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sim82's library [118 articles]

最近录入 sim82's 文献库.
  • The PyMOL Molecular Graphics System
    (2002)
    by WL Delano
    posted to pymol by sim82 on 2008-07-14 14:02:58 as **
  • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
    Protein Eng, Vol. 11, No. 9. (September 1998), pp. 739-747.
    by IN Shindyalov, PE Bourne
    posted to ce structural by sim82 on 2008-07-13 12:20:48 as ** along with 7 people and 2 groups nigham jwm analogAI dgront rabio siebertm Inchoate Radiation_Damage Stressosome
  • Protein structure comparison by alignment of distance matrices.
    J Mol Biol, Vol. 233, No. 1. (5 September 1993), pp. 123-138.
    by L Holm, C Sander
    posted to dali by sim82 on 2008-07-13 12:16:45 as ** along with 5 people and 2 groups BragilMassoud ana nigham dgront siebertm structural_bioinformatics Bioinformatics
  • Protein families and their evolution-a structural perspective.
    Annu Rev Biochem, Vol. 74 (2005), pp. 867-900.
    by CA Orengo, JM Thornton
    posted to review structure by sim82 on 2008-07-13 11:10:48 as ** along with 13 people and 6 groups ana barry tjimenez jwm chad_davis Einat Schmidtc marcius sriram_s ezotenko redelings medic0747 nigham structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF SGU-CIPF
  • Vorolignfast structural alignment using Voronoi contacts
    Bioinformatics, Vol. 23, No. 2. (15 January 2007), pp. e205-e211.
    by Birzele, Fabian, Gewehr, E Jan, Csaba, Gergely, Zimmer, Ralf
    posted to alignment structural vorolign voronoi by sim82 on 2008-07-12 20:21:15 as **
  • Application of a Theory of Enzyme Specificity to Protein Synthesis.
    Proc Natl Acad Sci U S A, Vol. 44, No. 2. (February 1958), pp. 98-104.
    by DE Koshland
    posted to fit induced by sim82 on 2008-07-12 20:18:08 as ** along with 5 people apostola robert kazemi nigham boris_aguilar
  • Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme.
    Journal of molecular biology, Vol. 103, No. 2. (15 May 1976), pp. 227-249.
    by A Warshel, M Levitt
    posted to qmmm warshel by sim82 on 2008-07-12 17:45:55 as **
  • Biochemistry
    (2002)
    by JM Berg, JL Tymoczko, L Stryer
    posted to book by sim82 on 2008-07-12 15:32:57 as **
  • Transition-state stabilization in the mechanism of tyrosyl-tRNA synthetase revealed by protein engineering.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 82, No. 23. (December 1985), pp. 7840-7844.
    by RJ Leatherbarrow, AR Fersht, G Winter
    posted to catalysis mutagenesis by sim82 on 2008-07-12 14:56:33 as **
  • COMPUTER SIMULATIONS OF ENZYME CATALYSIS: Methods, Progress, and Insights
    Annual Review of Biophysics and Biomolecular Structure, Vol. 32, No. 1. (2003), pp. 425-443.
    by Arieh Warshel
    posted to qmmm review warshel by sim82 on 2008-07-12 14:29:59 as **
  • ENZYMATIC TRANSITION STATES AND TRANSITION STATE ANALOG DESIGN
    Annual Review of Biochemistry, Vol. 67, No. 1. (1998), pp. 693-720.
    by Vern L Schramm
    posted to review states transition by sim82 on 2008-07-11 18:36:53 as **
  • Genetic Modification of Bacillus subtilis for Production of D-chiro-Inositol, an Investigational Drug Candidate for Treatment of Type 2 Diabetes and Polycystic Ovary Syndrome
    Appl. Environ. Microbiol., Vol. 72, No. 2. (1 February 2006), pp. 1310-1315.
