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zwang prediction [68 articles]

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  • Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking.
    Proceedings of the National Academy of Sciences of the United States of America (29 May 2008)
    by Hocine Madaoui, Raphaël Guerois
    posted to structure prediction interface interaction co-evolution by zwang on 2008-08-06 07:42:22 as *** along with 4 people chad_davis bicko phoenixzxl cabbagesofdoom
  • 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 structure protein prediction network interaction by zwang on 2008-07-30 03:51:04 as **** along with 3 people phoenixzxl icq242500260 roys
  • ProCope - Protein Complex Prediction and Evaluation
    Bioinformatics (17 July 2008), btn376.
    by Jan Krumsiek, Caroline C Friedel, Ralf Zimmer
    posted to protein prediction complex by zwang on 2008-07-26 10:52:18 as ** along with 1 person chad_davis
  • PIGS: Automatic prediction of antibody structures
    Bioinformatics (19 July 2008), btn341.
    by Paolo Marcatili, Alessandra Rosi, Anna Tramontano
    posted to structure prediction antibody by zwang on 2008-07-26 10:47:53 as ***
  • Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements
    BMC Bioinformatics, Vol. 9 (23 July 2008), 320.
    by Qingwu Yang, Sing-Hoi Sze
    posted to structure protein prediction interaction folding by zwang on 2008-07-26 10:43:26 as *
  • Tertiary Interactions Determine the Accuracy of RNA Folding
    posted to rna prediction folding by zwang on 2008-07-13 08:36:12 as **
  • Predicting protein function from domain content
    Bioinformatics (30 June 2008), btn312.
    by Kristoffer Forslund, Erik L Sonnhammer
    posted to protein prediction domain by zwang on 2008-07-01 02:44:42 as *** along with 2 people reyez phoenixzxl
  • Progress and challenges in protein structure prediction
    Current Opinion in Structural Biology, Vol. 18, No. 3. (June 2008), pp. 342-348.
    by Yang Zhang
    posted to structure protein prediction by zwang on 2008-06-27 03:37:25 as ** along with 2 people marck phoenixzxl
  • 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 svm protein prediction interaction by zwang on 2008-06-16 03:51:12 as **** along with 4 people marck phoenixzxl tmmurali jyuh
  • Predicting novel RNA-RNA interactions.
    Current opinion in structural biology (14 May 2008)
    by Irmtraud M M Meyer
    posted to structure rna prediction interaction by zwang on 2008-06-16 03:49:12 as ***** along with 1 person marck
  • 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 protein prediction interaction bayesian by zwang on 2008-06-03 04:01:29 as ** along with 2 people renatomilani jyuh
  • 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 prediction network human gene by zwang on 2008-05-09 02:59:01 as **** along with 6 people Borelli ptrobajo bootsy maralena jyuh biomcgary
  • Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
    Bioinformatics, Vol. 24, No. 3. (1 February 2008), pp. 333-340.
    by SD Dunn, LM Wahl, GB Gloor
    posted to residue prediction phylogeny mi interaction contact by zwang on 2008-05-09 02:44:06 as *** along with 3 people and 1 group marck bicko sobolevnrm baker-group
  • Predicting Human Interactive Learning by Regret-Driven Neural Networks
    Science, Vol. 319, No. 5866. (22 February 2008), pp. 1111-1113.
    by Davide Marchiori, Massimo Warglien
    posted to interaction network neural prediction by zwang on 2008-04-12 13:33:57 as **** along with 5 people and 1 group mdimmic brian Koh shigepong shivakmr VisionLab
  • 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 2 people and 3 groups barry sobolevnrm structural_bioinformatics Bioinformatics baker-group
  • 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 11 people and 3 groups joseph_x_zhou ucbcjbm barry aalibes jwm aprasad dgront sobolevnrm davidlott msuarezdiez scienbox McCammon structural_bioinformatics baker-group
  • The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
    Nature, Vol. 452, No. 7183., pp. 51-55.
    by Marc Parisien, François Major
    posted to prediction rna sequence structure by zwang on 2008-03-07 02:48:26 as *** along with 3 people reyez austin elfar
  • 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
  • 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 tmmurali debasis kentsis bootsy biomcgary cabbagezs westoll shikin shung
  • Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method
    Mol Syst Biol, Vol. 4 (12 February 2008)
    by Lukas Burger, Erik van Nimwegen
    posted to alignment bayesian interaction prediction protein sequence by zwang on 2008-02-17 10:10:43 as **** along with 10 people pansapiens kengg grahamc laughcry biomcgary cabbagezs roys cdeane gjuggler phoenixzxl
  • 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
  • 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 4 people eckart_bindewald skhadar asddd hpaces
  • 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
  • Detecting Coevolution in and among Protein Domains
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e211.
