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de massivemayhem library [252 articles]

Articles dernièrement stockés dans la bibliothèque de massivemayhem .
  • Conformational Sampling of Bioactive Molecules: A Comparative Study
    J. Chem. Inf. Model. (6 April 2007)
    by DK Agrafiotis, AC Gibbs, F Zhu, S Izrailev, E Martin
    posted to conformers by massivemayhem on 2008-10-08 14:53:32 as ** along with 3 people apaydin daevans superpyrin
  • Discarding Functional Residues from the Substitution Table Improves Predictions of Active Sites within Three-Dimensional Structures
    PLoS Comput Biol, Vol. 4, No. 10. (3 October 2008), e1000179.
    by Sungsam Gong, Tom L Blundell
    posted to esst by massivemayhem on 2008-10-07 13:08:20 as ** along with 1 person reyez
  • Can we separate active from inactive conformations?
    Journal of computer-aided molecular design, Vol. 16, No. 2. (February 2002), pp. 105-112.
    by DJ Diller, KM Merz
    posted to conformers by massivemayhem on 2008-09-30 16:37:01 as **
  • Distinguishing between Bioactive and Modeled Compound Conformations through Mining of Emerging Chemical Patterns
    J. Chem. Inf. Model. (13 August 2008)
    by Jens Auer, Jürgen Bajorath
    posted to conformers by massivemayhem on 2008-09-30 16:24:09 as ** along with 2 people sschurer zimbo1
  • Diverse, high-quality test set for the validation of protein-ligand docking performance.
    J Med Chem, Vol. 50, No. 4. (22 February 2007), pp. 726-741.
    by MJ Hartshorn, ML Verdonk, G Chessari, SC Brewerton, WT Mooij, PN Mortenson, CW Murray
    posted to pdb docking by massivemayhem on 2008-09-25 12:02:39 as ** along with 8 people GermanErlenkamp higueruelo BragilMassoud daevans ramensky hmk superpyrin thanatos
  • Concept of Combinatorial De Novo Design of Drug-like Molecules by Particle Swarm Optimization
    Chemical Biology & Drug Design, Vol. 72, No. 1. (2008), pp. 16-26.
    by Markus Hartenfeller, Ewgenij Proschak, Andreas Schuller, Gisbert Schneider
    posted to fragments by massivemayhem on 2008-09-24 14:58:34 as ** along with 1 person reyez
  • Deconstructing fragment-based inhibitor discovery.
    Nature chemical biology, Vol. 2, No. 12. (December 2006), pp. 720-723.
    by K Babaoglu, BK Shoichet
    posted to fragments by massivemayhem on 2008-09-24 14:57:42 as **
  • Chemical Substructures that Enrich for Biological Activity.
    Bioinformatics (Oxford, England) (11 September 2008)
    by Justin Klekota, Frederick P P Roth
    posted to fragments by massivemayhem on 2008-09-24 11:09:56 as ** along with 2 people thanatos higueruelo
  • Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit.
    Chemistry Central journal, Vol. 2 (2008)
    by NM O'Boyle, C Morley, GR Hutchison
    posted to cheminformatics openbabel pybel by massivemayhem on 2008-07-29 11:49:07 as **
  • Conceptual schema and relational database design (2nd ed.)
    (1996)
    by Terry Halpin
    posted to orm by massivemayhem on 2008-07-22 16:32:14 as ** along with 1 person nroovers
  • MSDmotif: exploring protein sites and motifs
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Adel Golovin, Kim Henrick
    posted to binding-site motifs by massivemayhem on 2008-07-21 11:32:41 as ** along with 3 people reyez chad_davis Evangelia
  • SuperPred: drug classification and target prediction.
    Nucleic acids research, Vol. 36, No. Web Server issue. (1 July 2008)
    by M Dunkel, S Günther, J Ahmed, B Wittig, R Preissner
    posted to drug-classification by massivemayhem on 2008-07-17 15:01:44 as **
  • Drugs in sport: a scientist-athlete's perspective: from ambition to neurochemistry
    Br J Pharmacol, Vol. 154, No. 3. (0000), pp. 496-501.
    by M Spedding, C Spedding
    posted to journal-club by massivemayhem on 2008-07-17 13:01:24 as **
  • Pharmacology of anabolic steroids
    Br J Pharmacol, Vol. 154, No. 3. (0000), pp. 502-521.
    by AT Kicman
    posted to journal-club by massivemayhem on 2008-07-17 12:54:43 as **
  • Structure of the catalytic domain of fibroblast collagenase complexed with an inhibitor.
