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Tag prediction [953 articles]

Recent papers classified by the tag prediction.
  • Evaluating and Learning from RNA Pseudotorsional Space: Quantitative Validation of a Reduced Representation for RNA Structure
    Journal of Molecular Biology, Vol. 372, No. 4. (28 September 2007), pp. 942-957.
    by Leven M Wadley, Kevin S Keating, Carlos M Duarte, Anna M Pyle
    posted to prediction rna structure by zwang on 2007-11-01 07:34:03 as ** along with 1 person reyez
  • Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e178.
    by Ramon Aragues, Andrej Sali, Jaume Bonet, Marc A Marti-Renom, Baldo Oliva
    posted to interaction interface motif prediction protein by zwang on 2007-10-22 05:23:09 as **** along with 3 people marti winterschlaefer Ema
  • Correlated substitution analysis and the prediction of amino acid structural contacts
    Brief Bioinform (13 November 2007), bbm052.
    by David S Horner, Walter Pirovano, Graziano Pesole
    posted to co-evolution contact prediction structure substitution by zwang on 2008-03-20 13:25:08 as *** along with 3 people and 3 groups barry sobolevnrm Lombardo_7 structural_bioinformatics Bioinformatics baker-group
  • Structure Prediction of Domain Insertion Proteins from Structures of Individual Domains
    Structure, Vol. 16, No. 4. (8 April 2008), pp. 513-527.
    by Monica Berrondo, Marc Ostermeier, Jeffrey J Gray
    posted to structure prediction peptide domain by zwang on 2008-11-12 01:40:59 as **** along with 2 people raik choonpeng
  • Methods and protocols for prediction of immunogenic epitopes
    Brief Bioinform, Vol. 8, No. 2. (1 March 2007), pp. 96-108.
    by Joo C Tong, Tin W Tan, Shoba Ranganathan
    posted to epitope prediction by zwang on 2007-04-24 15:51:48 as ** along with 1 person operon
  • Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences
    Nucl. Acids Res. (4 April 2008), gkn159.
    by Yanzhi Guo, Lezheng Yu, Zhining Wen, Menglong Li
    posted to interaction prediction protein svm by zwang on 2008-06-16 03:51:12 as **** along with 4 people guhjy marck phoenixzxl tmmurali
  • Predicting protein function from sequence and structure
    Nat Rev Mol Cell Biol, Vol. 8, No. 12. (December 2007), pp. 995-1005.
    by David Lee, Oliver Redfern, Christine Orengo
    posted to function prediction protein review sequence structure by zwang on 2007-12-08 08:55:16 as *** along with 9 people and 1 group skhadar neils cjeans Evangelia hpaces Ema renatomilani kluck janasont MuraLab
  • Predicting synthetic rescues in metabolic networks
    Mol Syst Biol, Vol. 4 (12 February 2008)
    by Adilson E Motter, Natali Gulbahce, Eivind Almaas, Albert-Laszlo Barabasi
    posted to metabolism network prediction by zwang on 2008-02-17 10:43:10 as ** along with 9 people kentsis bootsy biomcgary cabbagezs westoll shikin shung debasis tmmurali
  • InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale
    Genome Biology, Vol. 8 (14 September 2007), R192.
    by Haidong Wang, Eran Segal, Asa Ben-Hur, Qianru Li, Marc Vidal, Daphne Koller
    posted to binding interaction prediction protein sites by zwang on 2008-08-22 09:47:16 as **** along with 2 people cjeans carlk
  • Prediction of structures of multidomain proteins from structures of the individual domains.
    Protein Sci (22 December 2006)
    by Andrew M M Wollacott, Alexandre Zanghellini, Paul Murphy, David Baker
    posted to domain prediction protein structure by zwang on 2007-04-16 13:37:00 as ** along with 4 people wouterboomsma choonpeng IrinaMoreira rph
  • Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e220.
    by Peter M Kasson, Vijay S Pande
    posted to dynamics prediction by zwang on 2007-12-10 04:34:31 as * along with 3 people and 1 group sobolevnrm paulschlesinger Ema baker-group
  • Probabilistic prediction and ranking of human protein-protein interactions
    BMC Bioinformatics, Vol. 8 (05 July 2007), 239.
    by Michelle S Scott, Geoffrey J Barton
    posted to interaction prediction protein by zwang on 2007-07-13 17:19:17 as **** along with 4 people and 1 group cerca wnpx grahamc mingzhi ParkinsonLab_at_MaRS
  • Integration of Genome and Chromatin Structure with Gene Expression Profiles To Predict c-MYC Recognition Site Binding and Function.
