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barry's library [663 articles]

Recent papers added to barry's library.
  • Darwinian Evolution on a Chip
    PLoS Biology, Vol. 6, No. 4. (1 April 2008), e85.
    by Brian M Paegel, Gerald F Joyce
    posted to journal_club directed_evolution by barry on 2008-04-29 20:13:18 as **** along with 11 people and 2 groups fdsayre cfleet stevanspringer operon xingxu Minty renatomilani TomQ phoenixzxl melting dlobo Bioinformatics GEB
  • A Microtubule Interactome: Complexes with Roles in Cell Cycle and Mitosis
    PLoS Biology, Vol. 6, No. 4. (1 April 2008), e98.
    by Julian R Hughes, Ana M Meireles, Katherine H Fisher, Angel Garcia, Philip R Antrobus, Alan Wainman, Nicole Zitzmann, Charlotte Deane, Hiroyuki Ohkura, James G Wakefield
    posted to tubulin protein_protein mts by barry on 2008-04-29 19:37:04 as ** along with 1 person and 1 group cdeane Bioinformatics
  • 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 2 people ttjoseph ffranca
  • 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 **
  • Molecular Dynamics Simulation of the Escherichia coli NikR Protein: Equilibrium Conformational Fluctuations Reveal Interdomain Allosteric Communication Pathways
    Journal of Molecular Biology, Vol. In Press, Corrected Proof
    by Michael J Bradley, Peter T Chivers, Nathan A Baker
    posted to md_simulation allosteric by barry on 2008-04-27 22:02:29 as * along with 2 people and 2 groups skoddet sobolevnrm structural_bioinformatics baker-group
  • Development of polyphosphate parameters for use with the AMBER force field
    Journal of Computational Chemistry, Vol. 24, No. 9. (2003), pp. 1016-1025.
    by Kristin L Meagher, Luke T Redman, Heather A Carlson
    posted to md_simulation amber by barry on 2008-04-25 20:57:25 as ** along with 1 person blackbart
  • Comparison of multiple Amber force fields and development of improved protein backbone parameters
    Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 3. (2006), pp. 712-725.
    by Viktor Hornak, Robert Abel, Asim Okur, Bentley Strockbine, Adrian Roitberg, Carlos Simmerling
    posted to md_simulation ff99sb amber by barry on 2008-04-25 20:56:25 as ** along with 5 people baaden lna allmensch choonpeng kazemi
  • Very fast empirical prediction and rationalization of protein pKa values.
    Proteins, Vol. 61, No. 4. (1 December 2005), pp. 704-721.
    by H Li, AD Robertson, JH Jensen
    posted to pka md_simulation bioinf_methods by barry on 2008-04-25 20:55:37 as ** along with 3 people and 1 group sunhwan bicko sim82 Bioinformatics
  • 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
  • notes Tracing evolutionary pressure
    Bioinformatics, Vol. 24, No. 7. (1 April 2008), pp. 908-915.
    by Kai Ye, Gert Vriend, Adriaan P Ijzerman
    posted to bioinf_methods phylogeny protein_evolution protein_sequence residue_annotation by barry on 2008-04-11 19:13:21 as *** along with 1 person and 2 groups sunhwan structural_bioinformatics Bioinformatics
  • 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 4 people and 1 group 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 45 people and 3 groups 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 laharrin dullhunk Bevan_Weir zeji gareth massivemayhem zwang GustavoLacerda GeeSharpMinor bmaust zambujo mingzhi starz1010101 maralena wchannels sunhwan jennifermbui kdelavega zhouyu FAB-lab Bioinformatics baker-group
  • notes Compensatory and Long-Range Changes in Picosecond-Nanosecond Main-Chain Dynamics upon Complex Formation: 15N Relaxation Analysis of the Free and Bound States of the Ubiquitin-like Domain of Human Plexin-B1 and the Small GTPase Rac1
    Journal of Molecular Biology, Vol. 377, No. 5. (11 April 2008), pp. 1474-1487.
