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sim82s library [91 articles]

Nye artikler sendt til sim82s bibliotek.
  • Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database.
    Biochemistry, Vol. 45, No. 8. (28 February 2006), pp. 2545-2555.
    by SC Pegg, SD Brown, S Ojha, J Seffernick, EC Meng, JH Morris, PJ Chang, CC Huang, TE Ferrin, PC Babbitt
    posted to catalytic by sim82 on 2008-07-05 17:56:18 as ** along with 3 people kuhn tny jdiggans
  • EzCatDB: the Enzyme Catalytic-mechanism Database.
    Nucleic Acids Res, Vol. 33 Database Issue (1 January 2005)
    by N Nagano
    posted to catalytic by sim82 on 2008-07-05 17:54:34 as ** along with 4 people Jporci ziquje eweaver tny
  • 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 macie catalysis by sim82 on 2008-07-05 17:12:26 as ** along with 6 people and 2 groups jwm barry ucbcjbm cjeans zwang grottenolm structural_bioinformatics Bioinformatics
  • Improving the Continuum Dielectric Approach to Calculating pKas of Ionizable Groups in Proteins
    J. Phys. Chem., Vol. 100, No. 43. (24 October 1996), pp. 17373-17387.
    by E Demchuk, RC Wade
    posted to pka electrostatics dielectric by sim82 on 2008-07-04 16:00:58 as **
  • A statistical approach to the prediction of pK(a) values in proteins.
    Proteins, Vol. 69, No. 1. (1 October 2007), pp. 75-82.
    by Y He, J Xu, XM Pan
    posted to statistics pka by sim82 on 2008-07-04 14:48:27 as **
  • Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations
    Journal of Computational Chemistry, Vol. 25, No. 15. (2004), pp. 1865-1872.
    by B Kuhn, PA Kollman, M Stahl
    posted to pka gb electrostatics born by sim82 on 2008-07-04 12:48:28 as **
  • pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model.
    Biochemistry, Vol. 29, No. 44. (6 November 1990), pp. 10219-10225.
    by D Bashford, M Karplus
    posted to pka electrostatics by sim82 on 2008-07-04 11:10:54 as **
  • Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods
    Journal of Computational Chemistry, Vol. 16, No. 3. (1995), pp. 337-364.
    by Michael J Holst, Faisal Saied
    posted to multigrid lpbe electrostatics by sim82 on 2008-07-04 10:01:00 as **
  • The Poisson-Boltzmann Equation: Analysis and Multilevel Numerical Solutions
    by MJ Holst
    posted to multigrid lpbe apbs by sim82 on 2008-07-04 09:55:45 as **
  • A rare form of burn injury sustained during defaecation
    Burns, Vol. 25, No. 5. (August 1999), pp. 463-464.
    by O Nahlieli, AM Baruchin, E Eliav, L Rosenberg
    posted to electrostatics by sim82 on 2008-07-03 14:54:30 as **
  • PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
    BMC Bioinformatics, Vol. 7, No. 1. (6 February 2006)
    by Marcin von Grotthuss, Dariusz Plewczynski, Krzysztof Ginalski, Leszek Rychlewski, Eugene I Shakhnovich
    posted to pdb-uf by sim82 on 2008-06-30 12:45:28 as ** along with 2 people and 3 groups marcius caporaso biomedical-nlp BioinfoCIPF SGU-CIPF
  • LIGAND: database of chemical compounds and reactions in biological pathways.
    Nucleic Acids Res, Vol. 30, No. 1. (1 January 2002), pp. 402-404.
    by S Goto, Y Okuno, M Hattori, T Nishioka, M Kanehisa
    posted to reaction kegg database by sim82 on 2008-06-28 16:12:39 as ** along with 6 people alexg blackbart koerner massivemayhem dagmar shung
  • Description of organic reactions based on imaginary transition structures. 1. Introduction of new concepts
    J. Chem. Inf. Comput. Sci., Vol. 26 (1986), pp. 205-212.
    by S Fujita
    posted to its by sim82 on 2008-06-28 15:46:35 as **
  • Automatic Determination of Reaction Mappings and Reaction Center Information. 1. The Imaginary Transition State Energy Approach.
    Journal of chemical information and modeling (6 June 2008)
    by Robert Körner, Joannis Apostolakis
    posted to its by sim82 on 2008-06-28 15:26:41 as ** along with 1 person apostola
  • Graph-Based Molecular Alignment (GMA)
    J. Chem. Inf. Model., Vol. 47, No. 2. (26 March 2007), pp. 591-601.
    by J Marialke, R Korner, S Tietze, J Apostolakis
    posted to homdock gma by sim82 on 2008-06-28 13:36:24 as ** along with 2 people schlauchi superpyrin
  • Similarity Based Docking.
