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massivemayhem database [53 articles]

Recent papers added to massivemayhem library classified by the tag database. You can also see everyone's database.
  • 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 protein-ligand database 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 protein-ligand database by massivemayhem on 2008-06-11 13:17:42 as ** along with 2 people bicko nickolay
  • 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 database chemistry by massivemayhem on 2008-05-15 10:31:19 as ** along with 3 people grottenolm irenas dullhunk
  • 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 pathways genome database by massivemayhem on 2008-05-15 10:28:42 as ** along with 9 people TheresaNiederberger natstreet hpaces irenas jyuh raiyar barriot renatomilani shung
  • 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 4 people higueruelo tjimenez chad_davis mingzhi
  • 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 8 people and 1 group skumagai kuhn dullhunk incovoma Garamonfok asddd loopback007 flexer 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 reyez allmensch
  • 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 sim82 alexg blackbart koerner dagmar shung
  • 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
  • Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions.
    J Mol Biol, Vol. 326, No. 2. (14 February 2003), pp. 607-620.
    by M Hendlich, A Bergner, J Günther, G Klebe
    posted to database protein-ligand by massivemayhem on 2008-01-18 10:10:31 as ** along with 2 people nickolay blackbart
  • PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by JM Shin, DH Cho
    posted to database protein-ligand by massivemayhem on 2008-01-18 10:09:22 as **
  • Binding MOAD, a high-quality protein-ligand database.
    Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008)
    by ML Benson, RD Smith, NA Khazanov, B Dimcheff, J Beaver, P Dresslar, J Nerothin, HA Carlson
    posted to binding-affinity database protein-ligand by massivemayhem on 2008-01-18 10:08:30 as ** along with 1 person higueruelo
  • AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by P Block, CA Sotriffer, I Dramburg, G Klebe
    posted to binding-affinity database protein-ligand by massivemayhem on 2008-01-18 10:07:06 as **
  • Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms
    BMC Bioinformatics, Vol. 8 (25 August 2007), 310.
    by Luis A Diago, Persy Morell, Longendri Aguilera, Ernesto Moreno
    posted to database protein-ligand by massivemayhem on 2008-01-09 18:16:15 as ** along with 1 person mdimmic
  • SuperTarget and Matador: resources for exploring drug-target relationships.
    Nucleic Acids Res (16 October 2007)
    by Stefan Günther, Michael Kuhn, Mathias Dunkel, Monica Campillos, Christian Senger, Evangelia Petsalaki, Jessica Ahmed, Eduardo Garcia G Urdiales, Andreas Gewiess, Lars Juhl J Jensen, Reinhard Schneider, Roman Skoblo, Robert B B Russell, Philip E E Bourne, Peer Bork, Robert Preissner
    posted to database drugs by massivemayhem on 2008-01-09 10:26:05 as ** along with 6 people jyuh mdimmic chad_davis daevans Evangelia larsjuhljensen
  • STITCH: interaction networks of chemicals and proteins.
    Nucleic Acids Res (15 December 2007)
    by Michael Kuhn, Christian von Mering, Monica Campillos, Lars Juhl J Jensen, Peer Bork
    posted to database networks protein-ligand by massivemayhem on 2008-01-09 10:14:20 as ** along with 6 people and 1 group higueruelo jyuh balicea bootsy sobolevnrm larsjuhljensen baker-group
  • Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes
    Bioinformatics, Vol. 19, No. 14. (22 September 2003), pp. 1856-1857.
    by Dushyanthan Puvanendrampillai, John B Mitchell
    posted to database protein-ligand by massivemayhem on 2008-01-08 13:57:10 as ** along with 1 person nickolay
  • Comparison of protein active site structures for functional annotation of proteins and drug design
    Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 1. (2006), pp. 124-135.
    by Robert Powers, Jennifer C Copeland, Katherine Germer, Kelly A Mercier, Viswanathan Ramanathan, Peter Revesz
    posted to database protein-ligand by massivemayhem on 2007-12-04 11:26:50 as ** along with 1 person conkymacro
  • Cognate Ligand Domain Mapping for Enzymes.
