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jwm structural_bioinformatics [76 articles]

最近 jwm さんのライブラリに追加された論文の中から タグ structural_bioinformatics. You can also see everyone's structural_bioinformatics.
  • Evolution of binding sites for zinc and calcium ions playing structural roles
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by James W Torrance, Malcolm W Macarthur, Janet M Thornton
    posted to structural_templates structural_bioinformatics by jwm on 2008-06-03 18:03:38 as ** along with 2 people tny grottenolm
  • 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 structural_bioinformatics by jwm on 2008-06-03 18:03:01 as ** along with 6 people and 2 groups sim82 barry ucbcjbm cjeans zwang grottenolm structural_bioinformatics Bioinformatics
  • Molecular docking for substrate identification: the short-chain dehydrogenases/reductases.
    J Mol Biol, Vol. 375, No. 3. (18 January 2008), pp. 855-874.
    by AD Favia, I Nobeli, F Glaser, JM Thornton
    posted to structural_bioinformatics by jwm on 2008-06-03 17:57:30 as ** along with 1 person grottenolm
  • The geometry of interactions between catalytic residues and their substrates.
    J Mol Biol, Vol. 369, No. 4. (15 June 2007), pp. 1140-1152.
    by JW Torrance, GL Holliday, JB Mitchell, JM Thornton
    posted to structural_bioinformatics by jwm on 2008-06-03 13:02:47 as ** along with 1 person grottenolm
  • Shape Variation in Protein Binding Pockets and their Ligands.
    J Mol Biol, Vol. 368, No. 1. (20 April 2007), pp. 283-301.
    by A Kahraman, RJ Morris, RA Laskowski, JM Thornton
    posted to structural_bioinformatics ligand_sites by jwm on 2008-06-03 13:02:23 as ** along with 3 people tjimenez martainn grottenolm
  • Towards Fully Automated Structure-based Function Prediction in Structural Genomics: A Case Study
    Journal of Molecular Biology, Vol. 367, No. 5. (13 April 2007), pp. 1511-1522.
    by James D Watson, Steve Sanderson, Alexandra Ezersky, Alexei Savchenko, Aled Edwards, Christine Orengo, Andrzej Joachimiak, Roman A Laskowski, Janet M Thornton
    posted to structural_genomics structural_bioinformatics by jwm on 2008-06-03 13:02:06 as ** along with 4 people and 2 groups ana tjimenez nickolay grottenolm structural_bioinformatics Bioinformatics
  • MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by GL Holliday, DE Almonacid, GJ Bartlett, NM O'Boyle, JW Torrance, P Murray-Rust, JB Mitchell, JM Thornton
    posted to structural_bioinformatics by jwm on 2008-06-03 13:01:39 as ** along with 2 people dullhunk grottenolm
  • Protein Superfamily Evolution and the Last Universal Common Ancestor (LUCA)
    Journal of Molecular Evolution
    by Juan AG Ranea, Antonio Sillero, Janet M Thornton, Christine A Orengo
    posted to structural_bioinformatics luca by jwm on 2008-06-03 13:01:22 as ** along with 4 people and 2 groups ana barry tny grottenolm structural_bioinformatics Bioinformatics
  • Understanding the molecular machinery of genetics through 3D structures.
    Nat Rev Genet (27 December 2007)
    by Roman A A Laskowski, Janet M M Thornton
    posted to structural_bioinformatics by jwm on 2008-06-03 12:59:47 as ** along with 3 people higueruelo sebastien_vigneau grottenolm
  • A practical and robust sequence search strategy for structural genomics target selection.
    Bioinformatics (Oxford, England), Vol. 20, No. 14. (22 September 2004), pp. 2288-2295.
    by JE Bray, RL Marsden, SC Rison, A Savchenko, AM Edwards, JM Thornton, CA Orengo
    posted to structural_genomics structural_bioinformatics by jwm on 2008-06-03 12:58:12 as **
  • Inactive Enzyme-homologues Find New Function in Regulatory Processes
    Journal of Molecular Biology, Vol. 340, No. 3. (9 July 2004), pp. 399-404.
    by Birgit Pils, Jorg Schultz
    posted to structural_bioinformatics by jwm on 2008-06-03 12:48:30 as ** along with 2 people Jporci tny
  • Catalysing new reactions during evolution: economy of residues and mechanism.
