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chad_davis's web_service [55 articles]

Recent papers added to chad_davis's library classified by the tag web_service. You can also see everyone's web_service.
  • APID: Agile Protein Interaction DataAnalyzer.
    Nucleic acids research, Vol. 34, No. Web Server issue. (1 July 2006)
    by C Prieto, J De Las Rivas
    posted to web_service proj_interprets proj_assembly ppi networks download database data_integration by chad_davis on 2008-10-08 10:53:05 as *** along with 1 person satre
  • WikiPathways: Pathway Editing for the People
    PLoS Biology, Vol. 6, No. 7. (1 July 2008), e184.
    by Alexander R Pico, Thomas Kelder, Martijn P van Iersel, Kristina Hanspers, Bruce R Conklin, Chris Evelo
    posted to web_service networks database annotation by chad_davis on 2008-10-07 11:12:37 as ** along with 14 people and 2 groups jyuh psique ptrobajo cerami AlexanderPico thomaskelder iBartomeus renatomilani ajaymalik jarredmccaffrey laurianw dullhunk amarois tharris ConklinLab behavior_flexibility
  • notes PRISM: protein interactions by structural matching.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by U Ogmen, O Keskin, AS Aytuna, R Nussinov, A Gursoy
    posted to web_service structure proj_interprets proj_assembly ppi binding algorithm by chad_davis on 2008-10-07 10:15:00 as ***** along with 4 people apaydin bicko j3xucite henschel
  • GraphCrunch: a tool for large network analyses
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Tijana Milenkovic, Jason Lai, Natasa Przulj
    posted to web_service proj_assembly networks download distributed clustering algorithm by chad_davis on 2008-10-06 16:41:38 as *** along with 7 people grahamc laughcry barriot jyuh maralena dullhunk ptrobajo
  • A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences
    BMC Bioinformatics, Vol. 9 (06 May 2008), 229.
    by Claudia Chica, Alberto Labarga, Cathryn M Gould, Rodrigo Lopez, Toby J Gibson
    posted to web_service statistics ppi evolution embl disorder classification annotation algorithm by chad_davis on 2008-10-06 12:49:02 as *** along with 4 people Evangelia cabbagesofdoom biehl alanrw
  • Local Function Conservation in Sequence and Structure Space
    PLoS Comput Biol, Vol. 4, No. 7. (4 July 2008), e1000105.
    by Nils Weinhold, Oliver Sander, Francisco S Domingues, Thomas Lengauer, Ingolf Sommer
    posted to web_service structure annotation algorithm by chad_davis on 2008-10-06 12:34:49 as *** along with 3 people and 3 groups barry cabbagesofdoom Ema structural_bioinformatics McCammon Bioinformatics
  • Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Andrew Bordner, Andrey Gorin
    posted to web_service structure proj_interprets proj_assembly non-redundant database clustering binding annotation by chad_davis on 2008-09-16 10:09:39 as **** along with 4 people jyuh neils phoenixzxl bicko
  • notes 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 web_service proj_assembly ppi embl database data_integration classic by chad_davis on 2008-09-16 09:59:56 as *** along with 12 people wenhui jyuh kuhn balajis fisherp raiyar massivemayhem larsjuhljensen higueruelo renatomilani carlk bicko
  • 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 web_service proj_interprets ppi database by chad_davis on 2008-09-16 09:57:32 as ** along with 2 people massivemayhem bicko
  • Using protein binding site prediction to improve protein docking.
    Gene (14 June 2008)
    by Bingding Huang, Michael Schroeder
    posted to web_service structure proj_assembly ppi ensemble download docking complexes binding algorithm by chad_davis on 2008-09-16 09:52:11 as ***** along with 2 people kintoki bicko
  • Protein structure search and local structure characterization
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Shih Y Ku, Yuh J Hu
    posted to web_service structure feature_selection clustering alignment algorithm by chad_davis on 2008-09-01 15:50:31 as ** along with 2 people neils reyez
  • DAPID: a 3D-domain annotated protein-protein interaction database.
    Genome informatics. International Conference on Genome Informatics, Vol. 17, No. 2. (2006), pp. 206-215.
    by YC Chen, HC Chen, JM Yang
    posted to database proj_assembly proj_interprets structure web_service by chad_davis on 2008-08-26 18:18:15 as *** along with 1 person bicko
  • HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures.