    by S Bouguet-Bonnet, M Buck
    posted to g_proteins nmr protein-protein rho by barry on 2008-03-21 19:30:36 as **
  • Drug discovery: Schistosome treatment
    Nature, Vol. 452, No. 7185. (20 March 2008), pp. 296-296.
    by Sadaf Shadan
    posted to alex test by barry on 2008-03-21 03:02:22 as *
  • STRUCTURAL BIOLOGY: Researchers Hone Their Homology Tools
    Science, Vol. 319, No. 5870. (21 March 2008), 1612.
    by Robert F Service
    posted to comparative_model protein_structure by barry on 2008-03-21 02:54:55 as * along with 1 group structural_bioinformatics
  • notes Three-Dimensional Structures of Apo- and Holo-l-Alanine Dehydrogenase from Mycobacterium tuberculosis Reveal Conformational Changes upon Coenzyme Binding
    Journal of Molecular Biology, Vol. 377, No. 4. (4 April 2008), pp. 1161-1173.
    by Daniel Agren, Matthias Stehr, Catrine L Berthold, Shobhna Kapoor, Wulf Oehlmann, Mahavir Singh, Gunter Schneider
    posted to test by barry on 2008-03-21 01:15:24 as *
  • notes Discrimination between Distant Homologs and Structural Analogs: Lessons from Manually Constructed, Reliable Data Sets
    Journal of Molecular Biology, Vol. 377, No. 4. (4 April 2008), pp. 1265-1278.
    by Hua Cheng, Bong-Hyun Kim, Nick V Grishin
    posted to protein_evolution protein_structure by barry on 2008-03-20 17:04:58 as ***** along with 1 person and 1 group cdeane structural_bioinformatics
  • notes Divergent Evolution Within Protein Superfolds Inferred from Profile-based Phylogenetics
    Journal of Molecular Biology, Vol. 354, No. 3. (2 December 2005), pp. 722-737.
    by Douglas L Theobald, Deborah S Wuttke
    posted to phylogeny protein_evolution protein_sequence by barry on 2008-03-20 02:16:55 as * along with 3 people and 3 groups ana dlr caporaso structural_bioinformatics Bioinformatics biomedical-nlp
  • notes Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange
    J. Chem. Theory Comput., Vol. 4, No. 3. (11 March 2008), pp. 477-487.
    by M Zacharias
    posted to coarse-grained domain_motions md_simulation nma by barry on 2008-03-20 01:18:55 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Protein interactions in human genetic diseases
    Genome Biology, Vol. 9, No. 1. (2008)
    by Benjamin S Bockler, Alex Bateman
    posted to protein_protein protein_structure by barry on 2008-03-20 01:10:21 as read along with 9 people and 1 group balicea frohike neils grahamc aconesa biomcgary barriot mingzhi mclarenv Bioinformatics
  • Faculty Positions: Seeking the Skills for a Successful Career in Academia
    Science Careers (2008)
    by E Hitt
    posted to career by barry on 2008-03-20 01:07:34 as read along with 1 person and 1 group sobolevnrm baker-group
  • Defining functional distances over Gene Ontology
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Angela D Pozo, Florencio Pazos, Alfonso Valencia
    posted to clustering gene_ontology protein_function by barry on 2008-03-20 01:06:15 as ** along with 4 people and 2 groups tny grahamc sobolevnrm barriot Bioinformatics baker-group
  • Ready, set, hire
    NatureJobs
    by G Bjorn
    posted to career by barry on 2008-03-20 00:44:21 as ** along with 1 person and 1 group sobolevnrm baker-group
  • notes Structural flexibility in proteins: impact of the crystal environment
    Bioinformatics, Vol. 24, No. 4. (15 February 2008), pp. 521-528.