    J Mol Biol, Vol. 331, No. 4. (22 August 2003), pp. 829-860.
    by GJ Bartlett, N Borkakoti, JM Thornton
    posted to structural_bioinformatics by jwm on 2008-06-03 12:48:14 as ** along with 2 people gbart nickolay
  • Searching for functional sites in protein structures
    Current Opinion in Chemical Biology, Vol. 8, No. 1. (February 2004), pp. 3-7.
    by Susan Jones, Janet M Thornton
    posted to structural_templates structural_bioinformatics by jwm on 2008-06-03 12:47:20 as ** along with 6 people and 1 group nickolay BragilMassoud LeightonP chrn Einat proteasome structural_bioinformatics
  • Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families.
    J Mol Biol, Vol. 347, No. 3. (1 April 2005), pp. 565-581.
    by JW Torrance, GJ Bartlett, CT Porter, JM Thornton
    posted to structural_templates structural_bioinformatics by jwm on 2008-06-03 12:46:47 as ** along with 4 people and 1 group chrn Einat alexg gbart structural_bioinformatics
  • Progress of structural genomics initiatives: an analysis of solved target structures.
    J Mol Biol, Vol. 348, No. 5. (20 May 2005), pp. 1235-1260.
    by AE Todd, RL Marsden, JM Thornton, CA Orengo
    posted to structural_bioinformatics by jwm on 2008-06-03 12:46:26 as ** along with 2 people and 2 groups bicko marcius BioinfoCIPF SGU-CIPF
  • The complement of enzymatic sets in different species.
    J Mol Biol, Vol. 349, No. 4. (17 June 2005), pp. 745-763.
    by S Freilich, RV Spriggs, RA George, B Al-Lazikani, M Swindells, JM Thornton
    posted to structural_bioinformatics by jwm on 2008-06-03 12:45:50 as ** along with 2 people gbart tny
  • Predicting protein function from sequence and structural data.
    Curr Opin Struct Biol, Vol. 15, No. 3. (June 2005), pp. 275-284.
    by JD Watson, RA Laskowski, JM Thornton
    posted to structural_bioinformatics by jwm on 2008-06-03 12:45:15 as ** along with 2 people tjimenez kuhn
  • Protein Function Prediction Using Local 3D Templates.
    J Mol Biol (11 July 2005)
    by Roman A A Laskowski, James D D Watson, Janet M M Thornton
    posted to structural_templates structural_bioinformatics by jwm on 2008-06-03 12:44:58 as ** along with 7 people mdimmic shadowman chrn gbart MaggieYe siebertm yoonk
  • A method for localizing ligand binding pockets in protein structures.
    Proteins, Vol. 62, No. 2. (1 February 2006), pp. 479-488.
    by F Glaser, RJ Morris, RJ Najmanovich, RA Laskowski, JM Thornton
    posted to structural_bioinformatics ligand_sites by jwm on 2008-06-03 12:44:33 as ** along with 4 people tjimenez nickolay sriram_s bilab
  • Introduction. Bioinformatics: from molecules to systems.
    Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Vol. 361, No. 1467. (29 March 2006), pp. 389-391.
    by DT Jones, MJ Sternberg, JM Thornton
    posted to structural_bioinformatics bioinformatics by jwm on 2008-06-03 12:44:07 as **
  • One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions.
    J Mol Biol, Vol. 321, No. 5. (30 August 2002), pp. 741-765.
    by N Nagano, CA Orengo, JM Thornton
    posted to tim_barrel structural_bioinformatics by jwm on 2008-06-03 12:42:44 as ** along with 1 person tjimenez
  • Conservation helps to identify biologically relevant crystal contacts.
    J Mol Biol, Vol. 313, No. 2. (19 October 2001), pp. 399-416.
    by WS Valdar, JM Thornton
    posted to structural_bioinformatics crystal_contacts by jwm on 2008-06-03 12:42:01 as ** along with 3 people bicko cjeans Evangelia
  • A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm.
    Nucleic acids research, Vol. 29, No. 1. (1 January 2001), pp. 228-229.
    by IN Shindyalov, PE Bourne
    posted to structural_bioinformatics by jwm on 2008-06-02 10:11:56 as **
  • Andante: Reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities.
    Bioinformatics (6 March 2007)
    by Richard E E Smith, Simon C C Lovell, David F F Burke, Rinaldo W W Montalvao, Tom L L Blundell
    posted to structural_bioinformatics protein_engineering by jwm on 2008-05-19 11:09:42 as ** along with 1 person carlk
  • A molecular viewer for the analysis of TLS rigid-body motion in macromolecules
    Acta Crystallographica Section D Biological Crystallography
    by P& Painter
    posted to structural_bioinformatics by jwm on 2008-04-15 12:57:30 as **
  • Transformations to optimize the superposition of similar structures
    Acta Crystallographica Section A, Vol. 35, No. 1. (Jan 1979), pp. 158-163.