    Science (New York, N.Y.), Vol. 263, No. 5145. (21 January 1994), pp. 375-377.
    by B Lovejoy, A Cleasby, AM Hassell, K Longley, MA Luther, D Weigl, G McGeehan, AB McElroy, D Drewry, MH Lambert
    posted to drug-discovery pdb by massivemayhem on 2008-07-01 14:02:40 as **
  • MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions.
    Nucleic acids research (8 May 2008)
    by Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov, Haim J J Wolfson
    posted to binding-site by massivemayhem on 2008-06-11 14:24:40 as ** along with 2 people higueruelo reyez
  • URL decay in MEDLINE - a 4-year follow-up study.
    Bioinformatics (Oxford, England) (15 April 2008)
    by Jonathan D Wren
    posted to computer-science by massivemayhem on 2008-06-11 13:32:39 as ** along with 1 person dullhunk
  • Ligand-protein database: linking protein-ligand complex structures to binding data.
    J Med Chem, Vol. 44, No. 22. (25 October 2001), pp. 3592-3598.
    by O Roche, R Kiyama, CL Brooks
    posted to database protein-ligand by massivemayhem on 2008-06-11 13:27:07 as ** along with 2 people nickolay blackbart
  • Automated analysis of interatomic contacts in proteins.
    Bioinformatics, Vol. 15, No. 4. (April 1999), pp. 327-332.
    by V Sobolev, A Sorokine, J Prilusky, EE Abola, M Edelman
    posted to database protein-ligand by massivemayhem on 2008-06-11 13:17:42 as ** along with 2 people bicko nickolay
  • A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships.
    J Chem Inf Model, Vol. 46, No. 2. (r 2006), pp. 736-742.
    by ND Gold, RM Jackson
    posted to binding-site protein-ligand by massivemayhem on 2008-06-11 13:15:21 as ** along with 3 people and 1 group caporaso blackbart reyez biomedical-nlp
  • Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions.
    J Med Chem, Vol. 47, No. 2. (15 January 2004), pp. 337-344.
    by Z Deng, C Chuaqui, J Singh
    posted to protein-ligand sift by massivemayhem on 2008-06-11 13:13:34 as ** along with 2 people and 2 groups apostola sangeetha Bioinformatics insilicodrug
  • Relating protein pharmacology by ligand chemistry
    Nature Biotechnology, Vol. 25, No. 2. (07 February 2007), pp. 197-206.
    by Michael J Keiser, Bryan L Roth, Blaine N Armbruster, Paul Ernsberger, John J Irwin, Brian K Shoichet
    posted to cheminformatics pharmacology by massivemayhem on 2008-06-10 14:34:56 as ** along with 7 people ucbcjbm Yanno tjimenez kuhn daevans dgront jerome_ucsf_slb
  • 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 protein-classification protein-structure by massivemayhem on 2008-06-10 11:38:52 as ** along with 9 people and 4 groups tjimenez dimka jwm chad_davis Einat caporaso sim82 jteyra gulkur structural_bioinformatics Radiation_Damage Stressosome biomedical-nlp
  • PDBcal: A Comprehensive Dataset for Receptor-Ligand Interactions with Three-dimensional Structures and Binding Thermodynamics from Isothermal Titration Calorimetry
    Chemical Biology & Drug Design, Vol. 71, No. 6. (2008), pp. 529-532.
    by Liwei Li, Justin J Dantzer, Jonathan Nowacki, Brian J O’callaghan, Samy O Meroueh
    posted to binding-affinity protein-ligand by massivemayhem on 2008-05-22 10:01:46 as ** along with 2 people higueruelo kintoki
  • Fast Polygon Area and Newell Normal Computation
    journal of graphics tools, Vol. 7, No. 2. (2002), pp. 9-13.
    by Daniel Sunday
    posted to geometry newell-normal by massivemayhem on 2008-05-20 15:36:14 as **
  • Halogen bonds in biological molecules
    Proceedings of the National Academy of Sciences, Vol. 101, No. 48. (30 November 2004), pp. 16789-16794.
    by Pascal Auffinger, Franklin A Hays, Eric Westhof, Shing P Ho
    posted to halogen-bond by massivemayhem on 2008-05-16 10:59:06 as **
  • SFCscore: Scoring functions for affinity prediction of protein-ligand complexes.
    Proteins (28 April 2008)
    by Christoph A A Sotriffer, Paul Sanschagrin, Hans Matter, Gerhard Klebe
    posted to binding-affinity by massivemayhem on 2008-05-15 13:17:33 as **
  • Directing macromolecular conformation through halogen bonds.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 15. (10 April 2007), pp. 6188-6193.
    by AR Voth, FA Hays, PS Ho
    posted to halogen-bond by massivemayhem on 2008-05-15 11:45:19 as **
  • ChEBI: a database and ontology for chemical entities of biological interest.
