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barry's review [99 articles]

Recent papers added to barry's library classified by the tag review. You can also see everyone's review.
  • The 2006 Automated Function Prediction Meeting
    BMC Bioinformatics, Vol. 8, No. Suppl 4. (2007)
    by Ana Rodrigues, Barry Grant, Adam Godzik, Iddo Friedberg
    posted to review mine afp by barry on 2008-06-26 20:06:58 as read
  • RNA dynamics: it is about time
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Hashim M Al-Hashimi, Nils G Walter
    posted to rna_dynamics rna review nice_figure by barry on 2008-06-17 18:18:55 as ** along with 1 person ruvido
  • notes Kinesin-8 molecular motors: putting the brakes on chromosome oscillations
    Trends in Cell Biology, Vol. In Press, Corrected Proof
    by Melissa K Gardner, David J Odde, Kerry Bloom
    posted to review kinesin kin8 by barry on 2008-06-02 19:54:52 as *
  • notes Investigating protein dynamics in collective coordinate space.
    Curr Opin Struct Biol, Vol. 9, No. 2. (April 1999), pp. 164-169.
    by A Kitao, N Go
    posted to review protein_structure protein_dynamics pca nma md_simulation by barry on 2008-04-29 00:04:52 as ** along with 4 people and 1 group sobolevnrm choonpeng ttjoseph ffranca baker-group
  • notes Collective protein dynamics in relation to function
    Current Opinion in Structural Biology, Vol. 10, No. 2. (1 April 2000), pp. 165-169.
    by Herman JC Berendsen, Steven Hayward
    posted to review protein_structure protein_dynamics pca nma md_simulation by barry on 2008-04-29 00:03:09 as **
  • Transition networks for modeling the kinetics of conformational change in macromolecules
    Current Opinion in Structural Biology, Vol. 18, No. 2. (April 2008), pp. 154-162.
    by Frank Noé, Stefan Fischer
    posted to protein_dynamics protein_structure review smd by barry on 2008-04-17 19:15:44 as *** along with 2 people and 2 groups paulschlesinger sobolevnrm structural_bioinformatics baker-group
  • Computational methods for transcriptional regulation.
    Curr Opin Genet Dev, Vol. 15, No. 2. (April 2005), pp. 214-221.
    by ED Siggia
    posted to microarrays review transcription_factor by barry on 2008-04-03 19:42:48 as ** along with 3 people and 2 groups bertelsen dpollard koller Bioinformatics EisenLab
  • Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play.
    J Mol Biol (29 February 2008)
    by Chung-Jung J Tsai, Antonio Del Sol, Ruth Nussinov
    posted to allosteric protein_dynamics protein_structure review by barry on 2008-03-31 18:11:48 as *** along with 5 people and 1 group higueruelo choonpeng cactus sobolevnrm CameronNeylon structural_bioinformatics
  • notes What is principal component analysis?
    Nature Biotechnology, Vol. 26, No. 3., pp. 303-304.
    by Markus Ringnér
    posted to pca review by barry on 2008-03-21 19:36:38 as read along with 48 people and 3 groups tharris rsantana kengg laharrin chrissp100 xingxu dekay23 rvosa i-stevenson dimka dayjm markusd ashko craigwilson06 abbie_riner quianominorleo bibay2004 jfr kristgy pavanghatty rchauhan waghsk hpaces adacier fryanpan sobolevnrm Yanno jyuh operon baaic dullhunk Bevan_Weir zeji gareth massivemayhem zwang GustavoLacerda GeeSharpMinor bmaust zambujo mingzhi starz1010101 maralena wchannels sunhwan jennifermbui kdelavega zhouyu FAB-lab Bioinformatics baker-group
  • The AAA+ superfamily -- a myriad of motions
    Current Opinion in Structural Biology, Vol. 17, No. 6. (December 2007), pp. 641-652.
    by Paul A Tucker, Laszlo Sallai
    posted to aaa protein_structure review by barry on 2007-12-04 23:05:50 as *** along with 1 person cactus
  • Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
    Current Opinion in Structural Biology, Vol. 17, No. 6. (December 2007), pp. 633-640.
    by Ivet Bahar, Chakra Chennubhotla, Dror Tobi
    posted to allosteric protein_dynamics protein_structure review by barry on 2007-12-04 22:56:25 as ** along with 7 people and 3 groups higueruelo LamBras aqeel ruvido cactus sobolevnrm jennifermbui structural_bioinformatics Bioinformatics baker-group
  • Comparative Analysis of Protein Structure Alignments
    BMC Structural Biology, Vol. 7 (26 July 2007), 50.
    by Gabriele Mayr, Francisco S Domingues, Peter Lackner
    posted to protein_structure review structure_comparison by barry on 2007-12-04 22:41:13 as * along with 2 people and 1 group bicko chad_davis structural_bioinformatics
  • Correlated substitution analysis and the prediction of amino acid structural contacts
    Brief Bioinform (13 November 2007), bbm052.
    by David S Horner, Walter Pirovano, Graziano Pesole
    posted to correlated_mutations review by barry on 2007-11-27 23:34:46 as * along with 2 people and 3 groups zwang sobolevnrm structural_bioinformatics Bioinformatics baker-group
  • GTPases: multifunctional molecular switches regulating vesicular traffic.
