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gbart library [292 articles]

Статьи, недавно добавленные в библиотеку gbart .
  • Dynamic domain threading.
    Proteins, Vol. 64, No. 3. (15 August 2006), pp. 601-614.
    by WR Taylor, K Lin, D Klose, F Fraternali, I Jonassen
    posted to threading by gbart on 2006-10-11 13:13:01 as **
  • Protein fold refinement: building models from idealized folds using motif constraints and multiple sequence data.
    Protein Eng, Vol. 6, No. 6. (August 1993), pp. 593-604.
    by WR Taylor
    posted to fold_refinement by gbart on 2006-10-11 11:22:07 as **
  • Protein structure comparison using bipartite graph matching and its application to protein structure classification.
    Mol Cell Proteomics, Vol. 1, No. 4. (April 2002), pp. 334-339.
    by WR Taylor
    posted to structure_classification structure_comparison by gbart on 2006-10-11 11:21:15 as **
  • MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
    BMC Bioinformatics, Vol. 5, No. 1. (19 August 2004)
    by RC Edgar
    posted to sequence_alignment software by gbart on 2006-10-11 11:19:09 as ** along with 14 people and 3 groups sebk wallacei knaseanka chrn jwm balajis caporaso sriram_s cdallett sanchezbuelna timflutre gisle urgi Ema Radiation_Damage Stressosome biomedical-nlp
  • Pfam: clans, web tools and services.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by RD Finn, J Mistry, B Schuster-Böckler, S Griffiths-Jones, V Hollich, T Lassmann, S Moxon, M Marshall, A Khanna, R Durbin, SR Eddy, EL Sonnhammer, A Bateman
    posted to database by gbart on 2006-10-11 11:18:26 as ** along with 10 people dullhunk massivemayhem cjeans siebertm lpfernandes pablomendes antonkratz natstreet Lombardo_7 phoenixzxl
  • Effective use of sequence correlation and conservation in fold recognition.
    J Mol Biol, Vol. 293, No. 5. (12 November 1999), pp. 1221-1239.
    by O Olmea, B Rost, A Valencia
    posted to correlated_mutations fold_discrimination fold_recognition by gbart on 2006-10-06 12:09:49 as ** along with 1 person cjeans
  • The prediction of protein contacts from multiple sequence alignments.
    Protein Eng, Vol. 9, No. 11. (November 1996), pp. 941-948.
    by DJ Thomas, G Casari, C Sander
    posted to correlated_mutations by gbart on 2006-10-06 12:09:04 as ** along with 1 person jteyra
  • Correlated mutations and residue contacts in proteins.
    Proteins, Vol. 18, No. 4. (April 1994), pp. 309-317.
    by U Göbel, C Sander, R Schneider, A Valencia
    posted to correlated_mutations by gbart on 2006-10-06 12:08:07 as ** along with 5 people analogAI dgront cjeans jteyra Lombardo_7
  • Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations.
    Proteins, Vol. 48, No. 4. (1 September 2002), pp. 611-617.
    by I Kass, A Horovitz
    posted to correlated_mutations by gbart on 2006-10-06 12:06:50 as **
  • Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions.
    J Mol Biol, Vol. 303, No. 3. (27 October 2000), pp. 433-446.
    by SM Larson, AA Di Nardo, AR Davidson
    posted to correlated_mutations by gbart on 2006-10-06 12:06:15 as ** along with 6 people and 2 groups ana analogAI Haggan cjeans tale bethbromley structural_bioinformatics Bioinformatics
  • Positional dependence, cliques, and predictive motifs in the bHLH protein domain.
    J Mol Evol, Vol. 48, No. 5. (May 1999), pp. 501-516.
    by WR Atchley, W Terhalle, A Dress
    posted to correlated_mutations by gbart on 2006-10-06 12:05:38 as **
  • How frequent are correlated changes in families of protein sequences?
    Proc Natl Acad Sci U S A, Vol. 91, No. 1. (4 January 1994), pp. 98-102.
    by E Neher
    posted to correlated_mutations by gbart on 2006-10-06 12:04:55 as ** along with 2 people Haggan friendpine
  • Toward High-Resolution de Novo Structure Prediction for Small Proteins
    Science, Vol. 309, No. 5742. (16 September 2005), pp. 1868-1871.
    by Philip Bradley, Kira M Misura, David Baker
    posted to structure_prediction by gbart on 2006-10-04 16:34:01 as ** along with 8 people and 4 groups BragilMassoud ana barry thaliana jwm vavi marcius thamelry structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions.
