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jteyra library [69 articles]

Статьи, недавно добавленные в библиотеку jteyra .
  • Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain.
    PLoS Comput Biol, Vol. 2, No. 1. (January 2006)
    by T Hou, K Chen, WA McLaughlin, B Lu, W Wang
    posted to example mm_pbsa by jteyra on 2008-08-28 14:38:48 as ** along with 4 people neils carlescorbi Evangelia biehl
  • A structural perspective on protein-protein interactions.
    Curr Opin Struct Biol, Vol. 14, No. 3. (June 2004), pp. 313-324.
    by RB Russell, F Alber, P Aloy, FP Davis, D Korkin, M Pichaud, M Topf, A Sali
    posted to ppi review by jteyra on 2008-08-28 11:13:12 as ** along with 13 people and 1 group baaden bicko anita chad_davis dgront sriram_s ruvido cjeans Evangelia Pao-Yang marti higueruelo timg structure-bii
  • Rapid retrieval of protein structures from databases
    Drug Discovery Today, Vol. 12, No. 17-18. (September 2007), pp. 732-739.
    by Zeyar Aung, Kian-Lee Tan
    posted to review straln_sse by jteyra on 2008-08-28 11:05:21 as ** along with 1 person nigham
  • Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Ryoichi Minai, Yo Matsuo, Hiroyuki Onuki, Hiroshi Hirota
    posted to binding software straln_br by jteyra on 2008-08-22 16:23:21 as ** along with 6 people ramensky tjimenez chad_davis massivemayhem mingzhi higueruelo
  • Chemokine:Receptor Structure, Interactions, and Antagonism
    Annual Review of Immunology, Vol. 25, No. 1. (2007), pp. 787-820.
    by Samantha J Allen, Susan E Crown, Tracy M Handel
    posted to ccr5_tys tys by jteyra on 2008-08-22 13:52:07 as ** along with 1 person HugoMarcelo
  • LINCS: A linear constraint solver for molecular simulations
    Journal of Computational Chemistry, Vol. 18, No. 12. (1997), pp. 1463-1472.
    by Berk Hess, Henk Bekker, Herman JC Berendsen, Johannes GEM Fraaije
    posted to gromacs by jteyra on 2008-08-20 10:44:48 as ** along with 3 people A_Coletta_Thesis tji ashaytan
  • A smooth particle mesh Ewald method
    The Journal of Chemical Physics, Vol. 103, No. 19. (1995), pp. 8577-8593.
    by Ulrich Essmann, Lalith Perera, Max L Berkowitz, Tom Darden, Hsing Lee, Lee G Pedersen
    posted to gromacs by jteyra on 2008-08-20 10:44:22 as ** along with 7 people lillekatt and_ped10 easybakemuffin RamuAnandakrishnan ashaytan mikaellund 6rheology
  • Molecular dynamics with coupling to an external bath
    The Journal of Chemical Physics, Vol. 81, No. 8. (1984), pp. 3684-3690.
    by HJC Berendsen, JPM Postma, WF van Gunsteren, A Dinola, JR Haak
    posted to gromacs by jteyra on 2008-08-20 10:43:44 as ** along with 6 people lillekatt allmensch jwagoner luisand tji choonpeng
  • Protein-protein recognition and interaction hot spots in an antigen-antibody complex: free energy decomposition identifies "efficient amino acids".
    Proteins, Vol. 67, No. 2. (1 May 2007), pp. 418-434.
    by V Lafont, M Schaefer, RH Stote, D Altschuh, A Dejaegere
    posted to decomposition mm_pbsa by jteyra on 2008-08-19 09:30:49 as ** along with 1 person higueruelo
  • Can correlated mutations in protein domain families be used for protein design?
    Brief Bioinform, Vol. 2, No. 3. (1 January 2001), pp. 279-288.
    by Sylvia B Nagl
    posted to correlated_mutations by jteyra on 2008-08-19 09:28:52 as ** along with 1 person Lombardo_7
  • 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 jteyra on 2008-08-19 09:23:36 as ** along with 1 person gbart
  • Structural Basis of Human Triosephosphate Isomerase Deficiency: MUTATION E104D IS RELATED TO ALTERATIONS OF A CONSERVED WATER NETWORK AT THE DIMER INTERFACE
    J. Biol. Chem., Vol. 283, No. 34. (22 August 2008), pp. 23254-23263.
    by Claudia Rodriguez-Almazan, Rodrigo Arreola, David Rodriguez-Larrea, Beatriz Aguirre-Lopez, Marietta T de Gomez-Puyou, Ruy Perez-Montfort, Miguel Costas, Armando Gomez-Puyou, Alfredo Torres-Larios
    posted to water_bioexample water_interface by jteyra on 2008-08-15 15:29:46 as **
  • Recognition of a CXCR4 Sulfotyrosine by the Chemokine Stromal Cell-derived Factor-1[alpha] (SDF-1[alpha]/CXCL12)
    Journal of Molecular Biology, Vol. 359, No. 5. (23 June 2006), pp. 1400-1409.
    by Christopher T Veldkamp, Christoph Seibert, Francis C Peterson, Thomas P Sakmar, Brian F Volkman
    posted to cxcr4 tys by jteyra on 2008-08-15 11:42:01 as **
  • CXCR4-CCR5: A couple modulating T cell functions.
