fusion specificity
    Proceedings of the National Academy of Sciences, Vol. 103, No. 8. (21 February 2006), pp. 2701-2706.
    by Dorothea Brandhorst, Daniel Zwilling, Silvio O Rizzoli, Undine Lippert, Thorsten Lang, Reinhard Jahn
    posted to snare coiled-coil by marck on 2008-07-01 08:25:09 as **
  • Systems biology: Merging data means more powerful networks
    Nat Rev Genet, Vol. 9, No. 7. (July 2008), pp. 501-501.
    by Patrick Goymer
    posted to integrated by marck on 2008-07-01 06:37:44 as ** along with 3 people renatomilani reyez kengg
  • Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects
    Trends in Genetics, Vol. In Press, Corrected Proof
    by Reiner A Veitia, Samuel Bottani, James A Birchler
    posted to regulation by marck on 2008-07-01 06:33:08 as ** along with 1 person bpcusack
  • Force-Based Analysis of Multidimensional Energy Landscapes: Application of Dynamic Force Spectroscopy and Steered Molecular Dynamics Simulations to an Antibody Fragment-Peptide Complex
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Julia Morfill, Jan Neumann, Kerstin Blank, Uta Steinbach, Elias M Puchner, Kay-E Gottschalk, Hermann E Gaub
    posted to energy-landscape by marck on 2008-07-01 06:06:15 as **
  • Coiled coils meet the chaperone world
    Trends in Biochemical Sciences, Vol. 29, No. 9. (September 2004), pp. 455-458.
    by Jörg Martin, Markus Gruber, Andrei N Lupas
    posted to coiled-coil by marck on 2008-07-01 06:01:35 as **
  • Comparative analysis of coiled-coil prediction methods.
    J Struct Biol, Vol. 155, No. 2. (August 2006), pp. 140-145.
    by M Gruber, J Söding, AN Lupas
    posted to coiled-coil by marck on 2008-06-30 10:26:08 as ** along with 2 people ca3295 cjeans
  • Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes
    posted to linear-motif lim-domain by marck on 2008-06-30 06:10:58 as **
  • Design of protein conformational switches.
    Curr Opin Struct Biol, Vol. 16, No. 4. (August 2006), pp. 525-530.
    by XI Ambroggio, B Kuhlman
    posted to protein-engineering by marck on 2008-06-30 06:05:41 as ** along with 4 people jwm rabio kevinchannon bethbromley
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