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Einat's library [163 articles]

Recent papers added to Einat's library.
  • Statistical evaluation of alternative models of human evolution
    Proceedings of the National Academy of Sciences (31 October 2007), 0708280104.
    by Nelson J Fagundes, Nicolas Ray, Mark Beaumont, Samuel Neuenschwander, Francisco M Salzano, Sandro L Bonatto, Laurent Excoffier
    posted to evolution human by Einat on 2007-11-11 06:55:35 as ** along with 7 people A_Olympia EsepBib joepickrell nurban ryanraaum wsjames xosepedro
  • Specialization and evolution of endogenous small RNA pathways
    Nat Rev Genet, Vol. 8, No. 11. (November 2007), pp. 884-896.
    by Elisabeth J Chapman, James C Carrington
    posted to sirna by Einat on 2007-11-11 06:43:09 as ** along with 5 people dchughes alwinpremanand cabbagezs dandaman maralena
  • 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 function-prediction by Einat on 2007-11-07 20:23:52 as ** along with 3 people and 2 groups barry biehl mingzhi structural_bioinformatics Bioinformatics
  • MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans
    BMC Bioinformatics, Vol. 8 (17 September 2007), 341.
    by Ting-Hua Huang, Bin Fan, Max F Rothschild, Zhi-Liang Hu, Kui Li, Shu-Hong Zhao
    posted to micro-rna by Einat on 2007-09-23 13:41:34 as **** along with 1 person maralena
  • Engineering by homologous recombination: exploring sequence and function within a conserved fold.
    Curr Opin Struct Biol (18 September 2007)
    by Martina N N Carbone, Frances H H Arnold
    posted to design evolution structure by Einat on 2007-09-23 13:29:59 as **** along with 2 people jyuh allPowerde
  • MicroRNA-34b and MicroRNA-34c Are Targets of p53 and Cooperate in Control of Cell Proliferation and Adhesion-Independent Growth.
    Cancer Res (6 September 2007)
    by David C C Corney, Andrea Flesken-Nikitin, Andrew K K Godwin, Wei Wang, Alexander Yu Y Nikitin
    posted to cancer micro-rna by Einat on 2007-09-10 16:17:59 as ** along with 4 people and 2 groups jyuh andersbj delenca maralena structural_bioinformatics microRNA
  • Occurrence of protein structure elements in conserved sequence regions
    BMC Structural Biology, Vol. 7 (09 January 2007), 3.
    by Einat Sitbon, Shmuel Pietrokovski
    posted to evolution secondary-structure sequence-structure superfunnel by Einat on 2007-09-02 16:06:53 as read along with 1 group structural_bioinformatics
  • 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 design interface protein_structure by Einat on 2007-09-02 16:02:53 as ***** along with 6 people and 3 groups jwm bicko dpollard Scis0000002 phoenixzxl marck structural_bioinformatics Bioinformatics EisenLab
  • Automated Protein Subfamily Identification and Classification
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e160.
    by Duncan P Brown, Nandini Krishnamurthy, Kimmen Sjölander
    posted to function-prediction sub-family by Einat on 2007-09-02 16:00:00 as ***** along with 3 people and 1 group cjeans mingzhi shung structural_bioinformatics
  • Automated Discovery of Functional Generality of Human Gene Expression Programs.
    PLoS Comput Biol, Vol. 3, No. 8. (10 August 2007)
    by Georg K K Gerber, Robin D D Dowell, Tommi S S Jaakkola, David K K Gifford
    posted to expression function-prediction by Einat on 2007-09-02 15:56:58 as ** along with 2 people and 1 group jfr sebastien_vigneau structural_bioinformatics
  • rMotifGen: random motif generator for DNA and protein sequences
    BMC Bioinformatics, Vol. 8 (07 August 2007), 292.
    by Eric C Rouchka, Timothy C Hardin
    posted to background-creation motifs sequence-alignment by Einat on 2007-08-12 19:34:07 as *** along with 1 person and 1 group niallhaslam structural_bioinformatics
  • notes Evolution of Function in the “Two Dinucleotide Binding Domains” Flavoproteins
    PLoS Computational Biology, Vol. 3, No. 7. (1 July 2007), e121.
    by Sunil Ojha, Elaine C Meng, Patricia C Babbitt
    posted to evolution fad-binding nucelotide_binding rossman by Einat on 2007-08-05 08:39:04 as ***** along with 3 people and 2 groups barry zwang mdimon structural_bioinformatics Bioinformatics
  • Clustering protein environments for function prediction: finding PROSITE motifs in 3D.