    PLoS Comput Biol, Vol. 3, No. 4. (6 April 2007)
    by Yili Chen, Thomas W W Blackwell, Ji Chen, Jing Gao, Angel W W Lee, David J J States
    posted to chromatin gene genome integration prediction structure by zwang on 2007-04-28 12:36:42 as ** along with 1 person and 2 groups kengg Bioinformatics Plantandetc
  • Optimal Design of Thermally Stable Proteins
    Bioinformatics (22 August 2008), btn450.
    by Vanitha Suresh, Ryan M Bannen, George N Phillips, Stephen J Wright, Julie C Mitchell
    posted to design prediction protein structure by zwang on 2008-08-27 07:30:16 as ** along with 2 people friendpine phoenixzxl
  • Toward high-resolution prediction and design of transmembrane helical protein structures
    Proceedings of the National Academy of Sciences, Vol. 104, No. 40. (2 October 2007), pp. 15682-15687.
    by P Barth, J Schonbrun, D Baker
    posted to expression prediction protein structure by zwang on 2007-10-08 19:01:24 as * along with 3 people hmk biehl Ema
  • Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins
    BMC Bioinformatics, Vol. 8 (05 May 2007), 147.
    by Qiwen Dong, Xiaolong Wang, Lei Lin, Yi Guan
    posted to binding interface prediction profile protein residue by zwang on 2007-05-06 09:28:10 as **** along with 2 people bicko marti
  • A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
    Proceedings of the National Academy of Sciences (28 December 2007), 0707684105.
    by Michal Brylinski, Jeffrey Skolnick
    posted to annotation binding prediction site structure threading by zwang on 2008-01-10 01:30:18 as ** along with 1 person cjeans
  • Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis
    Bioinformatics, Vol. 24, No. 18. (15 September 2008), pp. 2002-2009.
    by Majid Masso, Iosif I Vaisman
    posted to svm structure stability protein prediction by zwang on 2008-10-09 08:57:06 as ** along with 2 people kluck afon
  • Prediction of Functional Sites Based on the Fuzzy Oil Drop Model
    PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e94.
    by Michał Bryliński, Katarzyna Prymula, Wiktor Jurkowski, Marek Kochańczyk, Ewa Stawowczyk, Leszek Konieczny, Irena Roterman
    posted to prediction site by zwang on 2007-05-26 05:09:12 as * along with 1 person and 1 group Einat structural_bioinformatics
  • High-throughput identification of Interacting Protein-Protein Binding Sites
    BMC Bioinformatics, Vol. 8 (27 June 2007), 223.
    by Jo-Lan Chung, Wei Wang, Philip E Bourne
    posted to binding interaction prediction protein site svm by zwang on 2007-08-27 08:57:42 as ***** along with 3 people and 1 group bicko grahamc Evangelia ParkinsonLab_at_MaRS
  • Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices
    BMC Bioinformatics, Vol. 8 (09 January 2007), 6.
    by Roger A Craig, Li Liao
    posted to interaction phylogeny prediction protein by zwang on 2007-04-16 13:57:11 as *** along with 2 people marti iris_2001
  • Predicting functionally important residues from sequence conservation
    Bioinformatics (22 May 2007), btm270.
    by John A Capra, Mona Singh
    posted to prediction residue by zwang on 2007-06-10 16:23:10 as ** along with 7 people and 2 groups grahamc azazello cabbagezs Jporci niallhaslam santiago dgront ParkinsonLab_at_MaRS MBLAB
  • A statistical approach using network structure in the prediction of protein characteristics
    Bioinformatics (28 June 2007), btm342.
    by Pao-Yang Chen, Charlotte M Deane, Gesine Reinert
    posted to network prediction protein statistical structure by zwang on 2007-08-15 03:41:38 as * along with 5 people and 1 group grahamc iris_2001 cabbagezs cdeane Pao-Yang ParkinsonLab_at_MaRS
  • Prediction of the structure of symmetrical protein assemblies
    Proceedings of the National Academy of Sciences (31 October 2007), 0702626104.
    by Ingemar Andre, Philip Bradley, Chu Wang, David Baker
    posted to prediction protein structure by zwang on 2007-11-07 07:44:46 as * along with 4 people and 2 groups jwm jmrivort cjeans sobolevnrm Supramolecular baker-group
  • Network-based prediction of human tissue-specific metabolism.