    Nucleic acids research, Vol. 36, No. Web Server issue. (1 July 2008)
    by N Fukuhara, T Kawabata
    posted to binding algorithm complexes modelling proj_assembly structure web_service by chad_davis on 2008-08-21 16:31:17 as read along with 2 people jyuh bicko
  • Integrating biological data - the Distributed Annotation System
    BMC Bioinformatics, Vol. 9, No. Suppl 8. (2008)
    by Andrew Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas Down, Robert Finn, Henning Hermjakob, Tim Hubbard, Rafael Jimenez, Philip Jones, Andreas Kahari, Eugene Kulesha, Jose Macias, Gabrielle Reeves, Andreas Prlic
    posted to annotation data_integration distributed toolkit web_service by chad_davis on 2008-08-09 16:40:02 as *** along with 4 people jfr jyuh aconesa djkt
  • ProCope - Protein Complex Prediction and Evaluation
    Bioinformatics (17 July 2008), btn376.
    by Jan Krumsiek, Caroline C Friedel, Ralf Zimmer
    posted to algorithm complexes data_integration proj_assembly structure toolkit web_service by chad_davis on 2008-08-03 22:03:17 as read along with 2 people zwang jyuh
  • MSDmotif: exploring protein sites and motifs
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Adel Golovin, Kim Henrick
    posted to algorithm complexes database data_integration drug embl structure web_service binding by chad_davis on 2008-07-17 16:18:19 as read along with 3 people reyez massivemayhem Evangelia
  • The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications
    BMC Bioinformatics, Vol. 8 (19 November 2007), 456.
    by Christopher J Bare, Paul T Shannon, Amy K Schmid, Nitin S Baliga
    posted to data_mining data_integration download web_service by chad_davis on 2008-07-16 17:31:02 as *** along with 9 people and 1 group jyuh jfr dullhunk neils ryanraaum mircea srp33 selatham megraw NCCT Lab Reading Group
  • iTools: a framework for classification, categorization and integration of computational biology resources.
    PLoS ONE, Vol. 3, No. 5. (2008)
    by ID Dinov, D Rubin, W Lorensen, J Dugan, J Ma, S Murphy, B Kirschner, W Bug, M Sherman, A Floratos, D Kennedy, HV Jagadish, J Schmidt, B Athey, A Califano, M Musen, R Altman, R Kikinis, I Kohane, S Delp, DS Parker, AW Toga
    posted to data_integration download toolkit web_service by chad_davis on 2008-07-15 12:55:47 as *** along with 4 people jfr dullhunk jyuh srp33
  • notes Inference of macromolecular assemblies from crystalline state.
    J Mol Biol, Vol. 372, No. 3. (21 September 2007), pp. 774-797.
    by E Krissinel, K Henrick
    posted to algorithm annotation complexes database embl proj_assembly structure validation web_service binding by chad_davis on 2008-07-13 16:28:44 as **** along with 1 person bicko
  • PSIbase: a database of Protein Structural Interactome map (PSIMAP)
    Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2541-2543.
    by Sungsam Gong, Giseok Yoon, Insoo Jang, Dan Bolser, Panos Dafas, Michael Schroeder, Hansol Choi, Yoobok Cho, Kyungsook Han, Sunghoon Lee, Hwanho Choi, Michael Lappe, Liisa Holm, Sangsoo Kim, Donghoon Oh, Jonghwa Bhak
    posted to algorithm database proj_assembly structure web_service binding by chad_davis on 2008-07-01 14:43:04 as read along with 1 person medic0747
  • Intrinsic disorder prediction from the analysis of multiple protein fold recognition models.
    Bioinformatics (Oxford, England) (25 June 2008)
    by Liam JJ Mcguffin
    posted to algorithm classification data_integration disorder ensemble feature_selection proj_disocons structure web_service by chad_davis on 2008-06-29 10:59:50 as read
  • Calling on a million minds for community annotation in WikiProteins
    Genome Biology, Vol. 9, No. 5. (2008)
    by Barend Mons, Michael Ashburner, Christine Chichester, Erik van Mulligen, Marc Weeber, Johan den Dunnen, Gert J van Ommen, Mark Musen, Matthew Cockerill, Henning Hermjakob, Albert Mons, Abel Packer, Roberto Pacheco, Suzanna Lewis, Alfred Berkeley, William Melton, Nickolas Barris, Jimmy Wales, Gerard Meijssen, Erik Moeller, Peter Roes, Katy Borner, Amos Bairoch
    posted to annotation data_integration web_service by chad_davis on 2008-06-22 20:16:44 as *** along with 17 people and 1 group jfr yas AlexanderPico thomaskelder dullhunk tharris renatomilani neils fpattyn sjc Katje jamselem ChrisEvelo carlk jyuh xingxu rholz microbiology_nijmegen
  • MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline.