    Annu Rev Biochem, Vol. 63 (1994), pp. 949-990.
    by C Nuoffer, WE Balch
    posted to ntpases p-loop review by barry on 2007-11-08 18:44:54 as **
  • Wavelets, a modern tool for signal processing - Physics Today October 2007
    Physics Today, Vol. 60, No. 10. (2007), 78.
    by IW Selesnick
    posted to review wavelets by barry on 2007-10-26 22:40:21 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Exploring the range of protein flexibility, from a structural proteomics perspective
    Current Opinion in Chemical Biology, Vol. 8, No. 1. (February 2004), pp. 14-19.
    by Mark Gerstein, Nathaniel Echols
    posted to protein_dynamics protein_structure review by barry on 2007-09-27 19:19:21 as read
  • A complex profile of protein elongation: translating chemical energy into molecular movement
    Structure, Vol. 4, No. 3. (March 1996), pp. 229-238.
    by Kenton Abel, Frances Jurnak
    posted to ef-tu g_proteins ntpases review by barry on 2007-09-20 23:01:17 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • notes A Ras by Any Other Name
    Mol. Cell. Biol., Vol. 21, No. 5. (1 March 2001), pp. 1441-1443.
    by Dafna Bar-Sagi
    posted to ntpases ras review by barry on 2007-09-20 00:03:36 as ***** along with 2 groups structural_bioinformatics Bioinformatics
  • The pathway to signal achievement
    Nature, Vol. 365, No. 6449. (28 October 1993), pp. 781-783.
    by Sean E Egan, Robert A Weinberg
    posted to ras review by barry on 2007-09-19 23:54:45 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • The Chemistry of Protein Catalysis
    Journal of Molecular Biology, Vol. 372, No. 5. (5 October 2007), pp. 1261-1277.
    by Gemma L Holliday, Daniel E Almonacid, John B Mitchell, Janet M Thornton
    posted to catalytic_mechanism review by barry on 2007-09-17 17:53:36 as * along with 6 people and 2 groups sim82 jwm ucbcjbm cjeans zwang grottenolm structural_bioinformatics Bioinformatics
  • Keeping dry and crossing membranes.
    Nat Biotechnol, Vol. 22, No. 9. (September 2004), pp. 1081-1084.
    by A Fernández
    posted to dehydron review by barry on 2007-09-13 19:06:23 as read along with 1 person and 2 groups BragilMassoud structural_bioinformatics Bioinformatics
  • Analysis of computational approaches for motif discovery
    Algorithms for Molecular Biology, Vol. 1, No. 1. (19 May 2006), 8.
    by Nan Li, Martin Tompa
    posted to review sequence_comparison sequence_motif transcription_factor by barry on 2007-08-28 02:13:10 as ** along with 9 people and 2 groups ana tuck chad_davis dquest lusk nklee maximilianh xi03 csdhwang structural_bioinformatics Bioinformatics
  • Graph-based methods for analysing networks in cell biology.
    Brief Bioinform, Vol. 7, No. 3. (September 2006), pp. 243-255.
    by T Aittokallio, B Schwikowski
    posted to graph interaction_maps review by barry on 2007-08-27 20:04:16 as ** along with 5 people and 2 groups iris_2001 tmmurali aswin grahamc jmarcelino structural_bioinformatics Bioinformatics
  • Protein Flexibility and Mobility in Structure-Based Drug Design
    pp. 455-476.
    by Aqeel Ahmed
    posted to docking drug_design protein_dynamics protein_ligand protein_structure review by barry on 2007-08-13 19:47:46 as * along with 2 groups structural_bioinformatics Bioinformatics
  • notes Hydrogen bonding in globular proteins
    Progress in Biophysics and Molecular Biology, Vol. 44, No. 2. (1984), pp. 97-179.
    by EN Baker, RE Hubbard
    posted to hbond protein_structure review by barry on 2007-06-21 22:53:50 as read along with 2 groups structural_bioinformatics Bioinformatics
  • Evolution of protein fold in the presence of functional constraints
    Current Opinion in Structural Biology, Vol. 16, No. 3. (June 2006), pp. 399-408.
    by Antonina Andreeva, Alexey G Murzin
    posted to protein_evolution protein_structure review by barry on 2007-05-30 19:27:55 as **** along with 4 people and 2 groups ana Einat tny cjeans structural_bioinformatics Bioinformatics
  • Identification and analysis of eukaryotic promoters: recent computational approaches.