    by Konrad Hinsen
    posted to nma protein_dynamics protein_structure by barry on 2008-03-20 00:43:49 as ** along with 3 people and 1 group sobolevnrm jlh64 scienbox 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 correlated_mutations protein_sequence protein_structure by barry on 2008-03-20 00:40:27 as ** along with 7 people and 2 groups wilbur friendpine neils sobolevnrm mingzhi penpen926 scienbox structural_bioinformatics baker-group
  • In Person: Finding Opportunities in a Dysfunctional Job Market
    Science Careers (2008)
    by B Allen
    posted to career by barry on 2008-03-20 00:39:16 as read along with 1 person and 1 group sobolevnrm baker-group
  • Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds
    Proceedings of the National Academy of Sciences, Vol. 105, No. 7. (19 February 2008), pp. 2343-2348.
    by Christian G Roessler, Branwen M Hall, William J Anderson, Wendy M Ingram, Sue A Roberts, William R Montfort, Matthew H Cordes
    posted to fold_space protein_engineering protein_sequence protein_structure by barry on 2008-03-20 00:33:52 as ** along with 2 people and 1 group cactus sobolevnrm baker-group
  • De Novo Computational Design of Retro-Aldol Enzymes
    Science, Vol. 319, No. 5868. (7 March 2008), pp. 1387-1391.
    by Lin Jiang, Eric A Althoff, Fernando R Clemente, Lindsey Doyle, Daniela Rothlisberger, Alexandre Zanghellini, Jasmine L Gallaher, Jamie L Betker, Fujie Tanaka, Carlos F Barbas, Donald Hilvert, Kendall N Houk, Barry L Stoddard, David Baker
    posted to protein_design protein_ligand structure_refinement by barry on 2008-03-20 00:05:53 as **** along with 10 people and 2 groups ucbcjbm aalibes jwm aprasad dgront zwang sobolevnrm davidlott msuarezdiez scienbox structural_bioinformatics baker-group
  • Nucleotide-Mediated Conformational Changes of Monomeric Actin and Arp3 Studied by Molecular Dynamics Simulations.
    J Mol Biol (28 November 2007)
    by Paul Dalhaimer, Thomas D D Pollard, Brad J J Nolen
    posted to actin arp3 md_simulation protein_structure subfamily by barry on 2008-01-14 19:48:54 as ****
  • 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 coarse-grained protein_protein ubiqutin by barry on 2008-01-10 19:41:24 as ** along with 3 people and 3 groups sobolevnrm iantunbridge mikaellund structural_bioinformatics Bioinformatics baker-group
  • The structural basis of the activation of Ras by Sos.
    Nature, Vol. 394, No. 6691. (23 July 1998), pp. 337-343.
    by PA Boriack-Sjodin, SM Margarit, D Bar-Sagi, J Kuriyan
    posted to alex by barry on 2007-12-10 23:35:36 as **
  • Three-dimensional structures and properties of a transforming and a nontransforming glycine-12 mutant of p21H-ras.
    Biochemistry, Vol. 32, No. 33. (24 August 1993), pp. 8411-8420.
    by SM Franken, AJ Scheidig, U Krengel, H Rensland, A Lautwein, M Geyer, K Scheffzek, RS Goody, HR Kalbitzer, EF Pai
    posted to alex by barry on 2007-12-10 23:34:55 as **
  • 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 6 people and 3 groups 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 1 person and 1 group 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
  • Wordom: a program for efficient analysis of molecular dynamics simulations
    Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2625-2627.
    by Michele Seeber, Marco Cecchini, Francesco Rao, Giovanni Settanni, Amedeo Caflisch
    posted to bioinf_methods md_simulation by barry on 2007-11-27 23:33:00 as ** along with 6 people and 2 groups jyuh tmmurali choonpeng hmk sobolevnrm LamBras structural_bioinformatics baker-group
  • Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
    Proceedings of the National Academy of Sciences (13 November 2007), 0706443104.