    Proceedings of the National Academy of Sciences of the United States of America (15 July 2008)
    by Rita Lucia L Contento, Barbara Molon, Cedric Boularan, Tullio Pozzan, Santos Manes, Stefano Marullo, Antonella Viola
    posted to ccr5_cxcr4_binding by jteyra on 2008-08-15 10:36:00 as ** along with 1 person shimi002
  • Identification of protein interaction partners and protein-protein interaction sites
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Sophie Sacquin-Mora, Alessandra Carbone, Richard Lavery
    posted to ppi_homology ppi_quaternary software by jteyra on 2008-08-12 08:41:38 as ** along with 1 person kluck
  • Peptide Folding: When Simulation Meets Experiment
    Angewandte Chemie International Edition, Vol. 38, No. 1-2. (1999), pp. 236-240.
    by Xavier Daura, Karl Gademann, Bernhard Jaun, Dieter Seebach, Wilfred F van Gunsteren, Alan E Mark
    posted to remd_dauraalg by jteyra on 2008-08-08 10:55:19 as **
  • Crystal structure of GRIP1 PDZ6-peptide complex reveals the structural basis for class II PDZ target recognition and PDZ domain-mediated multimerization.
    The Journal of biological chemistry, Vol. 278, No. 10. (7 March 2003), pp. 8501-8507.
    by YJ Im, SH Park, SH Rho, JH Lee, GB Kang, M Sheng, E Kim, SH Eom
    posted to pdz_dimer pdz_peptide by jteyra on 2008-08-06 16:52:38 as **
  • DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions.
    Bioinformatics (19 January 2008)
    by Julie Bernauer, Ranjit Prasad P Bahadur, Francis Rodier, Joël Janin, Anne Poupon
    posted to packing ppi software by jteyra on 2008-08-06 10:19:40 as ** along with 3 people kintoki higueruelo bicko
  • MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)
    by IW Davis, A Leaver-Fay, VB Chen, JN Block, GJ Kapral, X Wang, LW Murray, WB Arendall, J Snoeyink, JS Richardson, DC Richardson
    posted to modeling_check noncovalent_bonds by jteyra on 2008-08-06 09:43:04 as ** along with 1 person jwm
  • Integration of small angle X-ray scattering data into structural modeling of proteins and their assemblies
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Friedrich Förster, Benjamin Webb, Kristin A Krukenberg, Hiro Tsuruta, David A Agard, Andrej Sali
    posted to ppi_quaternary by jteyra on 2008-08-05 14:38:00 as **
  • NOXclass: prediction of protein-protein interaction types.
    BMC Bioinformatics, Vol. 7 (2006)
    by H Zhu, FS Domingues, I Sommer, T Lengauer
    posted to packing ppi software by jteyra on 2008-08-04 11:04:40 as ** along with 4 people bicko chad_davis conkymacro marti
  • Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Dario Ghersi, Roberto Sanchez
    posted to docking_scowlp by jteyra on 2008-08-04 10:12:10 as **
  • PROSITE: A documented database using patterns and profiles as motif descriptors
    Brief Bioinform, Vol. 3, No. 3. (1 January 2002), pp. 265-274.
    by Christian J Sigrist, Lorenzo Cerutti, Nicolas Hulo, Alexandre Gattiker, Laurent Falquet, Marco Pagni, Amos Bairoch, Philipp Bucher
    posted to prosite protein_domains by jteyra on 2008-07-30 08:25:03 as ** along with 2 people siebertm shung
  • CDD: a curated Entrez database of conserved domain alignments.
    Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 383-387.
    by A Marchler-Bauer, JB Anderson, C DeWeese-Scott, ND Fedorova, LY Geer, S He, DI Hurwitz, JD Jackson, AR Jacobs, CJ Lanczycki, CA Liebert, C Liu, T Madej, GH Marchler, R Mazumder, AN Nikolskaya, AR Panchenko, BS Rao, BA Shoemaker, V Simonyan, JS Song, PA Thiessen, S Vasudevan, Y Wang, RA Yamashita, JJ Yin, SH Bryant
    posted to cdd protein_domains by jteyra on 2008-07-30 08:24:47 as ** along with 4 people balajis maryee cjeans gulkur
  • Pfam: multiple sequence alignments and HMM-profiles of protein domains.