    Nucleic Acids Res (11 October 2007)
    by Kirill Degtyarenko, Paula de D Matos, Marcus Ennis, Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcántara, Michael Darsow, Mickaël Guedj, Michael Ashburner
    posted to chemistry database by massivemayhem on 2008-05-15 10:31:19 as ** along with 3 people irenas dullhunk grottenolm
  • KEGG for linking genomes to life and the environment
    Nucl. Acids Res. (12 December 2007), gkm882.
    by Minoru Kanehisa, Michihiro Araki, Susumu Goto, Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu, Yoshihiro Yamanishi
    posted to database genome pathways by massivemayhem on 2008-05-15 10:28:42 as ** along with 10 people namunet irenas jyuh raiyar barriot renatomilani shung hpaces natstreet TheresaNiederberger
  • Chemistry for everyone
    Nature, Vol. 451, No. 7179. (7 February 2008), pp. 648-651.
    by Peter Murray-Rust
    posted to chemistry e-science by massivemayhem on 2008-05-06 14:32:49 as ** along with 6 people operon dullhunk hpiwowar sci91078 peterli jyuh
  • The use of protein-ligand interaction fingerprints in docking.
    Current opinion in drug discovery & development, Vol. 11, No. 3. (May 2008), pp. 356-364.
    by SC Brewerton
    posted to docking protein-ligand by massivemayhem on 2008-05-06 14:01:00 as ** along with 1 person higueruelo
  • What is principal component analysis?
    Nature Biotechnology, Vol. 26, No. 3., pp. 303-304.
    by Markus Ringnér
    posted to pca statistics by massivemayhem on 2008-03-26 13:46:22 as ** along with 54 people and 3 groups Yanno jyuh operon barry baaic dullhunk Bevan_Weir zeji gareth zwang GustavoLacerda GeeSharpMinor bmaust zambujo mingzhi starz1010101 maralena wchannels sunhwan jennifermbui kdelavega zhouyu rsantana laharrin sobolevnrm fryanpan kengg rvosa dekay23 adacier hpaces waghsk rchauhan pavanghatty kristgy jfr bibay2004 xingxu quianominorleo abbie_riner craigwilson06 ashko markusd dayjm dimka i-stevenson chrissp100 tharris ale mjoach HugoMarcelo jdiezperezj rrbarb Nici baker-group FAB-lab Bioinformatics
  • Fragment-based screening using X-ray crystallography and NMR spectroscopy.
    Curr Opin Chem Biol, Vol. 11, No. 5. (October 2007), pp. 485-493.
    by H Jhoti, A Cleasby, M Verdonk, G Williams
    posted to drug-design fragments by massivemayhem on 2008-03-20 14:34:57 as ** along with 1 person jwm
  • Statistical Analysis of the Effects of Common Chemical Substituents on Ligand Potency
    J. Med. Chem. (4 January 2008)
    by Philip J Hajduk, Daryl R Sauer
    posted to ligand medchem by massivemayhem on 2008-03-20 11:11:31 as ** along with 2 people jerome higueruelo
  • Genome-wide association studies: progress and potential for drug discovery and development
    Nat Rev Drug Discov, Vol. 7, No. 3. (February 2008), pp. 221-230.
    by Stephen F Kingsmore, Ingrid E Lindquist, Joann Mudge, Damian D Gessler, William D Beavis
    posted to drug-discovery reviews snps by massivemayhem on 2008-02-29 11:38:51 as ** along with 3 people and 1 group jyuh psique Petersarkies parkinson's disease references
  • LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
    Journal of Molecular Graphics and Modelling, Vol. 15, No. 6. (December 1997), pp. 359-363.
    by Manfred Hendlich, Friedrich Rippmann, Gerhard Barnickel
    posted to binding-site by massivemayhem on 2008-02-07 17:24:12 as ** along with 1 person trmr
  • Fast prediction and visualization of protein binding pockets with PASS
    Journal of Computer-Aided Molecular Design, Vol. 14, No. 4. (1 May 2000), pp. 383-401.
    by Patrick G Brady, Pieter F Stouten
    posted to algorithm binding-site by massivemayhem on 2008-02-07 11:36:04 as **
  • Predicting protein druggability.
    Drug Discov Today, Vol. 10, No. 23-24. (December 2005), pp. 1675-1682.
    by PJ Hajduk, JR Huth, C Tse
    posted to druggability by massivemayhem on 2008-02-07 11:30:07 as ** along with 4 people and 1 group tjimenez bicko caporaso higueruelo biomedical-nlp
  • Clique-detection algorithms for matching three-dimensional molecular structures.