    Trends Genet, Vol. 17, No. 2. (February 2001), pp. 56-60.
    by U Ohler, H Niemann
    posted to gene_finding promoter_identification review transcription_factor by barry on 2007-05-30 19:19:49 as *** along with 3 people and 2 groups rklancer ana chad_davis structural_bioinformatics Bioinformatics
  • notes Assessing computational tools for the discovery of transcription factor binding sites
    Nature Biotechnology, Vol. 23, No. 1. (06 January 2005), pp. 137-144.
    by Martin Tompa, Nan Li, Timothy L Bailey, George M Church, Bart D De Moor, Eleazar Eskin, Alexander V Favorov, Martin C Frith, Yutao Fu, James J Kent, Vsevolod J Makeev, Andrei A Mironov, William S Noble, Giulio Pavesi, Graziano Pesole, Mireille Régnier, Nicolas Simonis, Saurabh Sinha, Gert Thijs, Jacques v van Helden, Mathias Vandenbogaert, Zhiping Weng, Christopher Workman, Chun Ye, Zhou Zhu
    posted to promoter_finding review transcription_factor by barry on 2007-05-30 19:11:02 as *** along with 23 people and 6 groups nuin ep161302 icases ana aalibes aprasad jfr tuck chad_davis lyongu tabu dquest neveaire ranb johncumbers noano xiaobeizhao olympos GustavoLacerda nklee mdimon dandaman vietanh0 structural_bioinformatics Biostatistics Computational-Genomics Bioinformatics Neuroscience TNT
  • Supramolecular Structure and Dynamics Special Feature: Crystalline molecular machines: Encoding supramolecular dynamics into molecular structure
    PNAS, Vol. 102, No. 31. (2 August 2005), pp. 10771-10776.
    by Miguel A Garcia-Garibay
    posted to review superamolecular by barry on 2007-05-09 00:07:02 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • AAA+ superfamily ATPases: common structure-diverse function
    Genes to Cells, Vol. 6, No. 7. (2001), pp. 575-597.
    by Teru Ogura, Anthony J Wilkinson
    posted to aaa dynein protein_structure review by barry on 2007-04-13 23:27:10 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Conservation of gene order: a fingerprint of proteins that physically interact.
    Trends Biochem Sci, Vol. 23, No. 9. (September 1998), pp. 324-328.
    by T Dandekar, B Snel, M Huynen, P Bork
    posted to genomic_context review by barry on 2007-04-10 19:36:11 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • notes Conformational diversity and protein evolution--a 60-year-old hypothesis revisited.
    Trends Biochem Sci, Vol. 28, No. 7. (July 2003), pp. 361-368.
    by LC James, DS Tawfik
    posted to review protein_structure protein_sequence protein_evolution protein_dynamics by barry on 2007-01-18 19:39:58 as ***** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • Microarray data analysis: from disarray to consolidation and consensus
    Nature Reviews Genetics, Vol. 7, No. 1., pp. 55-65.
    by David B Allison, Xiangqin Cui, Grier P Page, Mahyar Sabripour
    posted to review microarrays by barry on 2007-01-18 18:58:17 as * along with 21 people and 2 groups jo_davies giovenko jyuh textoris jfr Ayest balicea sterovetta lhonigberg acidwizard ronaldozhou vpschulz rmk schuylrp Garamonfok debasis GeeSharpMinor dimatura heliopais shikin minostro structural_bioinformatics Bioinformatics
  • Human RAS superfamily proteins and related GTPases.
    Sci STKE, Vol. 2004, No. 250. (14 September 2004)
    by J Colicelli
    posted to review ras g_proteins by barry on 2007-01-17 01:59:15 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins.
    Science, Vol. 247, No. 4945. (23 February 1990), pp. 939-945.
    by MV Milburn, L Tong, AM deVos, A Brünger, Z Yamaizumi, S Nishimura, SH Kim
    posted to review ras p-loop ntp g_proteins allosteric by barry on 2007-01-16 20:21:14 as ** along with 4 people and 2 groups Einat laurabailey allmensch gloria structural_bioinformatics Bioinformatics
  • The structure of Ras protein: a model for a universal molecular switch
    Trends in Biochemical Sciences, Vol. 16 (1991), pp. 382-387.
    by Alfred Wittinghofer, Emil F Pal
    posted to review ras p-loop ntp g_proteins allosteric by barry on 2007-01-16 20:13:08 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Lucky 13-microtubule depolymerisation by kinesin-13 motors
    Journal Of Cell Science, Vol. 119, No. Part 19. (1 October 2006), pp. 3905-3913.
    by Carolyn A Moores, Ronald A Milligan
    posted to kin13 kinesin molecular_motors review by barry on 2006-11-06 20:25:49 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • CtBP family proteins: more than transcriptional corepressors.