    Nucleic Acids Res, Vol. 26, No. 1. (1 January 1998), pp. 320-322.
    by EL Sonnhammer, SR Eddy, E Birney, A Bateman, R Durbin
    posted to pfam protein_domains by jteyra on 2008-07-30 08:23:27 as ** along with 4 people and 1 group tharris cjeans antonkratz gulkur C. elegans / WormBase
  • SMART, a simple modular architecture research tool: Identification of signaling domains
    Proceedings of the National Academy of Sciences, Vol. 95, No. 11. (26 May 1998), pp. 5857-5864.
    by Jorg Schultz, Frank Milpetz, Peer Bork, Chris P Ponting
    posted to protein_domains smart by jteyra on 2008-07-30 08:22:17 as ** along with 1 person Evangelia
  • CATH--a hierarchic classification of protein domain structures.
    Structure, Vol. 5, No. 8. (15 August 1997), pp. 1093-1108.
    by CA Orengo, AD Michie, S Jones, DT Jones, MB Swindells, JM Thornton
    posted to cath fold_classification by jteyra on 2008-07-30 08:17:48 as ** along with 9 people and 4 groups tjimenez dimka jwm chad_davis Einat caporaso massivemayhem sim82 gulkur structural_bioinformatics Radiation_Damage Stressosome biomedical-nlp
  • Dali/FSSP classification of three-dimensional protein folds.
    Nucleic acids research, Vol. 25, No. 1. (1 January 1997), pp. 231-234.
    by L Holm, C Sander
    posted to fold_classification fssp by jteyra on 2008-07-30 08:14:56 as **
  • The universal protein resource (UniProt).
    Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008)
    by
    posted to database swissprot uniprot by jteyra on 2008-07-30 08:05:18 as ** along with 4 people jyuh renatomilani kintoki janasont
  • Structural insight into the pH-induced conformational changes within the native human transthyretin tetramer
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Satheesh K Palaninathan, Mohamed, William C Snee, Jeffery W Kelly, James C Sacchettini
    posted to il16_oligomer by jteyra on 2008-07-24 09:46:34 as **
  • Novel protein folds and their nonsequential structural analogs
    Protein Sci (26 June 2008), ps.035469.108.
    by Aysam Guerler, Ernst-Walter Knapp
    posted to straln_nonseq by jteyra on 2008-07-15 08:55:45 as **
  • The immunoglobulin fold. Structural classification, sequence patterns and common core.
    Journal of molecular biology, Vol. 242, No. 4. (30 September 1994), pp. 309-320.
    by P Bork, L Holm, C Sander
    posted to fold_ig by jteyra on 2008-07-14 18:06:04 as **
  • Classification of Water Molecules in Protein Binding Sites
    J. Am. Chem. Soc., Vol. 129, No. 9. (7 March 2007), pp. 2577-2587.
    by C Barillari, J Taylor, R Viner, JW Essex
    posted to water_interface by jteyra on 2008-07-14 18:04:32 as ** along with 3 people daevans dmobley LamBras
  • On itinerant water molecules and detectability of protein-protein interfaces through comparative analysis of homologues.
    J Mol Biol, Vol. 369, No. 2. (1 June 2007), pp. 584-595.
    by I Mihalek, I Res, O Lichtarge
    posted to water_bioexample water_interface by jteyra on 2008-07-14 18:03:00 as ** along with 1 person marti
  • MHC-peptide binding is assisted by bound water molecules.
    J Mol Biol, Vol. 338, No. 2. (23 April 2004), pp. 419-435.
    by PM Petrone, AE Garcia
    posted to water_bioexample by jteyra on 2008-07-14 18:00:24 as ** along with 2 people and 1 group ssomani fjc1 structure-bii
  • Solvent mobility and the protein 'glass' transition.
    Nat Struct Biol, Vol. 7, No. 1. (January 2000), pp. 34-38.
    by D Vitkup, D Ringe, GA Petsko, M Karplus
    posted to water by jteyra on 2008-07-14 16:18:56 as ** along with 2 people naitsabes onufriev
  • Structural systems biology: modelling protein interactions
    Nature Reviews Molecular Cell Biology, Vol. 7, No. 3., pp. 188-197.
    by Patrick Aloy, Robert B Russell
    posted to ppi_homology review by jteyra on 2008-07-11 14:40:51 as ** along with 19 people and 3 groups ana aalibes bicko xico dgront drastic choonpeng henschel ruvido massivemayhem cat_worth fishtank iris_2001 gvuister lpfernandes Evangelia andreas_foersch higueruelo chad_davis structural_bioinformatics Bioinformatics WetBiology
  • Hydrophobic patches on protein subunit interfaces: Characteristics and prediction
    Proteins: Structure, Function, and Genetics, Vol. 28, No. 3. (1997), pp. 333-343.
    by Philip Lijnzaad, Patrick Argos
    posted to ppi_analysis by jteyra on 2008-07-11 10:22:31 as **
  • Computational redesign of protein-protein interaction specificity.