    Nature biotechnology (17 August 2008)
    by Tomer Shlomi, Moran N N Cabili, Markus J J Herrgård, Bernhard Ø O Palsson, Eytan Ruppin
    posted to prediction network metabolism by zwang on 2008-09-10 07:26:54 as ** along with 8 people jfr roys mdstobbe klo peterli ptrobajo renatomilani guhjy
  • Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic Genomes
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e237.
    by Juan A Ranea, Corin Yeats, Alastair Grant, Christine A Orengo
    posted to eukaryota genome hierarchical phylogeny prediction protein by zwang on 2007-12-10 04:43:48 as *** along with 5 people marti eckart_bindewald skhadar asddd hpaces
  • ProCope - Protein Complex Prediction and Evaluation
    Bioinformatics (17 July 2008), btn376.
    by Jan Krumsiek, Caroline C Friedel, Ralf Zimmer
    posted to complex prediction protein by zwang on 2008-07-26 10:52:18 as ** along with 3 people saket guhjy chad_davis
  • Analysis on multi-domain cooperation for predicting protein-protein interactions
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Rui S Wang, Yong Wang, Ling Y Wu, Xiang S Zhang, Luonan Chen
    posted to co-evolution domain interaction prediction protein by zwang on 2007-10-22 01:55:10 as *** along with 2 people guhjy phoenixzxl
  • PIGS: Automatic prediction of antibody structures
    Bioinformatics (19 July 2008), btn341.
    by Paolo Marcatili, Alessandra Rosi, Anna Tramontano
    posted to antibody prediction structure by zwang on 2008-07-26 10:47:53 as *** along with 1 person niallhaslam
  • Predicting PDZ domain–peptide interactions from primary sequences
    Nature Biotechnology, Vol. 26, No. 9. (17 August 2008), pp. 1041-1045.
    by Jiunn R Chen, Bryan H Chang, John E Allen, Michael A Stiffler, Gavin Macbeath
    posted to protein prediction interaction domain by zwang on 2008-09-10 07:31:56 as **** along with 4 people yzlab phoenixzxl guhjy cabbagesofdoom
  • Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners
    PLoS Computational Biology, Vol. 3, No. 4. (1 April 2007), e43.
    by Benjamin A Shoemaker, Anna R Panchenko
    posted to domain interaction prediction protein by zwang on 2007-04-28 12:23:05 as *** along with 17 people zdai Robinder giovenko Yanno guhjy aalibes bicko jfr chad_davis cjeans iris_2001 lpfernandes groepl carlk Evangelia higueruelo phoenixzxl
  • Analysis and prediction of functionally important sites in proteins.
    Protein Sci, Vol. 16, No. 1. (January 2007), pp. 4-13.
    by S Chakrabarti, CJ Lanczycki
    posted to prediction protein site by zwang on 2007-04-16 14:09:26 as ** along with 4 people tjimenez annotator_2006 MaggieYe Jporci
  • Computational biology: Protein predictions
    Nature (14 October 2007)
    by Eleanor J Dodson
    posted to prediction protein by zwang on 2007-11-13 17:06:59 as * along with 5 people and 1 group dullhunk massivemayhem cjeans mingzhi saunders libr
  • Systematic Identification of cis-Regulatory Sequences Active in Mouse and Human Embryonic Stem Cells
    PLoS Genetics, Vol. 3, No. 8. (1 August 2007), e145.
    by Marica Grskovic, Christina Chaivorapol, Alexandre Gaspar-Maia, Hao Li, Miguel Ramalho-Santos
    posted to human motif prediction regulatory sequence systematic by zwang on 2007-09-03 04:40:58 as **
  • Structure-Templated Predictions of Novel Protein Interactions from Sequence Information
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e182.
    by Doron Betel, Kevin E Breitkreuz, Ruth Isserlin, Danielle Dewar-Darch, Mike Tyers, Christopher W Hogue
    posted to interaction prediction protein sequence structure by zwang on 2007-10-22 05:11:20 as **** along with 3 people agustinarce cjeans winterschlaefer
  • InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes
    BMC Bioinformatics, Vol. 8 (26 October 2007), 414.
    by Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao
    posted to bacterial genome interaction prediction protein by zwang on 2007-10-29 13:11:19 as ** along with 2 people and 1 group tmmurali iris_2001 csb_journal_club_public
  • I-TASSER server for protein 3D structure prediction
    BMC Bioinformatics, Vol. 9 (23 January 2008), 40.
    by Yang Zhang
    posted to prediction protein structure by zwang on 2008-02-24 13:43:46 as ** along with 4 people chad_davis mkurc rabio mclarenv
  • Computational prediction of small-molecule catalysts
    Nature, Vol. 455, No. 7211. (17 September 2008), pp. 309-313.
    by KN Houk, Paul H Cheong
    posted to structure prediction by zwang on 2008-10-16 14:04:21 as **
  • Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation
    Nature Methods, Vol. 4, No. 7. (24 June 2007), pp. 563-565.