    BMC Bioinformatics, Vol. 8 Suppl 4 (2007)
    by S Yoon, JC Ebert, EY Chung, G De Micheli, RB Altman
    posted to active-site protein_structure structural_enviroment by Einat on 2007-07-01 13:56:21 as **** along with 1 person and 1 group shadowman structural_bioinformatics
  • Prediction of Functional Sites Based on the Fuzzy Oil Drop Model
    PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e94.
    by Michał Bryliński, Katarzyna Prymula, Wiktor Jurkowski, Marek Kochańczyk, Ewa Stawowczyk, Leszek Konieczny, Irena Roterman
    posted to active-site by Einat on 2007-06-26 14:56:06 as ** along with 1 person and 1 group zwang structural_bioinformatics
  • Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization
    BMC Bioinformatics, Vol. 8 (20 June 2007), 213.
    by Namshin Kim, Christopher Lee
    posted to evolution protein_structure by Einat on 2007-06-26 14:49:57 as **** along with 1 group structural_bioinformatics
  • Relating destabilizing regions to known functional sites in proteins
    BMC Bioinformatics, Vol. 8 (30 April 2007), 141.
    by Benoit H Dessailly, Marc F Lensink, Shoshana J Wodak
    posted to function-prediction protein-stability by Einat on 2007-05-25 11:28:43 as ***** along with 1 group structural_bioinformatics
  • How accurate and statistically robust are catalytic site predictions based on closeness centrality?
    BMC Bioinformatics, Vol. 8 (11 May 2007), 153.
    by Eric Chea, Dennis R Livesay
    posted to centrality function-prediction by Einat on 2007-05-25 11:25:33 as ** along with 1 person and 1 group massivemayhem structural_bioinformatics
  • Improved prediction of critical residues for protein function based on network and phylogenetic analyses.
    BMC Bioinformatics, Vol. 6 (2005)
    by B Thibert, DE Bredesen, G del Rio
    posted to evolution function-prediction networks protein_structure by Einat on 2007-05-25 11:24:23 as **** along with 2 people and 1 group pansapiens sriram_s structural_bioinformatics
  • Domain swapping in the sporulation response regulator Spo0A.
    J Mol Biol, Vol. 297, No. 3. (31 March 2000), pp. 757-770.
    by RJ Lewis, K Muchová, JA Brannigan, I Barák, G Leonard, AJ Wilkinson
    posted to spo0a sporulation structure by Einat on 2007-05-07 14:18:23 as ** along with 1 group structural_bioinformatics
  • Phylogeny and functional conservation of sigma(E) in endospore-forming bacteria.
    Microbiology, Vol. 146 ( Pt 7) (July 2000), pp. 1593-1603.
    by EF Arcuri, M Wiedmann, KJ Boor
    posted to evolution sporulation by Einat on 2007-05-07 14:00:00 as ** along with 1 group structural_bioinformatics
  • PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes.
    Bioinformatics, Vol. 21, No. 15. (1 August 2005), pp. 3316-3317.
    by SP Gore, DF Burke, TL Blundell
    posted to complex protein_structure by Einat on 2007-04-16 17:14:27 as ***** along with 4 people and 1 group bicko skhadar massivemayhem medic0747 structural_bioinformatics
  • A comparative genomic view of clostridial sporulation and physiology
    Nature Reviews Microbiology, Vol. 3, No. 12. (24 October 2005), pp. 969-978.
    by Carlos J Paredes, Keith V Alsaker, Eleftherios T Papoutsakis
    posted to evolution sporulation by Einat on 2007-04-11 13:33:45 as ***** along with 1 group structural_bioinformatics
  • Cyanobacterial two-component proteins: structure, diversity, distribution, and evolution.
    Microbiol Mol Biol Rev, Vol. 70, No. 2. (June 2006), pp. 472-509.
    by MK Ashby, J Houmard
    posted to evolution sporulation by Einat on 2007-04-11 13:32:38 as ***** along with 1 group structural_bioinformatics
  • The Generation of New Protein Functions by the Combination of Domains
    Structure, Vol. 15, No. 1. (January 2007), pp. 85-99.
    by Matthew Bashton, Cyrus Chothia
    posted to domains protein-function by Einat on 2007-04-11 13:19:49 as ***** along with 5 people and 1 group tny madhadron choonpeng cjeans bioinfolib structural_bioinformatics
  • Structure, function and evolution of multidomain proteins.
    Curr Opin Struct Biol, Vol. 14, No. 2. (April 2004), pp. 208-216.
    by C Vogel, M Bashton, ND Kerrison, C Chothia, SA Teichmann
    posted to domains evolution protein-function protein_structure review by Einat on 2007-04-11 13:18:01 as ***** along with 3 people and 1 group Schmidtc cjeans cmzmasek structural_bioinformatics
  • The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins.