    Nat Struct Mol Biol, Vol. 11, No. 4. (April 2004), pp. 371-379.
    by T Kortemme, LA Joachimiak, AN Bullock, AD Schuler, BL Stoddard, D Baker
    posted to ppi_design ppi_homology rosetta by jteyra on 2008-07-11 09:59:58 as ** along with 6 people lna jwm bicko ruvido cjeans tale
  • SH3-SPOT: An Algorithm to Predict Preferred Ligands to Different Members of the SH3 Gene Family
    Journal of Molecular Biology (April 2000), pp. 313-328.
    by B Brannetti, A Via, G Cestra, G Cesareni, MH Citterich
    posted to algorithm ppii scoring sh3_specificity by jteyra on 2008-07-11 09:50:45 as **
  • Computational design of protein-protein interactions.
    Curr Opin Chem Biol, Vol. 8, No. 1. (February 2004), pp. 91-97.
    by T Kortemme, D Baker
    posted to ppi_design review rosetta by jteyra on 2008-07-11 09:39:05 as ** along with 5 people lna jwm bicko hmk cjeans
  • Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases
    Nature Biotechnology, Vol. 26, No. 7. (29 June 2008), pp. 808-816.
    by Elena E Perez, Jianbin Wang, Jeffrey C Miller, Yann Jouvenot, Kenneth A Kim, Olga Liu, Nathaniel Wang, Gary Lee, Victor V Bartsevich, Ya-Li Lee, Dmitry Y Guschin, Igor Rupniewski, Adam J Waite, Carmine Carpenito, Richard G Carroll, Jordan S Orange, Fyodor D Urnov, Edward J Rebar, Dale Ando, Philip D Gregory, James L Riley, Michael C Holmes, Carl H June
    posted to ccr5 cd4 hiv il16_disease by jteyra on 2008-07-11 09:13:15 as **
  • 3D Complex: A Structural Classification of Protein Complexes
    PLoS Computational Biology, Vol. 2, No. 11. (1 November 2006), e155.
    by Emmanuel D Levy, Jose B Pereira-Leal, Cyrus Chothia, Sarah A Teichmann
    posted to oligomerization packing ppi_homology by jteyra on 2008-07-10 17:13:15 as ** along with 2 people aalibes krishnaJCSG
  • Water structure and interactions with protein surfaces
    Current Opinion in Structural Biology, Vol. 16, No. 2. (April 2006), pp. 152-159.
    by Tanya M Raschke
    posted to water_surface by jteyra on 2008-07-10 16:09:44 as ** along with 1 person rabio
  • The Relationship between the Flexibility of Proteins and their Conformational States on Forming Protein-Protein Complexes with an Application to Protein-Protein Docking
    Journal of Molecular Biology, Vol. 347, No. 5. (15 April 2005), pp. 1077-1101.
    by Graham R Smith, Michael Sternberg, Paul A Bates
    posted to docking_flexible protein_flexibility by jteyra on 2008-07-10 16:08:06 as ** along with 6 people and 3 groups ana barry aqeel bicko yongzhao ttjoseph structural_bioinformatics Bioinformatics TSRI_MGL
  • Trapped water molecules are essential to structural dynamics and function of a ribozyme.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 36. (5 September 2006), pp. 13380-13385.
    by MM Rhodes, K Réblová, J Sponer, NG Walter
    posted to water_bioexample by jteyra on 2008-07-10 16:05:16 as **
  • Solvated docking: introducing water into the modelling of biomolecular complexes.
    Bioinformatics (9 August 2006)
    by Aalt D J D van Dijk, Alexandre M J J M Bonvin
    posted to docking_water by jteyra on 2008-07-10 16:04:12 as ** along with 5 people and 1 group arlam msuarezdiez BragilMassoud bicko Lombardo_7 group
  • Electrostatics calculations: latest methodological advances.
    Curr Opin Struct Biol (13 March 2006)
    by Patrice Koehl
    posted to electrostatics review by jteyra on 2008-07-10 16:02:43 as ** along with 3 people BragilMassoud qwermish RamuAnandakrishnan
  • 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 ppi by jteyra on 2008-07-10 15:58:36 as ** along with 5 people gbart analogAI dgront cjeans Lombardo_7
  • Thermodynamics of Buried Water Clusters at a Protein-Ligand Binding Interface
    J. Phys. Chem. B, Vol. 110, No. 3. (26 January 2006), pp. 1464-1475.
    by Z Li, T Lazaridis
    posted to water_bioexample by jteyra on 2008-07-10 15:55:27 as **
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