    J Chem Inf Model (29 November 2007)
    by J Marialke, S Tietze, Joannis Apostolakis
    posted to homdock by sim82 on 2008-06-28 13:26:12 as ** along with 2 people apostola daevans
  • Crystal Structure of Thermostable Aspartase from Bacillus sp. YM55-1: Structure-based Exploration of Functional Sites in the Aspartase Family
    Journal of Molecular Biology, Vol. 328, No. 3. (2 May 2003), pp. 635-654.
    by T Fujii, H Sakai, Y Kawata, Y Hata
    posted to its_ecd34 1j3u by sim82 on 2008-06-27 12:54:11 as **
  • sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank.
    J Chem Inf Model, Vol. 46, No. 2. (r 2006), pp. 717-727.
    by E Kellenberger, P Muller, C Schalon, G Bret, N Foata, D Rognan
    posted to scpdb dock by sim82 on 2008-06-24 14:24:22 as ** along with 5 people and 1 group BragilMassoud caporaso schlauchi daevans ramensky biomedical-nlp
  • Very fast prediction and rationalization of pKa values for protein-ligand complexes
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Delphine C Bas, David M Rogers, Jan H Jensen
    posted to propka prediction pka by sim82 on 2008-06-24 13:44:31 as **
  • Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility.
    Biophys. J., Vol. 69, No. 5. (1 November 1995), pp. 1721-1733.
    by TJ You, D Bashford
    posted to pka mead electrostatics by sim82 on 2008-06-23 16:00:43 as **
  • Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program
    Computer Physics Communications, Vol. 91, No. 1-3. (2 September 1995), pp. 57-95.
    by Jeffry D Madura, James M Briggs, Rebecca C Wade, Malcolm E Davis, Brock A Luty, Andrew Ilin, Jan Antosiewicz, Michael K Gilson, Babak Bagheri, Ridgway L Scott, Andrew J Mccammon
    posted to uhbd pka electrostatics by sim82 on 2008-06-23 15:52:05 as ** along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
  • Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties.
    Biophysical journal, Vol. 72, No. 5. (May 1997), pp. 2075-2093.
    by EG Alexov, MR Gunner
    posted to pka mcce electrostatics by sim82 on 2008-06-23 15:23:56 as **
  • A Self-Consistent, Microenvironment Modulated Screened Coulomb Potential Approximation to Calculate pH-Dependent Electrostatic Effects in Proteins
    Biophys. J., Vol. 77, No. 1. (1 July 1999), pp. 3-22.
    by Ernest L Mehler, Frank Guarnieri
    posted to pka h-bonds by sim82 on 2008-06-23 13:30:19 as **
  • The determinants of carboxyl pKa values in turkey ovomucoid third domain.
    Proteins, Vol. 55, No. 3. (15 May 2004), pp. 689-704.
    by H Li, AD Robertson, JH Jensen
    posted to pka h-bonds by sim82 on 2008-06-23 13:24:45 as **
  • MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms
    Nucleic Acids Research, Vol. 35, No. Supplement 1. (January 2007), pp. D515-D520.
    by GL Holliday, DE Almonacid, GJ Bartlett, NM O'Boyle, JW Torrance, P Murray-Rust, JBO Mitchell, JM Thornton
    posted to macie by sim82 on 2008-06-16 13:48:42 as **
  • Mutational Analysis of Duck delta 2 Crystallin and the Structure of an Inactive Mutant with Bound Substrate Provide Insight into the Enzymatic Mechanism of Argininosuccinate Lyase
    J. Biol. Chem., Vol. 277, No. 6. (1 February 2002), pp. 4166-4175.
    by LM Sampaleanu, B Yu, PL Howell
    posted to 1dcn_2j84 1dcn by sim82 on 2008-06-13 18:35:04 as **
  • Channeling of ammonia in glucosamine-6-phosphate synthase
    Journal of Molecular Biology, Vol. 313, No. 5. (9 November 2001), pp. 1093-1102.
    by A Teplyakov, G Obmolova, B Badet, M Badet-Denisot
    posted to tunnel its_ecd34 channeling 1jxa by sim82 on 2008-06-12 11:03:37 as **
  • Crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonate identifies the role of Glu357 in catalysis.