    J Mol Biol (20 September 2006)
    by Matthew Bashton, Irene Nobeli, Janet M M Thornton
    posted to cognate-ligand database protein-ligand by massivemayhem on 2007-11-30 10:30:12 as ** along with 3 people drastic cdallett grottenolm
  • ChemDB Update - Full-Text Search and Virtual Chemical Space.
    Bioinformatics (28 June 2007)
    by Jonathan H H Chen, Erik Linstead, S Joshua J Swamidass, Dennis Wang, Pierre Baldi
    posted to database drug-discovery small-molecules virtual-screening by massivemayhem on 2007-09-12 17:18:37 as ** along with 3 people jyuh kuhn baldigroup
  • Prediction of deleterious human alleles.
    Hum Mol Genet, Vol. 10, No. 6. (15 March 2001), pp. 591-597.
    by S Sunyaev, V Ramensky, I Koch, W Lathe, AS Kondrashov, P Bork
    posted to database snps by massivemayhem on 2007-06-24 14:20:01 as ** along with 4 people and 2 groups caporaso cat_worth lpfernandes adijr structural_bioinformatics biomedical-nlp
  • Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways
    Nucl. Acids Res. (30 May 2007), gkm232.
    by Alper Uzun, Chesley M Leslin, Alexej Abyzov, Valentin Ilyin
    posted to database snps by massivemayhem on 2007-06-24 14:01:40 as ** along with 2 people jyuh bicko
  • MSDsite: A database search and retrieval system for the analysis and viewing of bound ligands and active sites
    Proteins: Structure, Function, and Bioinformatics, Vol. 58, No. 1. (2005), pp. 190-199.
    by Adel Golovin, Dimitris Dimitropoulos, Tom Oldfield, Abdelkrim Rachedi, Kim Henrick
    posted to database protein-ligand by massivemayhem on 2007-06-20 15:08:51 as ** along with 2 people and 1 group nickolay caporaso biomedical-nlp
  • Relibase: Design and Development of a Database for Comprehensive Analysis of Protein-Ligand Interactions
    Journal of Molecular Biology, Vol. 326, No. 2. (14 February 2003), pp. 607-620.
    by M Hendlich, A Bergner, J Gunther, G Klebe
    posted to database protein-ligand by massivemayhem on 2007-06-20 14:00:04 as ** along with 1 person P2324548
  • dbSNP: the NCBI database of genetic variation.
    Nucleic Acids Res, Vol. 29, No. 1. (1 January 2001), pp. 308-311.
    by ST Sherry, MH Ward, M Kholodov, J Baker, L Phan, EM Smigielski, K Sirotkin
    posted to database snps by massivemayhem on 2007-06-20 12:02:10 as ** along with 3 people aalibes chad_davis fisherp
  • ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by MD Kumar, KA Bava, MM Gromiha, P Prabakaran, K Kitajima, H Uedaira, A Sarai
    posted to database snps by massivemayhem on 2007-06-16 12:52:55 as ** along with 3 people and 1 group aalibes cat_worth gisle structural_bioinformatics
  • HOMSTRAD: a database of protein structure alignments for homologous families.
    Protein Sci, Vol. 7, No. 11. (November 1998), pp. 2469-2471.
    by K Mizuguchi, CM Deane, TL Blundell, JP Overington
    posted to alignment database protein-structure by massivemayhem on 2007-06-12 13:26:36 as ** along with 5 people newton1234 chrn medic0747 cdeane sebk
  • The Universal Protein Resource (UniProt).