    Bioinformatics (Oxford, England) (9 April 2008)
    by Jung, Piotr Pezik, Dietrich R Schuhmann
    posted to data_mining algorithm embl web_service by chad_davis on 2008-06-15 13:11:16 as ** along with 4 people hpiwowar dullhunk Gaetan jyuh
  • PISCES: recent improvements to a PDB sequence culling server.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by G Wang, RL Dunbrack
    posted to alignment database data_integration non-redundant proj_assembly structure web_service by chad_davis on 2008-04-28 15:45:08 as **** along with 4 people kaarsinogen bicko blackbart chgjb
  • POODLE-S: Web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position specific scoring matrix.
    Bioinformatics (28 June 2007)
    by Kana Shimizu, Shuichi Hirose, Tamotsu Noguchi
    posted to algorithm classification disorder feature_selection proj_disocons web_service by chad_davis on 2008-04-28 15:27:18 as *
  • The Eukaryotic Promoter Database (EPD)
    Nucl. Acids Res., Vol. 28, No. 1. (1 January 2000), pp. 302-303.
    by Rouaida C Perier, Viviane Praz, Thomas Junier, Claude Bonnard, Philipp Bucher
    posted to database gene_regulation proj_credo web_service by chad_davis on 2008-03-10 10:18:59 as read
  • notes Jane: Suggesting Journals, Finding Experts.
    Bioinformatics (28 January 2008)
    by Martijn JJ Schuemie, Jan AA Kors
    posted to data_mining web_service by chad_davis on 2008-02-20 09:53:28 as **** along with 7 people jyuh dullhunk farhat idonaldson renatomilani Barend merj
  • A note on difficult structure alignment problems
    Bioinformatics, Vol. 24, No. 3. (1 February 2008), pp. 426-427.
    by Manfred J Sippl, Markus Wiederstein
    posted to alignment evolution review structure web_service by chad_davis on 2008-01-31 16:11:26 as read along with 2 people mclarenv janasont
  • The MPI Bioinformatics Toolkit for protein sequence analysis.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by A Biegert, C Mayer, M Remmert, J Söding, AN Lupas
    posted to algorithm alignment modelling mpi web_service by chad_davis on 2008-01-24 10:07:12 as *** along with 2 people moborg grottenolm
  • SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Ramon D Uriarte
    posted to classification feature_selection microarray web_service proj_stabperf by chad_davis on 2008-01-22 10:12:49 as read along with 4 people jyuh aalibes frohike jfr
  • Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)
    by T Okumura, H Makiguchi, Y Makita, R Yamashita, K Nakai
    posted to ensemble gene_regulation web_service proj_credo by chad_davis on 2007-11-16 13:36:52 as ***** along with 1 person jyuh
  • notes A Web interface generator for molecular biology programs in Unix.
    Bioinformatics, Vol. 17, No. 1. (January 2001), pp. 73-82.
    by C Letondal
    posted to classic data_integration web_service by chad_davis on 2007-11-16 11:56:39 as ****
  • Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator.
    BMC Bioinformatics, Vol. 6, No. 1. (2005)
    by AG Castro, S Thoraval, LJ Garcia, MA Ragan
    posted to data_integration web_service by chad_davis on 2007-11-16 11:19:14 as ** along with 3 people jyuh moborg fisherp
  • wEMBOSS: a web interface for EMBOSS.
    Bioinformatics, Vol. 21, No. 4. (15 February 2005), pp. 540-541.
    by M Sarachu, M Colet
    posted to data_integration review web_service by chad_davis on 2007-11-16 10:57:56 as read along with 2 people jyuh dullhunk
  • Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations.
    J Mol Biol, Vol. 320, No. 2. (5 July 2002), pp. 369-387.
    by R Guerois, JE Nielsen, L Serrano
    posted to algorithm classic complexes embl structure web_service binding by chad_davis on 2007-09-28 13:07:21 as **** along with 4 people apaydin aalibes hmk carlescorbi
  • A novel ensemble learning method for de novo computational identification of DNA binding sites
    BMC Bioinformatics, Vol. 8 (12 July 2007), 249.
    by Arijit Chakravarty, Jonathan M Carlson, Radhika S Khetani, Robert H Gross
    posted to algorithm download ensemble feature_selection gene_regulation web_service proj_credo by chad_davis on 2007-08-08 12:26:30 as read along with 2 people and 1 group GustavoLacerda nklee Bioinformatics
  • Protein solubility: sequence based prediction and experimental verification.