    Structure, Vol. 12, No. 6. (June 2004), pp. 917-925.
    by J Gough, C Chothia
    posted to conservation protein-function protein_structure by Einat on 2007-04-11 13:00:07 as ***** along with 1 person and 1 group cjeans structural_bioinformatics
  • Protein Family Expansions and Biological Complexity
    PLoS Computational Biology, Vol. 2, No. 5. (1 May 2006), e48.
    by Christine Vogel, Cyrus Chothia
    posted to complex protein-families by Einat on 2007-04-11 12:56:28 as ***** along with 4 people and 2 groups ccots caporaso cjeans cmzmasek structural_bioinformatics biomedical-nlp
  • The SUPERFAMILY database in 2007: families and functions.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by D Wilson, M Madera, C Vogel, C Chothia, J Gough
    posted to protein-families protein_structure by Einat on 2007-04-11 12:40:09 as ***** along with 1 person and 1 group siebertm structural_bioinformatics
  • 3D complex: a structural classification of protein complexes.
    PLoS Comput Biol, Vol. 2, No. 11. (17 November 2006)
    by ED Levy, JB Pereira-Leal, C Chothia, SA Teichmann
    posted to complex protein_structure by Einat on 2007-04-11 12:38:06 as ***** along with 2 people and 1 group bicko chad_davis structural_bioinformatics
  • A ?FRankenstein's monster? approach to comparative modeling: Merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation
    Proteins: Structure, Function, and Genetics, Vol. 53, No. S6. (2003), pp. 369-379.
    by Jan Kosinski, Iwona A Cymerman, Marcin Feder, Michal A Kurowski, Joanna M Sasin, Janusz M Bujnicki
    posted to fold-recognition structural_prediction by Einat on 2007-04-04 16:04:39 as ** along with 1 person and 1 group dgront structural_bioinformatics
  • Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease.
    Proteins, Vol. 65, No. 4. (1 December 2006), pp. 867-876.
    by IA Cymerman, A Obarska, KJ Skowronek, A Lubys, JM Bujnicki
    posted to hnh homing-endonuclease by Einat on 2007-04-04 15:38:31 as ** along with 1 group structural_bioinformatics
  • Structural determinants of the rate of protein evolution in yeast.
    Mol Biol Evol, Vol. 23, No. 9. (September 2006), pp. 1751-1761.
    by JD Bloom, DA Drummond, FH Arnold, CO Wilke
    posted to evolution protein-stability protein_structure by Einat on 2007-04-04 15:27:56 as ** along with 1 person and 1 group chad_davis structural_bioinformatics
  • Protein stability promotes evolvability
    PNAS, Vol. 103, No. 15. (11 April 2006), pp. 5869-5874.
    by Jesse D Bloom, Sy T Labthavikul, Christopher R Otey, Frances H Arnold
    posted to evolution protein-stability by Einat on 2007-04-04 15:24:17 as ** along with 10 people and 2 groups rklancer Retchless lna penka cmm redelings BioNica Cristiano wilbur cdeane structural_bioinformatics FAB-lab
  • Why highly expressed proteins evolve slowly.
    Proc Natl Acad Sci U S A (21 September 2005)
    by D Allan A Drummond, Jesse D D Bloom, Christoph Adami, Claus O O Wilke, Frances H H Arnold
    posted to evolution folding protein-stability protein_structure by Einat on 2007-04-04 15:21:31 as ** along with 14 people and 5 groups rklancer stevanspringer bjorns imouthesmp aprasad dayjm marcius xwbcn penka balabu malcook balicea RamuAnandakrishnan wilbur structural_bioinformatics Nie FAB-lab BioinfoCIPF SGU-CIPF
  • Destruction of long-range interactions by a single mutation in lysozyme.
    Proc Natl Acad Sci U S A (26 March 2007)
    by Ruhong Zhou, Maria Eleftheriou, Ajay K Royyuru, Bruce J J Berne
    posted to centrality folding_nucleation protein-stability protein_structure by Einat on 2007-04-02 14:44:05 as *** along with 3 people and 1 group allmensch choonpeng gisle structural_bioinformatics
  • Exploring the common dynamics of homologous proteins. Application to the globin family.
    Biophys J, Vol. 89, No. 1. (July 2005), pp. 3-13.
    by S Maguid, S Fernandez-Alberti, L Ferrelli, J Echave
    posted to globin protein-families protein-flexibility by Einat on 2007-02-20 14:29:01 as ** along with 4 people and 2 groups gisle barry jlh64 edvin structural_bioinformatics Bioinformatics
  • SNPs, Silent But Not Invisible.