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by
    posted to database protein by massivemayhem on 2007-06-12 13:18:28 as ** along with 6 people saunders sim82 jyuh dullhunk CitoJam cjeans
  • The PROSITE database.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by N Hulo, A Bairoch, V Bulliard, L Cerutti, E De Castro, PS Langendijk-Genevaux, M Pagni, CJ Sigrist
    posted to database protein-function by massivemayhem on 2007-06-12 13:09:54 as ** along with 5 people and 1 group yas happy_manatee sriram_s neils siebertm T_lab
  • Pfam: clans, web tools and services.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by RD Finn, J Mistry, B Schuster-Böckler, S Griffiths-Jones, V Hollich, T Lassmann, S Moxon, M Marshall, A Khanna, R Durbin, SR Eddy, EL Sonnhammer, A Bateman
    posted to database protein-function protein-structure by massivemayhem on 2007-06-12 13:08:50 as ** along with 8 people natstreet gbart dullhunk cjeans siebertm lpfernandes pablomendes antonkratz
  • 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 database protein-structure by massivemayhem on 2007-06-12 13:07:16 as ** along with 9 people sim82 dimka chrn chad_davis j3xucite sriram_s aengisch cjeans siebertm
  • The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by CT Porter, GJ Bartlett, JM Thornton
    posted to database protein-function by massivemayhem on 2007-06-12 13:05:20 as ** along with 8 people and 2 groups baaden chrn jwm gbart tny sriram_s siebertm grottenolm Radiation_Damage Stressosome
  • SuperDrug: a conformational drug database
    Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 1751-1753.
    by Andrean Goede, Mathias Dunkel, Cornelius Frommel, Robert Preissner
    posted to database drug-discovery by massivemayhem on 2007-06-11 15:52:43 as ** along with 3 people reyez nachtalp kuhn
  • DrugBank: a comprehensive resource for in silico drug discovery and exploration.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by DS Wishart, C Knox, AC Guo, S Shrivastava, M Hassanali, P Stothard, Z Chang, J Woolsey
    posted to bioinformatics database drug-discovery drug-targets small-molecules by massivemayhem on 2007-05-29 10:18:10 as ** along with 6 people and 2 groups kuhn maryee sangeetha madhadron jdiggans elvinado Bioinformatics insilicodrug
  • E-MSD: an integrated data resource for bioinformatics.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by S Velankar, P McNeil, V Mittard-Runte, A Suarez, D Barrell, R Apweiler, K Henrick
    posted to database by massivemayhem on 2007-05-29 10:07:06 as ** along with 2 people bicko chad_davis
  • The Protein Data Bank.
    Nucleic Acids Res, Vol. 28, No. 1. (1 January 2000), pp. 235-242.
    by HM Berman, J Westbrook, Z Feng, G Gilliland, TN Bhat, H Weissig, IN Shindyalov, PE Bourne
    posted to database protein-structure by massivemayhem on 2007-05-28 11:03:59 as ** along with 22 people and 4 groups sebk higueruelo boris_aguilar nigham lillekatt thaliana dimka kuhn jwm vavi bicko itmeson dgront caporaso condon leelarcombe aengisch debatebob gisle girschick selrac tji Radiation_Damage Stressosome biomedical-nlp beta
  • PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by AG Jegga, S Gowrisankar, J Chen, BJ Aronow
    posted to snps disease database by massivemayhem on 2007-01-26 11:47:42 as ** along with 2 people and 1 group bicko cat_worth structural_bioinformatics
  • FireDB--a database of functionally important residues from proteins of known structure.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by G Lopez, A Valencia, M Tress
    posted to protein-ligand protein-function database by massivemayhem on 2007-01-24 13:04:15 as **
  • CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by F Kolpakov, V Poroikov, R Sharipov, Y Kondrakhin, A Zakharov, A Lagunin, L Milanesi, A Kel
    posted to database cell-cycle cancer by massivemayhem on 2007-01-22 11:48:11 as ** along with 2 people jyuh jfr
  • CancerGenes: a gene selection resource for cancer genome projects.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by ME Higgins, M Claremont, JE Major, C Sander, AE Lash
    posted to snps database cancer by massivemayhem on 2007-01-19 14:41:19 as ** along with 5 people cerami jyuh textoris jfr frohike
  • Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by M Jayapandian, A Chapman, VG Tarcea, C Yu, A Elkiss, A Ianni, B Liu, A Nandi, C Santos, P Andrews, B Athey, D States, HV Jagadish
    posted to protein-protein-interactions database by massivemayhem on 2007-01-18 11:37:04 as ** along with 2 people jyuh cerami
  • MINT: the Molecular INTeraction database.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by A Chatr-aryamontri, A Ceol, LM Palazzi, G Nardelli, MV Schneider, L Castagnoli, G Cesareni
    posted to protein-protein-interactions database by massivemayhem on 2007-01-18 11:34:06 as **
  • Snap: an integrated SNP annotation platform.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by S Li, L Ma, H Li, S Vang, Y Hu, L Bolund, J Wang
    posted to snps database annotation by massivemayhem on 2007-01-18 11:30:51 as ** along with 2 people and 1 group jyuh cat_worth structural_bioinformatics
  • T1DBase, a community web-based resource for type 1 diabetes research.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by LJ Smink, EM Helton, BC Healy, CC Cavnor, AC Lam, D Flamez, OS Burren, Y Wang, GE Dolman, DB Burdick, VH Everett, G Glusman, D Laneri, L Rowen, H Schuilenburg, NM Walker, J Mychaleckyj, LS Wicker, DL Eizirik, JA Todd, N Goodman
    posted to t1d snps database by massivemayhem on 2007-01-18 11:17:03 as ** along with 1 person shikin
  • SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non synonymous SNPs.