    by Chen-Hsiang Yeang, David Haussler
    posted to co-evolution domain prediction protein by zwang on 2007-12-10 04:24:46 as ***** along with 11 people and 1 group pradiptaray balicea skhadar sobolevnrm niallhaslam hpaces mingzhi Ema phoenixzxl penpen926 friendpine baker-group
  • 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 janasont kluck skhadar neils cjeans Evangelia hpaces Ema renatomilani
  • High-resolution structure prediction and the crystallographic phase problem
    Nature (14 October 2007)
    by Bin Qian, Srivatsan Raman, Rhiju Das, Philip Bradley, Airlie J Mccoy, Randy J Read, David Baker
    posted to prediction structure by zwang on 2007-11-13 17:07:38 as *** along with 15 people and 2 groups ardalby apaydin aheilbut jwm chad_davis eckart_bindewald ffranca dgront massivemayhem cjeans cactus sobolevnrm boris_aguilar Ema chenway OPIG baker-group
  • 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 saunders dullhunk massivemayhem cjeans mingzhi libr
  • 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
  • Detecting Coevolution in and among Protein Domains
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e211.
    by Chen-Hsiang Yeang, David Haussler
    posted to co-evolution domain prediction protein by zwang on 2007-11-03 03:07:56 as **** along with 1 person cjeans
  • 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 2007-11-02 08:05:43 as *** along with 3 people bicko chad_davis dquest
  • 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
  • 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
  • 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
  • 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 2 people Ema winterschlaefer
  • 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 2 people winterschlaefer cjeans
  • 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 1 person 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
  • 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 **
  • 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 reyez jwm marcius eckart_bindewald physics Ema BioinfoCIPF SGU-CIPF
  • Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells
    Nat Meth, Vol. 4, No. 9. (2007), pp. 747-753.
    by Pierre-Alain Girod, Duc-Quang Nguyen, David Calabrese, Stefania Puttini, Melanie Grandjean, Danielle Martinet, Alexandre Regamey, Damien Saugy, Jacques S Beckmann, Philipp Bucher, Nicolas Mermod
    posted to expression gene genome-wide mammal prediction by zwang on 2007-08-31 16:22:46 as * along with 2 people sebastien_vigneau uz_labu_laimi
  • 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 higueruelo bicko dchughes grahamc cjeans Jporci Pao-Yang G4ID ParkinsonLab_at_MaRS Genetics-of-Gambling
  • 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
  • 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
  • CpG Island Mapping by Epigenome Prediction.
    PLoS Comput Biol, Vol. 3, No. 6. (8 June 2007)
    by Christoph Bock, Jörn Walter, Martina Paulsen, Thomas Lengauer
    posted to cpg-island genome prediction by zwang on 2007-08-18 15:22:12 as *** along with 6 people kaarsinogen sebastien_vigneau oelemento fpattyn rschulz inesdesantiago
  • Structure-based activity prediction for an enzyme of unknown function
    Nature (01 July 2007)
    by Johannes C Hermann, Ricardo Marti-Arbona, Alexander A Fedorov, Elena Fedorov, Steven C Almo, Brian K Shoichet, Frank M Raushel
    posted to function prediction protein structure by zwang on 2007-08-18 08:45:55 as *** along with 6 people aheilbut tjimenez daevans pkolb kimicc ivke
  • MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing.
    Mol Cell, Vol. 27, No. 1. (6 July 2007), pp. 91-105.
    by Andrew Grimson, Kyle Kai-How K Farh, Wendy K K Johnston, Philip Garrett-Engele, Lee P P Lim, David P P Bartel
    posted to mammal microrna prediction target by zwang on 2007-08-15 04:15:51 as ** along with 5 people and 1 group andersbj bootsy heliopais fpattyn maralena microRNA
  • An Approach to Predict Transcription Factor DNA Binding Site Specificity Based upon Gene and Transcription Factor Functional Categorization
    Bioinformatics (10 July 2007), btm348.
    by Ziliang Qian, Lingyi Lu, Xiaojun Liu, Yu-Dong Cai, Yixue Li
    posted to binding dna gene prediction site transcription by zwang on 2007-08-15 03:43:07 as *** along with 1 person xili03
  • 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
  • How does eukaryotic gene prediction work?
    Nature Biotechnology, Vol. 25, No. 8., pp. 883-885.
    by Michael R Brent
    posted to eukaryota gene prediction by zwang on 2007-08-14 08:01:16 as **** along with 7 people and 3 groups jyuh indigoviolet dchughes wenhan cabbagezs nklee ale EisenLab G4ID Genetics-of-Gambling
  • 3D models of yeast RNase P/MRP proteins Rpp1p and Pop3p
    RNA, Vol. 11, No. 2. (1 February 2005), pp. 123-127.
    by Mensur Dlakic
    posted to prediction protein rnasep structure subunit yeast by zwang on 2007-07-26 15:46:54 as ****
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