    Biochemistry, Vol. 40, No. 6. (13 February 2001), pp. 1560-1566.
    by CJ Jeffery, R Hardré, L Salmon
    posted to its_ecd34 1g98 by sim82 on 2008-06-11 18:50:38 as **
  • Crystal structure of an inactive duck delta II crystallin mutant with bound argininosuccinate.
    Biochemistry, Vol. 38, No. 8. (23 February 1999), pp. 2425-2434.
    by F Vallée, MA Turner, PL Lindley, PL Howell
    posted to 1dcn_2j84 1dcn by sim82 on 2008-06-11 18:39:02 as **
  • The structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter and intra-subunit complementation during evolution.
    Journal of molecular biology, Vol. 300, No. 4. (21 July 2000), pp. 917-933.
    by IP Korndörfer, WD Fessner, BW Matthews
    posted to its_ecd34 1de5 by sim82 on 2008-06-05 17:10:27 as **
  • Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase: implications for substrate binding and catalysis.
    Journal of molecular biology, Vol. 321, No. 4. (23 August 2002), pp. 601-612.
    by M Garrido-Franco, B Laber, R Huber, T Clausen
    posted to mechanism macie_ecd34 1ixn by sim82 on 2008-06-05 15:02:58 as **
  • The catalytic mechanism of indole-3-glycerol phosphate synthase: crystal structures of complexes of the enzyme from Sulfolobus solfataricus with substrate analogue, substrate, and product.
    Journal of molecular biology, Vol. 319, No. 3. (7 June 2002), pp. 757-766.
    by M Hennig, BD Darimont, JN Jansonius, K Kirschner
    posted to mechanism macie_ecd34 1a53 by sim82 on 2008-06-05 15:02:05 as **
  • DaliLite workbench for protein structure comparison
    Bioinformatics, Vol. 16, No. 6. (1 June 2000), pp. 566-567.
    by L Holm, J Park
    posted to dalilite dali by sim82 on 2008-06-04 13:09:02 as ** along with 1 person rabio
  • Removing near-neighbour redundancy from large protein sequence collections.
    Bioinformatics, Vol. 14, No. 5. (June 1998), pp. 423-429.
    by L Holm, C Sander
    posted to pdb90 dali by sim82 on 2008-06-04 11:35:37 as ** along with 1 person kaarsinogen
  • Crystal structure of human cholesterol sulfotransferase (SULT2B1b) in the presence of pregnenolone and 3'-phosphoadenosine 5'-phosphate. Rationale for specificity differences between prototypical SULT2A1 and the SULT2BG1 isoforms.
    The Journal of biological chemistry, Vol. 278, No. 45. (7 November 2003), pp. 44593-44599.
    by KA Lee, H Fuda, YC Lee, M Negishi, CA Strott, LC Pedersen
    posted to macie_ecd1 1q20 by sim82 on 2008-06-04 10:03:07 as **
  • Structures of chitobiase mutants complexed with the substrate Di-N-acetyl-d-glucosamine: the catalytic role of the conserved acidic pair, aspartate 539 and glutamate 540.
    Journal of molecular biology, Vol. 300, No. 3. (14 July 2000), pp. 611-617.
    by G Prag, Y Papanikolau, G Tavlas, CE Vorgias, K Petratos, AB Oppenheim
    posted to macie_ecd1 1c7t by sim82 on 2008-06-03 18:35:55 as **
  • Structural mapping of the catalytic mechanism for a mammalian phosphoinositide-specific phospholipase C.
    Biochemistry, Vol. 36, No. 7. (18 February 1997), pp. 1704-1718.
    by LO Essen, O Perisic, M Katan, Y Wu, MF Roberts, RL Williams
    posted to macie_ecd1 macie m0028 by sim82 on 2008-06-03 17:55:49 as **
  • The Crystal Structure of AMP-Bound PDE4 Suggests a Mechanism for Phosphodiesterase Catalysis
    Biochemistry, Vol. 42, No. 45. (18 November 2003), pp. 13220-13226.
    by Q Huai, J Colicelli, H Ke
    posted to macie_ecd1 camp 1tb5 by sim82 on 2008-06-03 16:28:14 as **
  • A Glutamine Switch Mechanism for Nucleotide Selectivity by Phosphodiesterases
    Molecular Cell, Vol. 15, No. 2. (23 July 2004), pp. 279-286.