    by WA Hendrickson
    posted to structural_alignment structural_bioinformatics by jwm on 2008-03-04 09:58:36 as **
  • Sequence alignment for molecular replacement
    Acta Crystallographica Section D Biological Crystallography
    by Barton
    posted to molecular_replacement structural_bioinformatics xtal_methods xtal_software by jwm on 2008-02-20 10:38:14 as **
  • 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 protein_structure_validation structural_bioinformatics xtal_methods by jwm on 2007-12-12 13:41:04 as **
  • MUSTANG: A multiple structural alignment algorithm
    Proteins: Structure, Function, and Bioinformatics, Vol. 64, No. 3. (2006), pp. 559-574.
    by Arun S Konagurthu, James C Whisstock, Peter J Stuckey, Arthur M Lesk
    posted to structural_alignment structural_bioinformatics by jwm on 2007-12-06 10:43:13 as ** along with 5 people and 3 groups granujilla karbak ana rabio Thaverkamp structural_bioinformatics Bioinformatics Microbial-Ecology
  • Multiple flexible structure alignment using partial order graphs.
    Bioinformatics (3 March 2005)
    by Yuzhen Ye, Adam Godzik
    posted to structural_alignment structural_bioinformatics by jwm on 2007-12-06 10:36:43 as ** along with 2 people and 2 groups ana aalibes structural_bioinformatics Bioinformatics
  • The Protein Data Bank: a computer-based archival file for macromolecular structures.
    J Mol Biol, Vol. 112, No. 3. (25 May 1977), pp. 535-542.
    by FC Bernstein, TF Koetzle, GJ Williams, EF Meyer, MD Brice, JR Rodgers, O Kennard, T Shimanouchi, M Tasumi
    posted to historical_interest structural_bioinformatics by jwm on 2007-11-30 17:05:07 as ** along with 1 person j3xucite
  • MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison
    Protein Sci, Vol. 11, No. 11. (1 November 2002), pp. 2606-2621.
    by Angel R Ortiz, Charlie E Strauss, Osvaldo Olmea
    posted to structural_bioinformatics by jwm on 2007-11-27 13:52:57 as ** along with 4 people and 2 groups ana iakes dimka analogAI structural_bioinformatics Bioinformatics
  • Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles.
    Biotechnol J, Vol. 2, No. 1. (January 2007), pp. 62-67.
    by J Damborský, M Petrek, P Banás, M Otyepka
    posted to caver cavities protein_channels structural_bioinformatics by jwm on 2007-11-23 15:17:20 as **
  • MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels.
    Structure, Vol. 15, No. 11. (13 November 2007), pp. 1357-1363.
    by Martin Petřek, Pavlína Košinová, Jaroslav Koča, Michal Otyepka
    posted to caver cavities protein_channels structural_bioinformatics by jwm on 2007-11-23 15:17:04 as ** along with 1 person and 1 group sobolevnrm baker-group
  • ZRANK: reranking protein docking predictions with an optimized energy function.
    Proteins, Vol. 67, No. 4. (1 June 2007), pp. 1078-1086.
    by B Pierce, Z Weng
    posted to protein_docking structural_bioinformatics by jwm on 2007-09-17 17:38:47 as ** along with 1 person and 2 groups bicko Radiation_Damage Stressosome
  • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    Journal of Molecular Biology, Vol. 272, No. 1. (12 September 1997), pp. 106-120.
    by Henry A Gabb, Richard M Jackson, Michael J Sternberg
    posted to protein_docking structural_bioinformatics by jwm on 2007-09-17 15:40:25 as ** along with 7 people and 3 groups bicko yongzhao ima ffranca cjeans selrac kintoki Radiation_Damage Stressosome TSRI_MGL
  • Modelling repressor proteins docking to DNA.
    Proteins, Vol. 33, No. 4. (1 December 1998), pp. 535-549.
    by P Aloy, G Moont, HA Gabb, E Querol, FX Aviles, MJ Sternberg
    posted to protein_docking structural_bioinformatics by jwm on 2007-09-17 15:33:40 as ** along with 1 person and 2 groups bpagano Radiation_Damage Stressosome
  • Use of pair potentials across protein interfaces in screening predicted docked complexes.
    Proteins, Vol. 35, No. 3. (15 May 1999), pp. 364-373.
    by G Moont, HA Gabb, MJ Sternberg
    posted to protein_docking structural_bioinformatics by jwm on 2007-09-17 14:50:05 as ** along with 3 people and 2 groups bicko chaleil selrac Radiation_Damage Stressosome
  • Model building of disulfide bonds in proteins with known three-dimensional structure.