    J Biol Chem, Vol. 279, No. 9. (27 February 2004), pp. 8126-8132.
    by S Madabushi, AK Gross, A Philippi, EC Meng, TG Wensel, O Lichtarge
    posted to evolutionary_trace gpcr by gbart on 2006-10-04 16:30:56 as ** along with 2 people and 1 group xdeupi sriram_s LabCompMed
  • Protein model refinement using structural fragment tessellation.
    Comput Biol Chem, Vol. 30, No. 5. (October 2006), pp. 360-366.
    by I Jonassen, D Klose, WR Taylor
    posted to furball by gbart on 2006-10-04 16:29:58 as **
  • A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments.
    Bioinformatics, Vol. 20, No. 10. (10 July 2004), pp. 1565-1572.
    by JP Dekker, A Fodor, RW Aldrich, G Yellen
    posted to statistical_coupling by gbart on 2006-10-04 16:29:19 as ** along with 3 people Haggan cjeans ca3295
  • On evolutionary conservation of thermodynamic coupling in proteins.
    J Biol Chem, Vol. 279, No. 18. (30 April 2004), pp. 19046-19050.
    by AA Fodor, RW Aldrich
    posted to statistical_coupling by gbart on 2006-10-04 16:28:42 as ** along with 7 people and 2 groups ana barry cjeans tale friendpine ca3295 Lombardo_7 structural_bioinformatics Bioinformatics
  • Influence of conservation on calculations of amino acid covariance in multiple sequence alignments.
    Proteins, Vol. 56, No. 2. (1 August 2004), pp. 211-221.
    by AA Fodor, RW Aldrich
    posted to statistical_coupling by gbart on 2006-10-04 16:28:16 as ** along with 6 people and 2 groups ana cjeans jlh64 mingzhi dgront Lombardo_7 structural_bioinformatics Bioinformatics
  • Statistical coevolution analysis and molecular dynamics: identification of amino acid pairs essential for catalysis.
    Proc Natl Acad Sci U S A, Vol. 102, No. 4. (25 January 2005), pp. 994-999.
    by RA Estabrook, J Luo, MM Purdy, V Sharma, P Weakliem, TC Bruice, NO Reich
    posted to cat_res molecular_dynamics statistical_coupling by gbart on 2006-10-04 16:27:38 as ** along with 4 people and 2 groups ana barry pansapiens dimka structural_bioinformatics Bioinformatics
  • Detection and reduction of evolutionary noise in correlated mutation analysis
    Protein Engineering, Design and Selection, Vol. 18, No. 5. (1 May 2005), pp. 247-253.
    by Orly Noivirt, Miriam Eisenstein, Amnon Horovitz
    posted to correlated_mutations by gbart on 2006-10-04 16:26:46 as ** along with 2 people and 2 groups barry cjeans structural_bioinformatics Bioinformatics
  • Determination of network of residues that regulate allostery in protein families using sequence analysis.
    Protein Sci, Vol. 15, No. 2. (February 2006), pp. 258-268.
    by RI Dima, D Thirumalai
    posted to statistical_coupling by gbart on 2006-10-04 16:26:11 as ** along with 5 people and 1 group xdeupi nirfriedman choonpeng tale mingzhi LabCompMed
  • Natural Selection for Kinetic Stability Is a Likely Origin of Correlations between Mutational Effects on Protein Energetics and Frequencies of Amino Acid Occurrences in Sequence Alignments.
    J Mol Biol, Vol. 362, No. 5. (6 October 2006), pp. 966-978.
    by R Godoy-Ruiz, F Ariza, D Rodriguez-Larrea, R Perez-Jimenez, B Ibarra-Molero, JM Sanchez-Ruiz
    posted to correlated_mutations by gbart on 2006-10-04 16:25:41 as **
  • A simple tool to explore the distance distribution of correlated mutations in proteins.
    Biophys Chem, Vol. 119, No. 3. (1 February 2006), pp. 240-246.
    by R Perez-Jimenez, R Godoy-Ruiz, A Parody-Morreale, B Ibarra-Molero, JM Sanchez-Ruiz
    posted to correlated_mutations by gbart on 2006-10-04 16:24:52 as ** along with 1 person Lombardo_7
  • Correlated mutations: Advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families.
    Proteins (28 February 2006)
    by Inbal Halperin, Haim Wolfson, Ruth Nussinov
    posted to correlated_mutations by gbart on 2006-10-04 16:24:06 as ** along with 7 people bicko ramensky cjeans tale mingzhi friendpine Lombardo_7
  • A simple approach for protein structure discrimination based on the network pattern of conserved hydrophobic residues.