    by Laurence Ettwiller, Benedict Paten, Mirana Ramialison, Ewan Birney, Joachim Wittbrodt
    posted to chromatin motif prediction regulatory by zwang on 2007-08-28 03:56:29 as * along with 3 people and 1 group brant maximilianh fpattyn EisenLab
  • 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 substitution structure residue prediction by zwang on 2008-11-03 09:15:32 as **** along with 4 people joseph_x_zhou bicko massivemayhem reyez
  • Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
    Mol Syst Biol, Vol. 3 (10 July 2007)
    by Robert Schuetz, Lars Kuepfer, Uwe Sauer
    posted to bacterial prediction systematic by zwang on 2007-07-11 19:28:02 as ** along with 4 people and 1 group alexg fishtank Ema michaelbarton Bioinformatics
  • A Bayesian Estimator of Protein-Protein Association Probabilities
    Bioinformatics (22 May 2008), btn238.
    by JM Gilmore, DL Auberry, JL Sharp, AM White, KK Anderson, DS Daly
    posted to bayesian interaction prediction protein by zwang on 2008-06-03 04:01:29 as ** along with 2 people guhjy renatomilani
  • Automated de novo prediction of native-like RNA tertiary structures
    PNAS (28 August 2007), 0703836104.
    by Rhiju Das, David Baker
    posted to prediction rna structure by zwang on 2007-08-31 16:23:25 as **** along with 6 people and 2 groups jwm marcius eckart_bindewald physics Ema reyez BioinfoCIPF SGU-CIPF
  • Predicting and Validating Protein Interactions Using Network Structure
    PLoS Comput Biol, Vol. 4, No. 7. (25 July 2008), e1000118.
    by Pao-Yang Chen, Charlotte M Deane, Gesine Reinert
    posted to interaction network prediction protein structure by zwang on 2008-07-30 03:51:04 as **** along with 4 people icq242500260 phoenixzxl roys mingzhi
  • Protein-Protein Interaction Hotspots Carved into Sequences.
    PLoS Comput Biol, Vol. 3, No. 7. (13 July 2007)
    by Yanay Ofran, Burkhard Rost
    posted to insilico interaction prediction protein sequence by zwang on 2007-08-29 02:25:39 as *** along with 7 people and 3 groups bicko dchughes grahamc cjeans Jporci Pao-Yang higueruelo G4ID ParkinsonLab_at_MaRS Genetics-of-Gambling
  • Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000151.
    by Raja Mazumder, Sona Vasudevan
    posted to structure protein prediction function by zwang on 2008-10-07 11:19:53 as ** along with 9 people and 2 groups i000 pengchy raik chad_davis druvus reyez mdstobbe barry jameswasmuth structural_bioinformatics Bioinformatics
  • Predicting novel RNA-RNA interactions.
    Current opinion in structural biology (14 May 2008)
    by Irmtraud M M Meyer
    posted to interaction prediction rna structure by zwang on 2008-06-16 03:49:12 as ***** along with 2 people and 1 group Hosna marck beta
  • Network-based global inference of human disease genes
    Mol Syst Biol, Vol. 4 (6 May 2008)
    by Xuebing Wu, Rui Jiang, Michael Q Zhang, Shao Li
    posted to gene human network prediction by zwang on 2008-05-09 02:59:01 as **** along with 9 people tmmurali diamantis jfr maralena bootsy biomcgary guhjy ptrobajo Borelli
  • A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types.
    Mol Cell, Vol. 28, No. 2. (26 October 2007), pp. 337-350.
    by O Elemento, N Slonim, S Tavazoie
    posted to clustering genome motif prediction yeast by zwang on 2007-11-01 02:15:02 as *** along with 12 people and 2 groups ana brant cwbrown aswin cjeans cabbagezs nklee maximilianh idonaldson sb_journal_club kristen barwil EisenLab Motif Discovery
  • De Novo Computational Design of Retro-Aldol Enzymes
    Science, Vol. 319, No. 5868. (7 March 2008), pp. 1387-1391.
    by Lin Jiang, Eric A Althoff, Fernando R Clemente, Lindsey Doyle, Daniela Rothlisberger, Alexandre Zanghellini, Jasmine L Gallaher, Jamie L Betker, Fujie Tanaka, Carlos F Barbas, Donald Hilvert, Kendall N Houk, Barry L Stoddard, David Baker
    posted to design prediction protein by zwang on 2008-03-07 03:02:39 as ** along with 12 people and 3 groups barry aalibes jwm aprasad dgront sobolevnrm davidlott msuarezdiez scienbox ucbcjbm joseph_x_zhou cambray structural_bioinformatics baker-group McCammon
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