    by Ken-Ichi Yoshida, Masanori Yamaguchi, Tetsuro Morinaga, Maya Ikeuchi, Masaki Kinehara, Hitoshi Ashida
    posted to ioli by sim82 on 2008-07-10 19:37:27 as **
  • Atom Pairs as Molecular Features in Structure-Activity Studies: Definition and Applications
    Journal of Chemical Information and Computer Sciences, Vol. 25 (1985), pp. 64-73.
    by RE Carhart, DH Smith, R Venkataraghavan
    posted to fingerprint similarity by sim82 on 2008-07-08 13:10:06 as ** along with 1 person nachtalp
  • BRENDA, the enzyme database: updates and major new developments.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by I Schomburg, A Chang, C Ebeling, M Gremse, C Heldt, G Huhn, D Schomburg
    posted to brenda database by sim82 on 2008-07-08 12:18:16 as ** along with 4 people and 2 groups alexg jberro helliontroy shung biomedical-nlp Projet_ENSIMAG
  • The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
    Nucleic Acids Research, Vol. 32 (2004), pp. D129-D133.
    by CT Porter, GJ Bartlett, JM Thornton
    posted to csa database by sim82 on 2008-07-08 12:16:59 as **
  • The Universal Protein Resource (UniProt).
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by
    posted to database uniprot by sim82 on 2008-07-08 11:22:42 as ** along with 7 people jyuh dullhunk CitoJam massivemayhem cjeans saunders sgoetz
  • Evolution of Enzymes in Metabolism: A Network Perspective
    Journal of Molecular Biology, Vol. 320, No. 4. (19 July 2002), pp. 751-770.
    by Rui Alves, Raphael A Chaleil, Michael J Sternberg
    posted to evolution pathway by sim82 on 2008-07-08 10:10:38 as ** along with 1 person tny
  • The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli.
    J Mol Biol, Vol. 311, No. 4. (24 August 2001), pp. 693-708.
    by SA Teichmann, SC Rison, JM Thornton, M Riley, J Gough, C Chothia
    posted to evolution pathway by sim82 on 2008-07-08 10:03:31 as ** along with 3 people tjimenez kuhn tny
  • Enzyme nomenclature. Reccomendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology
    (1992)
    by EC Webb
    posted to no-tag by sim82 on 2008-07-07 19:22:34 as **
  • Evolution of function in protein superfamilies, from a structural perspective
    Journal of Molecular Biology, Vol. 307, No. 4. (6 April 2001), pp. 1113-1143.
    by AE Todd, CA Orengo, JM Thornton
    posted to enzyme evolution by sim82 on 2008-07-07 16:57:21 as ** along with 8 people and 2 groups ana kuhn chad_davis tny sriram_s choonpeng cdallett uz_labu_laimi structural_bioinformatics Bioinformatics
  • Understanding Enzyme Superfamilies. Chemistry as the fundamental determinant in the evolution of new catalytic activities
    J. Biol. Chem., Vol. 272, No. 49. (5 December 1997), pp. 30591-30594.
    by PC Babbitt, JA Gerlt
    posted to catalytic evolution by sim82 on 2008-07-07 16:50:32 as **
  • SCOP: a structural classification of proteins database for the investigation of sequences and structures.
    J Mol Biol, Vol. 247, No. 4. (7 April 1995), pp. 536-540.
    by AG Murzin, SE Brenner, T Hubbard, C Chothia
    posted to classification enzyme scop by sim82 on 2008-07-07 15:33:05 as ** along with 9 people dimka chrn chad_davis j3xucite sriram_s aengisch massivemayhem cjeans siebertm
  • 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 classification enzyme by sim82 on 2008-07-07 15:32:05 as ** along with 9 people and 4 groups tjimenez dimka jwm chad_davis Einat caporaso massivemayhem jteyra gulkur structural_bioinformatics Radiation_Damage Stressosome biomedical-nlp
  • Understanding nature's catalytic toolkit.