    Protein Eng Des Sel, Vol. 19, No. 6. (June 2006), pp. 265-275.
    by UK Muppirala, Z Li
    posted to fold_discrimination by gbart on 2006-10-04 16:23:41 as **
  • Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
    Protein Eng, Vol. 7, No. 3. (March 1994), pp. 349-358.
    by IN Shindyalov, NA Kolchanov, C Sander
    posted to 3d_contacts correlated_mutations by gbart on 2006-10-04 16:22:16 as ** along with 2 people nirfriedman kieran101
  • Global fold determination from a small number of distance restraints.
    J Mol Biol, Vol. 251, No. 2. (11 August 1995), pp. 308-326.
    by A Aszódi, MJ Gradwell, WR Taylor
    posted to fold_recognition by gbart on 2006-10-04 16:21:38 as ** along with 1 person nigham
  • Ab initio folding of proteins using restraints derived from evolutionary information.
    Proteins, Vol. Suppl 3 (1999), pp. 177-185.
    by AR Ortiz, A Kolinski, P Rotkiewicz, B Ilkowski, J Skolnick
    posted to evolutionary_information protein_folding restraints by gbart on 2006-10-04 16:20:35 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Knowledge-based potential functions in protein design.
    Curr Opin Struct Biol, Vol. 12, No. 4. (August 2002), pp. 447-452.
    by WP Russ, R Ranganathan
    posted to statistical_coupling by gbart on 2006-03-09 14:54:26 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Local complexity of amino acid interactions in a protein core.
    Proc Natl Acad Sci U S A, Vol. 101, No. 1. (6 January 2004), pp. 111-116.
    by RK Jain, R Ranganathan
    posted to statistical_coupling by gbart on 2006-03-09 14:53:17 as ** along with 5 people and 4 groups ana barry lna marcius choonpeng structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Structural determinants of allosteric ligand activation in RXR heterodimers.
    Cell, Vol. 116, No. 3. (6 February 2004), pp. 417-429.
    by AI Shulman, C Larson, DJ Mangelsdorf, R Ranganathan
    posted to allostery evolution statistical_coupling by gbart on 2006-03-09 14:52:03 as ** along with 3 people and 3 groups lna marcius caporaso biomedical-nlp BioinfoCIPF SGU-CIPF
  • Predicting enzyme function from protein sequence.
    Curr Opin Chem Biol, Vol. 9, No. 2. (April 2005), pp. 202-209.
    by J Minshull, JE Ness, C Gustafsson, S Govindarajan
    posted to enzyme function by gbart on 2006-01-04 15:48:58 as *****
  • Predicting solvent accessibility: higher accuracy using Bayesian statistics and optimized residue substitution classes.
    Proteins, Vol. 25, No. 1. (May 1996), pp. 38-47.
    by MJ Thompson, RA Goldstein
    posted to solv_acc by gbart on 2005-12-07 11:00:59 as **
  • A Fourier analysis of symmetry in protein structure
    Protein Engineering, Vol. 15, No. 2. (February 2002), pp. 79-89.
    by William R Taylor, Jaap Heringa, Franck Baud, Tomas P Flores
    posted to ramble by gbart on 2005-12-02 13:50:20 as **
  • Protein fold comparison by the alignment of topological strings.
    Protein Eng, Vol. 16, No. 12. (December 2003), pp. 949-955.
    by LO Johannissen, WR Taylor
    posted to fold_recognition topology by gbart on 2005-12-02 13:47:27 as ** along with 1 person martainn
  • Structural trees for protein superfamilies.
    Proteins, Vol. 28, No. 2. (June 1997), pp. 241-260.
    by AV Efimov
    posted to evolution strutural_trees superfamily by gbart on 2005-11-24 14:52:20 as **
  • Threading using neural nEtwork (TUNE): the measure of protein sequence-structure compatibility.
    Bioinformatics, Vol. 18, No. 10. (October 2002), pp. 1350-1357.
    by K Lin, AC May, WR Taylor
    posted to fold_recognition neural_network threading by gbart on 2005-11-23 17:34:28 as ** along with 2 people KuangLin owarburg
  • Is allostery an intrinsic property of all dynamic proteins?