    Bioinformatics (29 June 2006)
    by Joke Reumers, Sebastian Maurer-Stroh, Joost Schymkowitz, Frederic Rousseau
    posted to snps database by massivemayhem on 2007-01-18 11:12:37 as ** along with 4 people and 3 groups skoddet chad_davis caporaso cat_worth Nielsen group structural_bioinformatics biomedical-nlp
  • LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources
    Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2814-2820.
    by Rachel Karchin, Mark Diekhans, Libusha Kelly, Daryl J Thomas, Ursula Pieper, Narayanan Eswar, David Haussler, Andrej Sali
    posted to snps database annotation by massivemayhem on 2007-01-18 11:02:46 as ** along with 3 people and 3 groups mattjb cat_worth lpfernandes structural_bioinformatics ComplexAdaptiveSystems DSTO-CAS
  • STRING 7--recent developments in the integration and prediction of protein interactions.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by C von Mering, LJ Jensen, M Kuhn, S Chaffron, T Doerks, B Krüger, B Snel, P Bork
    posted to protein-protein-interactions database by massivemayhem on 2007-01-16 18:14:13 as ** along with 9 people higueruelo carlk renatomilani jyuh kuhn balajis fisherp raiyar larsjuhljensen
  • CellCircuits: a database of protein network models.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by HC Mak, M Daly, B Gruebel, T Ideker
    posted to networks database by massivemayhem on 2007-01-16 18:09:58 as ** along with 1 person jyuh
  • IntAct--open source resource for molecular interaction data.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by S Kerrien, Y Alam-Faruque, B Aranda, I Bancarz, A Bridge, C Derow, E Dimmer, M Feuermann, A Friedrichsen, R Huntley, C Kohler, J Khadake, C Leroy, A Liban, C Lieftink, L Montecchi-Palazzi, S Orchard, J Risse, K Robbe, B Roechert, D Thorneycroft, Y Zhang, R Apweiler, H Hermjakob
    posted to protein-protein-interactions database by massivemayhem on 2007-01-16 08:54:15 as ** along with 1 person balajis
  • HMDB: the Human Metabolome Database.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by DS Wishart, D Tzur, C Knox, R Eisner, AC Guo, N Young, D Cheng, K Jewell, D Arndt, S Sawhney, C Fung, L Nikolai, M Lewis, MA Coutouly, I Forsythe, P Tang, S Shrivastava, K Jeroncic, P Stothard, G Amegbey, D Block, DD Hau, J Wagner, J Miniaci, M Clements, M Gebremedhin, N Guo, Y Zhang, GE Duggan, GD Macinnis, AM Weljie, R Dowlatabadi, F Bamforth, D Clive, R Greiner, L Li, T Marrie, BD Sykes, HJ Vogel, L Querengesser
    posted to metabolome database by massivemayhem on 2007-01-15 21:38:41 as ** along with 1 person frohike
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