    Trends Biochem Sci (5 October 2005)
    by A Gutteridge, JM Thornton
    posted to catalysis catalytic by sim82 on 2008-07-07 15:07:44 as ** along with 10 people and 4 groups ana jwm Einat alexg gbart eweaver tny noby siebertm grottenolm structural_bioinformatics Radiation_Damage Stressosome Bioinformatics
  • Very fast prediction and rationalization of pKa values for protein-ligand complexes
    Proteins: Structure, Function, and Bioinformatics, Vol. Epub ahead of print (May 2008)
    by DC Bas, DM Rogers, JH Jensen
    posted to no-tag by sim82 on 2008-07-07 15:01:15 as **
  • Role of Conserved Histidines in Catalytic Activity and Inhibitor Binding of Human Recombinant Phosphodiesterase 4A
    Mol Pharmacol, Vol. 51, No. 6. (1 June 1997), pp. 999-1006.
    by S Jacobitz, MD Ryan, MM Mclaughlin, GP Livi, WE Dewolf, TJ Torphy
    posted to 1ptw mutagenesis mutation by sim82 on 2008-07-07 13:05:41 as **
  • Potential Roles of Conserved Amino Acids in the Catalytic Domain of the cGMP-binding cGMP-specific Phosphodiesterase (PDE5)
    J. Biol. Chem., Vol. 273, No. 11. (13 March 1998), pp. 6460-6466.
    by IV Turko, SH Francis, JD Corbin
    posted to 1ptw mutagenesis mutation by sim82 on 2008-07-07 13:01:29 as **
  • Using Reaction Mechanism to Measure Enzyme Similarity
    Journal of Molecular Biology, Vol. 368, No. 5. (18 May 2007), pp. 1484-1499.
    by NM O'Boyle, GL Holliday, DE Almonacid, JBO Mitchell
    posted to enzyme macie by sim82 on 2008-07-07 12:37:19 as ** along with 3 people ucbcjbm daevans gemmalholliday
  • 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 ziquje eweaver tny Jporci
  • The Chemistry of Protein Catalysis
    Journal of Molecular Biology, Vol. 372, No. 5. (5 October 2007), pp. 1261-1277.
    by GL Holliday, DE Almonacid, JBO Mitchell, JM Thornton
    posted to catalysis macie by sim82 on 2008-07-05 17:12:26 as ** along with 7 people and 2 groups barry ucbcjbm cjeans zwang grottenolm jwm gemmalholliday 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 dielectric electrostatics pka by sim82 on 2008-07-04 16:00:58 as ** along with 1 person RamuAnandakrishnan
  • 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 pka statistics 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 born electrostatics gb pka 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 electrostatics pka 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 MJ Holst, F Saied
    posted to electrostatics lpbe multigrid by sim82 on 2008-07-04 10:01:00 as **
  • The Poisson-Boltzmann Equation: Analysis and Multilevel Numerical Solutions
    by MJ Holst
    posted to apbs lpbe multigrid 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 M von Grotthuss, D Plewczynski, K Ginalski, L Rychlewski, EI 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 database kegg reaction 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, Vol. 48, No. 6. (6 June 2008), pp. 1181-1189.
    by R Körner, J 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 Körner, S Tietze, J Apostolakis
    posted to gma homdock 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, J 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 1j3u its_ecd34 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 dock scpdb by sim82 on 2008-06-24 14:24:22 as ** along with 6 people and 1 group BragilMassoud caporaso schlauchi daevans ramensky nickolay biomedical-nlp
  • 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 electrostatics mead pka 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 electrostatics pka uhbd 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 electrostatics mcce pka by sim82 on 2008-06-23 15:23:56 as ** along with 1 person RamuAnandakrishnan
  • 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 EL Mehler, F Guarnieri
    posted to h-bonds pka by sim82 on 2008-06-23 13:30:19 as ** along with 1 person RamuAnandakrishnan
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