    by Kam Y Zhang, Graeme L Card, Yoshihisa Suzuki, Richard D Artis, Daniel Fong, Sam Gillette, Davin Hsieh, Joshua Neiman, Brian L West, Chao Zhang, Michael V Milburn, Sung-Hou Kim, Joseph Schlessinger, Gideon Bollag
    posted to macie_ecd1 1tb5 by sim82 on 2008-06-03 16:02:26 as **
  • Observations of Reaction Intermediates and the Mechanism of Aldose-Ketose Interconversion by D-Xylose Isomerase
    Proceedings of the National Academy of Sciences, Vol. 87, No. 4. (15 February 1990), pp. 1362-1366.
    by CA Collyer, DM Blow
    posted to macie_ecd1 1did by sim82 on 2008-06-03 15:11:55 as **
  • Crystal Structures of Fructose 1,6-Bisphosphatase: Mechanism of Catalysis and Allosteric Inhibition Revealed in Product Complexes
    Biochemistry, Vol. 39, No. 29. (25 July 2000), pp. 8565-8574.
    by JY Choe, HJ Fromm, RB Honzatko
    posted to macie_ecd1 1eyk by sim82 on 2008-06-03 14:41:03 as **
  • Structure of Acinetobacter Strain ADP1 Protocatechuate 3,4-Dioxygenase at 2.2 A Resolution: Implications for the Mechanism of an Intradiol Dioxygenase
    Biochemistry, Vol. 39, No. 27. (11 July 2000), pp. 7943-7955.
    by MW Vetting, DA D'Argenio, LN Ornston, DH Ohlendorf
    posted to macie_ecd1 1eob by sim82 on 2008-06-03 14:13:09 as **
  • Evolution of Enzymatic Activities in the Orotidine 5'-Monophosphate Decarboxylase Suprafamily: Mechanistic Evidence for a Proton Relay System in the Active Site of 3-Keto-L-gulonate 6-Phosphate Decarboxylase
    Biochemistry, Vol. 43, No. 21. (1 June 2004), pp. 6427-6437.
    by WS Yew, EL Wise, I Rayment, JA Gerlt
    posted to mutagenesis macie_ecd1 1q6o by sim82 on 2008-06-02 15:23:11 as **
  • Mapping the protein universe.
    Science, Vol. 273, No. 5275. (2 August 1996), pp. 595-603.
    by L Holm, C Sander
    posted to dali by sim82 on 2008-05-14 13:32:36 as ** along with 5 people and 2 groups ana barry dimka robert AbnerCYH structural_bioinformatics Bioinformatics
  • Web services at the European bioinformatics institute.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)
    by A Labarga, F Valentin, M Anderson, R Lopez
    posted to webserver ebi by sim82 on 2008-05-13 15:08:05 as ** along with 6 people alanrw moborg dullhunk sujaikumar sgoetz niallhaslam
  • The Rap[ndash]RapGAP complex: GTP hydrolysis without catalytic glutamine and arginine residues
    The EMBO Journal, Vol. aop, No. current. (28 February 2008)
    by Andrea Scrima, Christoph Thomas, Delia Deaconescu, Alfred Wittinghofer
    posted to rapgap 1dcn_2j84 by sim82 on 2008-05-09 14:30:09 as **
  • Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon
    Journal of Molecular Biology, Vol. 372, No. 3. (21 September 2007), pp. 817-845.
    by Pier F Gherardini, Mark N Wass, Manuela Helmer-Citterich, Michael J Sternberg
    posted to structural convergent by sim82 on 2008-05-08 10:55:49 as ** along with 6 people and 2 groups barry tjimenez jjray chad_davis tny Minty structural_bioinformatics Bioinformatics
  • Mutational analysis of amino acid residues involved in argininosuccinate lyase activity in duck delta II crystallin.
    Biochemistry, Vol. 38, No. 8. (23 February 1999), pp. 2435-2443.
    by AR Chakraborty, A Davidson, PL Howell
    posted to mutation lyase argininosuccinate 1dcn_2j84 by sim82 on 2008-05-07 15:42:49 as **
  • Gln212, Asn270, and Arg301 are critical for catalysis by adenylosuccinate lyase from Bacillus subtilis.
    Biochemistry, Vol. 43, No. 23. (15 June 2004), pp. 7391-7402.
    by ML Segall, RF Colman
    posted to subtilis mutation lyase bacillus adenylosuccinate 1dcn_2j84 by sim82 on 2008-05-07 15:40:48 as **
  • GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein-Ligand Complexes.
    J Chem Inf Model, Vol. 47, No. 4. (g 2007), pp. 1657-1672.
    by S Tietze, J Apostolakis
    posted to glamdock dock by sim82 on 2008-04-30 14:48:29 as ** along with 1 person schlauchi
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