    Bioinformatics (6 December 2006)
    by Pawel Smialowski, Antonio, Aleksandra Mikolajka, Tobias Girschick, Tad AA Holak, Dmitrij Frishman
    posted to algorithm classification web_service proj_disocons by chad_davis on 2007-06-07 16:20:04 as **** along with 3 people jyuh bobychan girschick
  • Multiple sequence alignment with the Clustal series of programs.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3497-3500.
    by R Chenna, H Sugawara, T Koike, R Lopez, TJ Gibson, DG Higgins, JD Thompson
    posted to algorithm classic clustering download embl evolution web_service by chad_davis on 2007-04-18 09:17:52 as *** along with 5 people and 1 group miguel beatrizfernandez raylim xingxu marck Microbial-Ecology
  • Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases.
    Trends Biochem Sci, Vol. 23, No. 11. (November 1998), pp. 444-447.
    by SF Altschul, EV Koonin
    posted to algorithm alignment classic download evolution statistics web_service by chad_davis on 2007-04-16 16:04:17 as * along with 2 people cerca newton1234
  • Tools for comparative protein structure modeling and analysis.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3375-3380.
    by N Eswar, B John, N Mirkovic, A Fiser, VA Ilyin, U Pieper, AC Stuart, Marti MA Renom, MS Madhusudhan, B Yerkovich, A Sali
    posted to database download modelling structure web_service by chad_davis on 2007-04-10 11:28:50 as read along with 2 people and 2 groups vavi marcius BioinfoCIPF SGU-CIPF
  • notes SMART 5: domains in the context of genomes and networks.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by I Letunic, RR Copley, B Pils, S Pinkert, J Schultz, P Bork
    posted to classic classification disorder embl web_service proj_disocons by chad_davis on 2007-04-02 19:40:37 as *** along with 1 person siebertm
  • notes PHD -- an automatic mail server for protein secondary structure prediction.
    Comput Appl Biosci, Vol. 10, No. 1. (February 1994), pp. 53-60.
    by B Rost, C Sander, R Schneider
    posted to classic classification structure web_service proj_disocons by chad_davis on 2007-01-09 14:19:05 as * along with 2 people j3xucite dgront
  • SCRATCH: a protein structure and structural feature prediction server.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by J Cheng, AZ Randall, MJ Sweredoski, P Baldi
    posted to classification structure web_service by chad_davis on 2007-01-02 13:07:37 as *
  • iHOPerator: User-scripting a personalized bioinformatics Web, starting with the iHOP website
    BMC Bioinformatics, Vol. 7 (15 December 2006), 534.
    by Benjamin M Good, Edward A Kawas, Byron Y Kuo, Mark D Wilkinson
    posted to data_integration web_service by chad_davis on 2006-12-22 13:56:33 as *** along with 7 people textoris jfr dullhunk egonw equipediaz cerami jyuh
  • The FoldX web server: an online force field.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by J Schymkowitz, J Borg, F Stricher, R Nys, F Rousseau, L Serrano
    posted to algorithm disease embl structure web_service by chad_davis on 2006-11-29 13:35:33 as *** along with 2 people aalibes neils
  • Babel's tower revisited: a universal resource for cross-referencing across annotation databases.
    Bioinformatics (26 October 2006)
    by Sorin Draghici, Sivakumar Sellamuthu, Purvesh Khatri
    posted to annotation database data_integration web_service proj_disocons by chad_davis on 2006-11-18 21:02:23 as **** along with 6 people jyuh aalibes dullhunk fisherp plofje kynn
  • Human non-synonymous SNPs: server and survey.
    Nucleic Acids Res, Vol. 30, No. 17. (1 September 2002), pp. 3894-3900.
    by V Ramensky, P Bork, S Sunyaev
    posted to classification disease embl web_service proj_disocons by chad_davis on 2006-11-03 13:41:41 as ***** along with 3 people and 1 group chrn happy_manatee cat_worth structural_bioinformatics
  • PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs
    BMC Bioinformatics, Vol. 7 (27 July 2006), 365.
    by Sylvain Pitre, Frank Dehne, Albert Chan, Jim Cheetham, Alex Duong, Andrew Emili, Marinella Gebbia, Jack Greenblatt, Mathew Jessulat, Nevan Krogan, Xuemei Luo, Ashkan Golshani
    posted to download yeast web_service binding by chad_davis on 2006-08-08 11:12:28 as *** along with 1 person gurkanbebek
  • NORSp: Predictions of long regions without regular secondary structure.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3833-3835.
    by J Liu, B Rost
    posted to disorder web_service proj_disocons by chad_davis on 2006-07-22 17:25:19 as ****
  • notes The DISOPRED server for the prediction of protein disorder.
    Bioinformatics, Vol. 20, No. 13. (1 September 2004), pp. 2138-2139.
    by JJ Ward, LJ Mcguffin, K Bryson, BF Buxton, DT Jones
    posted to disorder download web_service proj_disocons by chad_davis on 2006-07-21 17:01:21 as read
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