    Bioessays, Vol. 25, No. 1. (January 2003), pp. 9-12.
    by G Chinnadurai
    posted to ctbp review by barry on 2006-09-29 21:13:42 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Kinesin-8s: motoring and depolymerizing
    Nature Cell Biology, Vol. 8, No. 9., pp. 903-905.
    by Claire E Walczak
    posted to kin8 kinesin mitosis molecular_motors review by barry on 2006-09-04 20:12:49 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • The nicotinamide dinucleotide binding motif: a comparison of nucleotide binding proteins
    The FASEB Journal: Official Publication Of The Federation Of American Societies For Experimental Biology, Vol. 10, No. 11. (September 1996), pp. 1257-1269.
    by CR Bellamacina
    posted to ctbp nad nadp review by barry on 2006-08-15 20:01:17 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Structure and mechanism of liver alcohol dehydrogenase, lactate dehydrogenase and glyceraldehyde-3-phosphate dehydrogenase.
    Experientia Suppl, Vol. 36 (1980), pp. 40-84.
    by CI Brändén, H Eklund
    posted to adh ctbp mdh review by barry on 2006-08-15 02:14:00 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Alcohol dehydrogenases.
    Adv Exp Med Biol, Vol. 414 (1997), pp. 591-594.
    by B Persson
    posted to adh ctbp review by barry on 2006-08-15 02:02:20 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Multiprotein-DNA complexes in transcriptional regulation.
    Annu Rev Biophys Biomol Struct, Vol. 28 (1999), pp. 29-56.
    by C Wolberger
    posted to ctbp review by barry on 2006-08-03 02:05:46 as ** along with 1 person and 3 groups nickluscombe structural_bioinformatics Bioinformatics EBI-regulation
  • CtBP, an unconventional transcriptional corepressor in development and oncogenesis.
    Mol Cell, Vol. 9, No. 2. (February 2002), pp. 213-224.
    by G Chinnadurai
    posted to ctbp review by barry on 2006-08-02 22:29:53 as *** along with 2 groups structural_bioinformatics Bioinformatics
  • Dehydrogenases, NAD, and transcription--what's the connection?
    Structure, Vol. 10, No. 11. (November 2002), pp. 1465-1466.
    by R Marmorstein
    posted to ctbp review by barry on 2006-08-02 22:20:09 as *** along with 2 groups structural_bioinformatics Bioinformatics
  • Regulation of corepressor function by nuclear NADH.
    Science, Vol. 295, No. 5561. (8 March 2002), pp. 1895-1897.
    by Q Zhang, DW Piston, RH Goodman
    posted to ctbp nadh review by barry on 2006-08-02 22:13:14 as *** along with 1 person and 2 groups yedmonds structural_bioinformatics Bioinformatics
  • The CtBP family: enigmatic and enzymatic transcriptional co-repressors.
    Bioessays, Vol. 23, No. 8. (August 2001), pp. 683-690.
    by J Turner, M Crossley
    posted to ctbp review by barry on 2006-08-02 22:04:24 as *** along with 2 groups structural_bioinformatics Bioinformatics
  • How kinesins walk, assemble and transport: A birds-eye-view of some unresolved questions
    Physica A: Statistical Mechanics and its Applications, Vol. In Press, Uncorrected Proof
    by Krishanu Ray
    posted to kinesin molecular_motors review by barry on 2006-06-05 19:40:40 as ***** along with 1 person and 2 groups qwermish structural_bioinformatics Bioinformatics
  • Molecular motors as cargo transporters in the cell--The good, the bad and the ugly
    Physica A: Statistical Mechanics and its Applications, Vol. In Press, Uncorrected Proof
    by Roop Mallik, Steven P Gross
    posted to dynein kinesin molecular_motors myosin review by barry on 2006-06-05 19:36:53 as ***** along with 2 groups structural_bioinformatics Bioinformatics
  • Genomics and the Irreducible Nature of Eukaryote Cells
    Science, Vol. 312, No. 5776. (19 May 2006), pp. 1011-1014.
    by CG Kurland, LJ Collins, D Penny
    posted to comparative_genomics review by barry on 2006-05-19 02:31:07 as ** along with 7 people and 7 groups cmzmasek kuhn dayjm dchughes cmm azuma mattjb structural_bioinformatics Bioinformatics FAB-lab G4ID ComplexAdaptiveSystems DSTO-CAS Genetics-of-Gambling
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