    Science (21 December 2006)
    by Anton A A Komar
    posted to folding protein_structure snps by Einat on 2007-02-20 14:27:10 as ** along with 3 people and 3 groups dchughes massivemayhem cat_worth structural_bioinformatics G4ID Genetics-of-Gambling
  • 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 evolution protein-function protein_structure by Einat on 2007-02-20 13:45:01 as ** along with 4 people and 2 groups ana barry tny cjeans 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 allostery protein_structure by Einat on 2007-02-20 13:43:17 as ** along with 4 people and 2 groups barry laurabailey allmensch gloria structural_bioinformatics Bioinformatics
  • Analysis of chameleon sequences and their implications in biological processes.
    Proteins (13 February 2007)
    by Jun-Tao T Guo, Jerzy W W Jaromczyk, Ying Xu
    posted to chameleon by Einat on 2007-02-18 13:08:28 as ** along with 1 group structural_bioinformatics
  • Conserved residues and the mechanism of protein folding.
    Nature, Vol. 379, No. 6560. (4 January 1996), pp. 96-98.
    by E Shakhnovich, V Abkevich, O Ptitsyn
    posted to conservation folding by Einat on 2007-02-18 13:07:51 as ** along with 2 people and 1 group cat_worth medic0747 structural_bioinformatics
  • SNPs, protein structure, and disease.
    Hum Mutat, Vol. 17, No. 4. (April 2001), pp. 263-270.
    by Z Wang, J Moult
    posted to protein_structure snps by Einat on 2007-02-18 13:07:16 as ** along with 2 people and 1 group massivemayhem cat_worth structural_bioinformatics
  • Predicting the Effects of Amino Acid Substitutions on Protein Function.
    Annu Rev Genomics Hum Genet (9 August 2005)
    by Pauline C C Ng, Steven Henikoff
    posted to amino-acid-propensities protein-function by Einat on 2007-02-18 13:06:18 as ** along with 6 people and 2 groups caporaso hdopazo ramensky massivemayhem cat_worth lpfernandes structural_bioinformatics biomedical-nlp
  • Allosteric determinants in guanine nucleotide-binding proteins.
    Proc Natl Acad Sci U S A, Vol. 100, No. 24. (25 November 2003), pp. 14445-14450.
    by ME Hatley, SW Lockless, SK Gibson, AG Gilman, R Ranganathan
    posted to allostery by Einat on 2007-02-18 13:04:57 as ** along with 4 people and 5 groups barry lna marcius caporaso structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
  • Flavin-dependent enzymes
    (1998), pp. 84-100.
    by BA Palfey, V Massey
    edited by M Sinnot
    posted to fad-binding by Einat on 2007-02-18 13:04:08 as ** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • Hydrogen bonding increases packing density in the protein interior
    Proteins: Structure, Function, and Bioinformatics, Vol. 63, No. 2. (2006), pp. 278-282.
    by David Schell, Jerry Tsai, Martin J Scholtz, Nick C Pace
    posted to hydrogen-bonds protein-stability by Einat on 2007-02-18 13:03:27 as ** along with 1 person and 1 group cat_worth structural_bioinformatics
  • Low-throughput model design of protein folding inhibitors.
    Proteins (12 February 2007)
    by R A A Broglia, G Tiana, L Sutto, D Provasi, V Perelli
    posted to protein-stability by Einat on 2007-02-18 12:40:44 as ** along with 1 group structural_bioinformatics
  • Local motions in a benchmark of allosteric proteins.
    Proteins (12 February 2007)
    by Michael D D Daily, Jeffrey J J Gray
    posted to allostery protein_structure by Einat on 2007-02-18 12:34:47 as ** along with 2 people and 1 group lna choonpeng structural_bioinformatics
  • Relating three-dimensional structures to protein networks provides evolutionary insights.
    Science, Vol. 314, No. 5807. (22 December 2006), pp. 1938-1941.
    by PM Kim, LJ Lu, Y Xia, MB Gerstein
    posted to evolution networks protein_structure by Einat on 2007-01-07 11:40:57 as ** along with 17 people and 2 groups bicko lfriedl chad_davis tny choonpeng timflutre grahamc ramensky massivemayhem efge lpfernandes cdeane Pao-Yang phoenixzxl carlk paolomarcatili saket structural_bioinformatics kdl
  • Bio3d: an R package for the comparative analysis of protein structures.
    Bioinformatics (29 August 2006)
    by Barry J J Grant, Ana P C P Rodrigues, Karim M M Elsawy, J Andrew A McCammon, Leo S D S Caves
    posted to protein_structure r_package by Einat on 2006-11-02 10:06:42 as ** along with 6 people and 2 groups ana barry plofje krishnaJCSG insectopalo cdeane structural_bioinformatics Bioinformatics
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