    Protein Eng, Vol. 2, No. 2. (July 1988), pp. 119-125.
    by B Hazes, BW Dijkstra
    posted to xtal_software structural_bioinformatics protein_engineering disulfide by jwm on 2007-09-14 13:19:58 as ** along with 2 groups Radiation_Damage Stressosome
  • PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes
    Bioinformatics, Vol. 21, No. 15. (1 August 2005), pp. 3316-3317.
    by Swanand P Gore, David F Burke, Tom L Blundell
    posted to skeletonization structural_bioinformatics by jwm on 2007-08-25 18:07:14 as ** along with 3 people and 2 groups cat_worth siebertm sebk Radiation_Damage Stressosome
  • Shape complementarity at protein/protein interfaces.
    J Mol Biol, Vol. 234, No. 4. (20 December 1993), pp. 946-950.
    by MC Lawrence, PM Colman
    posted to ccp4 docking protein_docking structural_bioinformatics xtal_methods xtal_software by jwm on 2007-08-07 13:35:44 as ** along with 1 person and 2 groups kintoki Radiation_Damage Stressosome
  • 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 bioinformatics protein_classification structural_bioinformatics by jwm on 2007-08-07 13:19:05 as ** along with 7 people and 4 groups sim82 massivemayhem tjimenez dimka chad_davis Einat caporaso structural_bioinformatics Radiation_Damage Stressosome biomedical-nlp
  • Molecular speleology: the exploration of crevices in proteins for prediction of binding sites, design of drugs and analysis of surface recognition
    Acta Crystallographica, Vol. A42 (1986), pp. 83-85.
    by AM Lesk
    posted to cavities structural_bioinformatics by jwm on 2007-07-30 13:22:19 as ** along with 2 groups Radiation_Damage Stressosome
  • Speleologie des hydrogenases a nickel et a fer
    Les Ecoles Physique et Chimie du Vivant, Vol. 1 (April 1999), pp. 47-52.
    by Anne Volbeda
    posted to cavenv cavities cavity structural_bioinformatics by jwm on 2007-07-29 15:54:58 as ** along with 2 groups Radiation_Damage Stressosome
  • A survey of left-handed helices in protein structures.
    J Mol Biol, Vol. 347, No. 2. (25 March 2005), pp. 231-241.
    by M Novotny, GJ Kleywegt
    posted to structural_bioinformatics by jwm on 2007-01-23 11:32:01 as ** along with 1 person and 2 groups martainn Radiation_Damage Stressosome
  • Protein families and their evolution-a structural perspective.
    Annu Rev Biochem, Vol. 74 (2005), pp. 867-900.
    by CA Orengo, JM Thornton
    posted to protein_families structural_bioinformatics by jwm on 2006-11-27 16:35:46 as ** along with 12 people and 6 groups nigham ana barry tjimenez chad_davis Einat Schmidtc marcius sriram_s ezotenko redelings medic0747 structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF SGU-CIPF
  • HOLE: a program for the analysis of the pore dimensions of ion channel structural models.
    J Mol Graph, Vol. 14, No. 6. (December 1996)
    by OS Smart, JG Neduvelil, X Wang, BA Wallace, MS Sansom
    posted to cavities pore structural_bioinformatics by jwm on 2006-10-17 15:48:00 as ** along with 2 groups Radiation_Damage Stressosome
  • 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 structural_bioinformatics by jwm on 2006-10-16 16:35:46 as ** along with 12 people and 3 groups sanchezbuelna wallacei knaseanka chrn balajis gbart caporaso sriram_s cdallett timflutre gisle urgi Radiation_Damage Stressosome biomedical-nlp
  • MUSCLE: multiple sequence alignment with high accuracy and high throughput.
    Nucleic Acids Res, Vol. 32, No. 5. (2004), pp. 1792-1797.
    by RC Edgar
    posted to structural_bioinformatics by jwm on 2006-10-16 16:35:40 as ** along with 13 people and 2 groups sconlan newton1234 skumagai edvin sanchezbuelna bmaust nachtalp bpb chrn Haggan timflutre olympos martainn Radiation_Damage Stressosome
  • SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces.
    BMC Bioinformatics, Vol. 7, No. 1. (2 March 2006)
    by Joan Teyra, Andreas Doms, Michael Schroeder, M Teresa T Pisabarro
    posted to docking structural_bioinformatics by jwm on 2006-09-06 17:37:23 as ** along with 4 people and 2 groups jteyra bicko chad_davis choonpeng Radiation_Damage Stressosome
    • 注: このページを引用する時は次のURLでどうぞ: http://www.citeulike.org/user/jwm/tag/structural_bioinformatics

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