    J Mol Graph Model, Vol. 15, No. 4. (August 1997), pp. 245-253.
    by EJ Gardiner, PJ Artymiuk, P Willett
    posted to algorithms graph-theory by massivemayhem on 2008-02-07 11:12:44 as ** along with 2 people tjimenez BarrosH
  • A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology
    Journal of Molecular Biology, Vol. 323, No. 2. (18 October 2002), pp. 387-406.
    by Stefan Schmitt, Daniel Kuhn, Gerhard Klebe
    posted to binding-site ligands by massivemayhem on 2008-02-07 10:28:07 as **
  • An anticancer C-Kit kinase inhibitor is reengineered to make it more active and less cardiotoxic.
    J Clin Invest, Vol. 117, No. 12. (December 2007), pp. 4044-4054.
    by A Fernández, A Sanguino, Z Peng, E Ozturk, J Chen, A Crespo, S Wulf, A Shavrin, C Qin, J Ma, J Trent, Y Lin, HD Han, LS Mangala, JA Bankson, J Gelovani, A Samarel, W Bornmann, AK Sood, G Lopez-Berestein
    posted to desolvation drug-design imatinib kinases water by massivemayhem on 2008-02-05 14:41:58 as **
  • 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-site database prediction protein-drug protein-ligand by massivemayhem on 2008-01-24 12:06:30 as ** along with 6 people ramensky tjimenez chad_davis jteyra mingzhi higueruelo
  • SMARTS
    http://www.daylight.com/dayhtml/doc/theory/index.html
    by CA James, D Weininger, J Delay
    posted to chemistry chemoinformatics by massivemayhem on 2008-01-22 12:10:06 as ** along with 1 person noby
  • SMILES, a chemical language and information system. 1. introduction to methodology and encoding rules
    J. Chem. Inf. Comput. Sci., Vol. 28, No. 1. (February 1988), pp. 31-36.
    by David Weininger
    posted to chemoinformatics smiles by massivemayhem on 2008-01-22 12:08:54 as ** along with 2 people and 2 groups camster dbk streptomyces dbk-lab
  • Ensembl 2007.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by TJ Hubbard, BL Aken, K Beal, B Ballester, M Caccamo, Y Chen, L Clarke, G Coates, F Cunningham, T Cutts, T Down, SC Dyer, S Fitzgerald, J Fernandez-Banet, S Graf, S Haider, M Hammond, J Herrero, R Holland, K Howe, K Howe, N Johnson, A Kahari, D Keefe, F Kokocinski, E Kulesha, D Lawson, I Longden, C Melsopp, K Megy, P Meidl, B Ouverdin, A Parker, A Prlic, S Rice, D Rios, M Schuster, I Sealy, J Severin, G Slater, D Smedley, G Spudich, S Trevanion, A Vilella, J Vogel, S White, M Wood, T Cox, V Curwen, R Durbin, XM Fernandez-Suarez, P Flicek, A Kasprzyk, G Proctor, S Searle, J Smith, A Ureta-Vidal, E Birney
    posted to database genome sequence by massivemayhem on 2008-01-22 11:37:40 as ** along with 9 people and 1 group kuhn dullhunk incovoma Garamonfok asddd loopback007 flexer skumagai kcrawlik Cancer_Stem_Cells
  • Announcing the worldwide Protein Data Bank
    Nat Struct Mol Biol, Vol. 10, No. 12. (December 2003), pp. 980-980.
    by Helen Berman, Kim Henrick, Haruki Nakamura
    posted to database protein-structure by massivemayhem on 2008-01-21 15:17:54 as ** along with 2 people allmensch reyez
  • Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design
    Chem Biol, Vol. 3, No. 12. (Dec 1996), pp. 973-980.
    by JE Ladbury
    posted to drug-design protein-ligand water by massivemayhem on 2008-01-18 13:30:57 as **
  • 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 pathways protein-ligand by massivemayhem on 2008-01-18 10:12:36 as ** along with 6 people alexg blackbart koerner dagmar shung sim82
  • Het-PDB Navi.: A Database for Protein-Small Molecule Interactions
    J Biochem (Tokyo), Vol. 135, No. 1. (1 January 2004), pp. 79-84.
    by Akihiro Yamaguchi, Kei Iida, Nobuaki Matsui, Shirou Tomoda, Kei Yura, Mitiko Go
    posted to database protein-ligand by massivemayhem on 2008-01-18 10:11:28 as ** along with 1 person blackbart
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