sim82's library 133 articles Export

	Obesity alters gut microbial ecology. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 31. (2 August 2005), pp. 11070-11075. by Ruth E. Ley, Fredrik Bäckhed, Peter Turnbaugh, Catherine A. Lozupone, Robin D. Knight, Jeffrey I. Gordon posted to no-tag by sim82 on 2009-07-30 11:24:25 as along with 4 people and 2 groups robertrentzsch Zephyrus marimo michC Orengo Group Journal Picks MathBio
	ARB: a software environment for sequence data [My Copy] Nucl. Acids Res., Vol. 32, No. 4. (25 February 2004), pp. 1363-1371. by Wolfgang Ludwig, Oliver Strunk, Ralf Westram, et al.Lothar Richter, Harald Meier, Yadhukumar, Arno Buchner, Tina Lai, Susanne Steppi, Gangolf Jobb, Wolfram Forster, Igor Brettske, Stefan Gerber, Anton W. Ginhart, Oliver Gross, Silke Grumann, Stefan Hermann, Ralf Jost, Andreas Konig, Thomas Liss, Ralph Lussmann, Michael May, Bjorn Nonhoff, Boris Reichel, Robert Strehlow, Alexandros Stamatakis, Norbert Stuckmann, Alexander Vilbig, Michael Lenke, Thomas Ludwig, Arndt Bode, Karl-Heinz Schleifer posted to arb by sim82 on 2009-07-29 15:00:48 as along with 5 people stharward suzannevdVelde florisbuijzen Vincent_Rouilly mcox
	NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes [My Copy] Nucl. Acids Res., Vol. 34, No. suppl_2. (1 July 2006), pp. W394-399. by T. Z. Desantis, P. Hugenholtz, K. Keller, et al.E. L. Brodie, N. Larsen, Y. M. Piceno, R. Phan, G. L. Andersen posted to no-tag by sim82 on 2009-07-29 14:50:33 as along with 5 people and 1 group esyoun jmeppley nghoffma mcox djkt iSEEM
	A Rapid Bootstrap Algorithm for the RAxML Web Servers [My Copy] Syst Biol, Vol. 57, No. 5. (1 October 2008), pp. 758-771. by Alexandros Stamatakis, Paul Hoover, Jacques Rougemont posted to raxml by sim82 on 2009-07-23 13:54:04 as along with 2 people druvus aprasad
	The Holy Grail of the Perfect Character: The Cladistic Treatment of Morphometric Data [My Copy] Cladistics, Vol. 9, No. 3., pp. 275-304. by Kevin Thiele posted to morph_calib by sim82 on 2009-05-14 12:03:54 as
	Phenetics in Camouflage [My Copy] Vol. 6, No. 1., pp. 91-100. by James S. Farris posted to morph_calib by sim82 on 2009-05-14 12:01:58 as
	Character Analysis in Morphological Phylogenetics: Problems and Solutions [My Copy] Systematic Biology, Vol. 50, No. 5., pp. 689-699. by John Wiens posted to morph_calib by sim82 on 2009-05-14 11:54:48 as
	Phylogeny and Subfamilial Classification of the Grasses (Poaceae) [My Copy] Annals of the Missouri Botanical Garden, Vol. 88 (2001), pp. 373-457. by Grass Phylogeny Working Group posted to gpwg morph_calib by sim82 on 2009-05-13 13:06:42 as
	Hylid Frog Phylogeny and Sampling Strategies for Speciose Clades [My Copy] Systematic Biology, Vol. 54, No. 5. (October 2005), pp. 719-748. by John Wiens, James Fetzner, Christopher Parkinson, Tod Reeder posted to hylid2005 morph_calib by sim82 on 2009-05-13 12:57:18 as
	Ontogeny Discombobulates Phylogeny: Paedomorphosis and Higher-Level Salamander Relationships [My Copy] Systematic Biology, Vol. 54, No. 1. (February 2005), pp. 91-110. by John Wiens, Ronald Bonett, Paul Chippindale posted to morph_calib salamander2005 by sim82 on 2009-05-13 12:55:40 as
	ReXSpecies - a tool for the analysis of the evolution of generegulation across species [My Copy] BMC evolutionary biology, Vol. 8 (14 April 2008), 111. by Stephan Struckmann, Marcos J. Arauzo-Bravo, Hans R. Schoeler, Rolland A. Reinbold, Georg Fuellen posted to morph_calib rexspecies by sim82 on 2009-05-13 09:59:39 as along with 3 people and 1 group isimpson maximilianh cisevol cis-regulatory-evolution
	Data congruence, paedomorphosis and salamanders [My Copy] Frontiers in Zoology, Vol. 4 (31 October 2007), 22. by Torsten H. Struck posted to salamander2005 by sim82 on 2009-05-13 09:54:36 as
	Phylogeny of Extant and Fossil Juglandaceae Inferred from the Integration of Molecular and Morphological Data Sets [My Copy] Systematic Biology, Vol. 56, No. 3. (2007), pp. 412-430. by Paul S. Manos, Pamela S. Soltis, Douglas E. Soltis, et al.Steven R. Manchester, Sang-Hun Oh, Charles D. Bell, David L. Dilcher, Donald E. Stone posted to manos2007 morph_calib by sim82 on 2009-05-13 09:52:53 as
	Australia's Oldest Marsupial Fossils and their Biogeographical Implications [My Copy] PLoS ONE, Vol. 3, No. 3. (26 March 2008), e1858. by Robin M. Beck, Henk Godthelp, Vera Weisbecker, Michael Archer, Suzanne J. Hand posted to beck_djha_2008 morph_calib by sim82 on 2009-05-13 09:50:25 as
	Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics [My Copy] Syst Biol, Vol. 57, No. 5. (1 October 2008), pp. 750-757. by Kasper Munch, Wouter Boomsma, John P. Huelsenbeck, Eske Willerslev, Rasmus Nielsen posted to phylo by sim82 on 2008-10-14 13:08:09 as along with 3 people and 1 group polivares druvus djkt iSEEM
	The PyMOL Molecular Graphics System [My Copy] (2002) by W. L. 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. [My Copy] Protein Eng, Vol. 11, No. 9. (September 1998), pp. 739-747. by I. N. Shindyalov, P. E. Bourne posted to ce structural by sim82 on 2008-07-13 12:20:48 as along with 11 people and 2 groups medic0747 sebk reyez pjcite nigham jwm analogAI dgront rabio siebertm Inchoate Radiation_Damage Stressosome
	Protein structure comparison by alignment of distance matrices. [My Copy] Journal of molecular biology, 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 7 people and 2 groups jwm tjimenez BragilMassoud ana nigham dgront siebertm structural_bioinformatics Bioinformatics
	Protein families and their evolution-a structural perspective. [My Copy] Annu Rev Biochem, Vol. 74 (2005), pp. 867-900. by C. A. Orengo, J. M. Thornton posted to review structure by sim82 on 2008-07-13 11:10:48 as along with 19 people and 6 groups dfdong ucbcjbm flbarroso kumar_physics yuslinaz ssgong 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 [My Copy] Bioinformatics, Vol. 23, No. 2. (15 January 2007), pp. e205-e211. by Birzele, Fabian, Gewehr, et al.E. Jan, Csaba, Gergely, Zimmer, Ralf posted to alignment structural vorolign voronoi by sim82 on 2008-07-12 20:21:15 as along with 1 person mijam
	Application of a Theory of Enzyme Specificity to Protein Synthesis [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 44, No. 2. (February 1958), pp. 98-104. by D. E. Koshland posted to fit induced by sim82 on 2008-07-12 20:18:08 as along with 7 people aqeel cen4ik 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. [My Copy] 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 along with 2 people flbarroso xavierprat
	Biochemistry [My Copy] (2002) by J. M. Berg, J. L. 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. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 82, No. 23. (December 1985), pp. 7840-7844. by R. J. Leatherbarrow, A. R. 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. [My Copy] Annual review of biophysics and biomolecular structure, Vol. 32, No. 1. (2003), pp. 425-443. by A. Warshel posted to qmmm review warshel by sim82 on 2008-07-12 14:29:59 as along with 1 person flbarroso
	ENZYMATIC TRANSITION STATES AND TRANSITION STATE ANALOG DESIGN [My Copy] 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 [My Copy] 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 [My Copy] Journal of Chemical Information and Computer Sciences, Vol. 25 (1985), pp. 64-73. by R. E. Carhart, D. H. Smith, R. Venkataraghavan posted to fingerprint similarity by sim82 on 2008-07-08 13:10:06 as along with 2 people Eliamar nachtalp
	BRENDA, the enzyme database: updates and major new developments [My Copy] Nucl. Acids Res., Vol. 32, No. suppl_1. (1 January 2004), pp. D431-433. by Ida Schomburg, Antje Chang, Christian Ebeling, et al.Marion Gremse, Christian Heldt, Gregor Huhn, Dietmar Schomburg posted to brenda database by sim82 on 2008-07-08 12:18:16 as along with 5 people and 2 groups flbarroso 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 [My Copy] Nucleic Acids Research, Vol. 32 (2004), pp. D129-D133. by C. T. Porter, G. J. Bartlett, J. M. Thornton posted to csa database by sim82 on 2008-07-08 12:16:59 as
	The Universal Protein Resource (UniProt). [My Copy] 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 8 people and 1 group flbarroso sgoetz guhjy dullhunk CitoJam massivemayhem cjeans saunders References for 3DSim paper
	Evolution of Enzymes in Metabolism: A Network Perspective [My Copy] 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. [My Copy] J Mol Biol, Vol. 311, No. 4. (24 August 2001), pp. 693-708. by S. A. Teichmann, S. C. Rison, J. M. 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 [My Copy] (1992) by E. C. 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 [My Copy] Journal of Molecular Biology, Vol. 307, No. 4. (6 April 2001), pp. 1113-1143. by A. E. Todd, C. A. Orengo, J. M. Thornton posted to enzyme evolution by sim82 on 2008-07-07 16:57:21 as along with 10 people and 2 groups ucbcjbm flbarroso yuslinaz sgoetz ana kuhn tny sriram_s cdallett uz_labu_laimi structural_bioinformatics Bioinformatics