    Proteins, Vol. 57, No. 3. (15 November 2004), pp. 433-443.
    by K Gunasekaran, B Ma, R Nussinov
    posted to allostery by gbart on 2005-11-23 09:56:31 as read along with 5 people lna leemary4 choonpeng ruvido cactus
  • Evolutionarily conserved networks of residues mediate allosteric communication in proteins.
    Nat Struct Biol, Vol. 10, No. 1. (January 2003), pp. 59-69.
    by GM Süel, SW Lockless, MA Wall, R Ranganathan
    posted to allostery evolution statistical_coupling by gbart on 2005-11-22 16:52:28 as ** along with 15 people and 3 groups lna dimka marcius eckart_bindewald analogAI nirfriedman dgront caporaso choonpeng efge carlescorbi mingzhi yalexeev weisblum ca3295 biomedical-nlp BioinfoCIPF SGU-CIPF
  • Shared promiscuous activities and evolutionary features in various members of the amidohydrolase superfamily.
    Biochemistry, Vol. 44, No. 38. (27 September 2005), pp. 12728-12736.
    by C Roodveldt, DS Tawfik
    posted to enzyme mechanism plasticity struct_func by gbart on 2005-11-18 12:08:42 as ****
  • Evolutionarily conserved pathways of energetic connectivity in protein families.
    Science, Vol. 286, No. 5438. (8 October 1999), pp. 295-299.
    by SW Lockless, R Ranganathan
    posted to protein_folding statistical_coupling struct_func by gbart on 2005-11-16 15:13:38 as ** along with 2 people lna analogAI
  • The family feud: do proteins with similar structures fold via the same pathway?
    Curr Opin Struct Biol, Vol. 15, No. 1. (February 2005), pp. 42-49.
    by A Zarrine-Afsar, SM Larson, AR Davidson
    posted to phi_analysis protein_folding by gbart on 2005-11-16 13:21:54 as ** along with 1 person apaydin
  • Phi value versus psi analysis.
    Proc Natl Acad Sci U S A, Vol. 101, No. 50. (14 December 2004), pp. 17327-17328.
    by AR Fersht
    posted to phi_analysis protein_folding by gbart on 2005-11-16 13:21:18 as **
  • The protein folding transition state: what are Phi-values really telling us?
    Protein Pept Lett, Vol. 12, No. 2. (February 2005), pp. 117-122.
    by DP Raleigh, KW Plaxco
    posted to phi_analysis protein_folding by gbart on 2005-11-16 13:20:28 as **
  • Differences in the folding transition state of ubiquitin indicated by phi and psi analyses.
    Proc Natl Acad Sci U S A, Vol. 101, No. 50. (14 December 2004), pp. 17377-17382.
    by TR Sosnick, RS Dothager, BA Krantz
    posted to phi_analysis protein_folding by gbart on 2005-11-16 13:19:36 as ****
  • Simulating protein evolution in sequence and structure space.
    Curr Opin Struct Biol, Vol. 14, No. 2. (April 2004), pp. 202-207.
    by Y Xia, M Levitt
    posted to evolution protein simulation by gbart on 2005-11-14 16:01:37 as ** along with 10 people and 4 groups betainverse korakot mdimmic karbak rmj001 ana barry aalibes analogAI insectopalo Philosophy_of_Information Blog_and_Wiki_Research structural_bioinformatics Bioinformatics
  • Evolutionary information for specifying a protein fold
    Nature, Vol. 437, No. 7058., pp. 512-518.
    by Michael Socolich, Steve W Lockless, William P Russ, Heather Lee, Kevin H Gardner, Rama Ranganathan
    posted to popcorn protein_design protein_folding by gbart on 2005-11-14 13:40:33 as read along with 14 people and 5 groups ana barry lna bpb Einat balajis marcius analogAI nirfriedman caporaso massivemayhem mingzhi bethbromley ca3295 structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
  • Multiple sequence threading: an analysis of alignment quality and stability.
    J Mol Biol, Vol. 269, No. 5. (27 June 1997), pp. 902-943.
    by WR Taylor
    posted to algorithm alignment threading by gbart on 2005-11-14 10:34:12 as **
  • A template based method of pattern matching in protein sequences.
    Prog Biophys Mol Biol, Vol. 54, No. 3. (1989), pp. 159-252.
    by WR Taylor
    posted to pattern_matching template by gbart on 2005-11-14 10:21:59 as ***** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • Defining linear segments in protein structure.
    J Mol Biol, Vol. 310, No. 5. (27 July 2001), pp. 1135-1150.
    by WR Taylor
    posted to prediction secondary_structure by gbart on 2005-11-14 09:39:31 as *****
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