    by Karunesh Arora, Charles L Brooks
    posted to allosteric kinases md_simulation by barry on 2007-11-27 23:23:58 as ** along with 5 people and 2 groups allmensch cactus sobolevnrm jlh64 karunesh structural_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 **
  • Functional Specificity Lies within the Properties and Evolutionary Changes of Amino Acids
    Journal of Molecular Biology, Vol. 373, No. 3. (26 October 2007), pp. 801-810.
    by Saikat Chakrabarti, Stephen H Bryant, Anna R Panchenko
    posted to clustering protein_sequence subfamily by barry on 2007-10-31 21:58:01 as ** along with 3 people and 2 groups Einat biehl mingzhi structural_bioinformatics Bioinformatics
  • Predicting Allosteric Communication in Myosin via a Pathway ofConserved Residues
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Susan Tang, Jung-Chi Liao, Alexander R Dunn, Russ B Altman, James A Spudich, Jeanette P Schmidt
    posted to allosteric molecular_motors myosin protein_sequence protein_structure sequence_comparison by barry on 2007-10-31 21:53:37 as read along with 5 people and 2 groups choonpeng cactus sobolevnrm jlh64 melting structural_bioinformatics baker-group
  • Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
    J. Chem. Theory Comput. (6 October 2007)
    by J Shao, SW Tanner, N Thompson, TE Cheatham
    posted to clustering md_simulation protein_structure by barry on 2007-10-26 22:44:54 as **** along with 4 people and 2 groups allmensch daevans sobolevnrm LamBras structural_bioinformatics baker-group
  • On the paper trail
    Nature, Vol. 449, No. 7162. (4 October 2007), pp. 508-508.
    posted to career funding by barry on 2007-10-26 22:42:02 as ** along with 1 person and 1 group sobolevnrm baker-group
  • 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
  • Determination of electrostatic interaction energies and protonation state populations in enzyme active sites
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Chresten R Sondergaard, Lawrence P Mcintosh, Gianluca Pollastri, Jens E Nielsen
    posted to electrostatics solvent by barry on 2007-10-26 22:39:25 as ** along with 2 people and 2 groups sobolevnrm skoddet structural_bioinformatics baker-group
  • Supercharging Proteins Can Impart Unusual Resilience
    J. Am. Chem. Soc., Vol. 129, No. 33. (22 August 2007), pp. 10110-10112.
    by MS Lawrence, KJ Phillips, DR Liu
    posted to electrostatics journal_club protein_design protein_evolution protein_folding by barry on 2007-10-26 22:37:58 as read along with 2 people and 3 groups samjlord sobolevnrm structural_bioinformatics moernerlab baker-group
  • How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: A theoretical study.
    Protein Sci (7 March 2006)
    by Yuhui Cheng, Yingkai Zhang, J Andrew A McCammon
    posted to correlated_motions kinases md_simulation pca phosphorylation by barry on 2007-10-12 01:11:45 as * along with 1 person and 1 group nknii TCR_Signaling
  • Insights into Correlated Motions and Long-Range Interactions in CheY Derived from Molecular Dynamics Simulations.
    Biophys J, Vol. 92, No. 6. (15 March 2007), pp. 2062-2079.
    by MH Knaggs, FR Salsbury, MH Edgell, JS Fetrow
    posted to contacts correlated_motions md_simulation by barry on 2007-10-12 01:04:36 as * along with 1 person choonpeng
  • Complementarity of Structure Ensembles in Protein-Protein Binding
    Structure, Vol. 12, No. 12. (December 2004), pp. 2125-2136.
    by Raik Gruenberg, Johan Leckner, Michael Nilges
    posted to md_simulation protein_dynamics protein_protein by barry on 2007-10-02 03:05:14 as read along with 3 people and 3 groups lna allmensch cursonivel1 structural_bioinformatics Bioinformatics cursonivel1
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