	Understanding Enzyme Superfamilies. Chemistry as the fundamental determinant in the evolution of new catalytic activities [My Copy] J. Biol. Chem., Vol. 272, No. 49. (5 December 1997), pp. 30591-30594. by P. C. Babbitt, J. A. Gerlt posted to catalytic evolution by sim82 on 2008-07-07 16:50:32 as along with 1 person flbarroso
	SCOP: a structural classification of proteins database for the investigation of sequences and structures. [My Copy] Journal of molecular biology, Vol. 247, No. 4. (7 April 1995), pp. 536-540. by A. G. Murzin, S. E. Brenner, T. Hubbard, C. Chothia posted to classification enzyme scop by sim82 on 2008-07-07 15:33:05 as along with 14 people timhubbard flbarroso yuslinaz semin pjcite dimka chrn chad_davis j3xucite sriram_s aengisch massivemayhem cjeans siebertm
	CATH--a hierarchic classification of protein domain structures. [My Copy] Structure (London, England : 1993), Vol. 5, No. 8. (15 August 1997), pp. 1093-1108. by C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, J. M. Thornton posted to cath classification enzyme by sim82 on 2008-07-07 15:32:05 as along with 14 people and 4 groups ucbcjbm flbarroso kumar_physics semin sebk tjimenez dimka jwm chad_davis Einat caporaso massivemayhem jteyra gulkur structural_bioinformatics Radiation_Damage Stressosome biomedical-nlp
	Understanding nature's catalytic toolkit. [My Copy] Trends Biochem Sci (5 October 2005) by A. Gutteridge, J. M. Thornton posted to catalysis catalytic by sim82 on 2008-07-07 15:07:44 as along with 11 people and 4 groups ucbcjbm 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 [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. Epub ahead of print (May 2008) by D. C. Bas, D. M. Rogers, J. H. 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 [My Copy] Mol Pharmacol, Vol. 51, No. 6. (1 June 1997), pp. 999-1006. by S. Jacobitz, M. D. Ryan, M. M. Mclaughlin, G. P. Livi, W. E. Dewolf, T. J. 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) [My Copy] J. Biol. Chem., Vol. 273, No. 11. (13 March 1998), pp. 6460-6466. by I. V. Turko, S. H. Francis, J. D. Corbin posted to 1ptw mutagenesis mutation by sim82 on 2008-07-07 13:01:29 as
	Using Reaction Mechanism to Measure Enzyme Similarity [My Copy] Journal of Molecular Biology, Vol. 368, No. 5. (18 May 2007), pp. 1484-1499. by N. M. O'Boyle, G. L. Holliday, D. E. Almonacid, J. B. O. 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. [My Copy] Biochemistry, Vol. 45, No. 8. (28 February 2006), pp. 2545-2555. by Scott C-H C. Pegg, Shoshana D. Brown, Sunil Ojha, et al.Jennifer Seffernick, Elaine C. Meng, John H. Morris, Patricia J. Chang, Conrad C. Huang, Thomas E. Ferrin, Patricia C. Babbitt posted to catalytic by sim82 on 2008-07-05 17:56:18 as along with 7 people NickFurnham grottenolm yzlab ucbcjbm kuhn tny jdiggans
	EzCatDB: the Enzyme Catalytic-mechanism Database. [My Copy] Nucleic acids research, Vol. 33, No. Database issue. (1 January 2005) by N. Nagano posted to catalytic by sim82 on 2008-07-05 17:54:34 as along with 5 people grottenolm ziquje eweaver tny Jporci
	The Chemistry of Protein Catalysis [My Copy] Journal of Molecular Biology, Vol. 372, No. 5. (5 October 2007), pp. 1261-1277. by G. L. Holliday, D. E. Almonacid, J. B. O. Mitchell, J. M. 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 [My Copy] J. Phys. Chem., Vol. 100, No. 43. (24 October 1996), pp. 17373-17387. by E. Demchuk, R. C. Wade posted to dielectric electrostatics pka by sim82 on 2008-07-04 16:00:58 as along with 2 people flbarroso RamuAnandakrishnan
	A statistical approach to the prediction of pK(a) values in proteins. [My Copy] Proteins, Vol. 69, No. 1. (1 October 2007), pp. 75-82. by Y. He, J. Xu, X. M. Pan posted to pka statistics by sim82 on 2008-07-04 14:48:27 as along with 1 person flbarroso
	Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations [My Copy] Journal of Computational Chemistry, Vol. 25, No. 15. (2004), pp. 1865-1872. by B. Kuhn, P. A. Kollman, M. Stahl posted to born electrostatics gb pka by sim82 on 2008-07-04 12:48:28 as along with 3 people and 1 group flbarroso sobolevnrm dfgreen baker-group
	pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. [My Copy] 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 along with 1 person flbarroso

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macie	35
pka	14
electrostatics	10
macie_ecd1	9
morph_calib	9
1a0i	6
1dcn_2j84	5
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dali	4
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dock	2
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voronoi	1
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