Partially-supervised protein subclass discovery with simultaneous annotation of functional residues

January 2009
BMC Structural Biology;2009, Vol. 9, p68
Academic Journal
No abstract available.


Related Articles

  • Graph kernels and applications in protein classification. Jiang Qiangrong; Xiong Zhikang; Zhai Can // Journal of Chemical & Pharmaceutical Research;2014, Vol. 6 Issue 2, p563 

    Protein classification is a well established research field concerned with the discovery of molecule's properties through informational techniques. Graph-based kernels provide a nice framework combining machine learning techniques with graph theory. In this paper we introduce a novel graph...

  • ProSAT2–Protein Structure Annotation Server. Gabdoulline, R. R.; Ulbrich, S.; Richter, S.; Wade, R. C. // Nucleic Acids Research;Jul2006, Vol. 34 Issue 11, pw79 

    ProSAT2 is a server to facilitate interactive visualization of sequence-based, residue-specific annotations mapped onto 3D protein structures. As the successor of ProSAT (Protein Structure Annotation Tool), it includes its features for visualizing SwissProt and PROSITE functional annotations....

  • Protein family alignment annotation.  // Briefings in Bioinformatics;Jun2003, Vol. 4 Issue 2, p192 

    For bioscientists studying protein structure and function, the Protein Family Alignment Annotation Tool (Pfaat) is a useful and simple program for annotating collections of proteins. This open-source software includes methods for viewing and aligning protein families, and for annotating sequence...

  • 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data. Cox, Juergen; Mann, Matthias // BMC Bioinformatics;2012, Vol. 13 Issue Suppl 16, p1 

    Quantitative proteomics now provides abundance ratios for thousands of proteins upon perturbations. These need to be functionally interpreted and correlated to other types of quantitative genome-wide data such as the corresponding transcriptome changes. We describe a new method, 2D annotation...

  • Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes. Haynes, Chad; Oldfield, Christopher J.; Fei Ji; Klitgord, Niels; Cusick, Michael E.; Radivojac, Predrag; Uversky, Vladimir N.; Vidal, Marc; Iakoucheva, Lilia M. // PLoS Computational Biology;Aug2006, Vol. 2 Issue 8, pe100 

    Recent proteome-wide screening approaches have provided a wealth of information about interacting proteins in various organisms. To test for a potential association between protein connectivity and the amount of predicted structural disorder, the disorder propensities of proteins with various...

  • WSsas: a web service for the annotation of functional residues through structural homologues. David Talavera; Roman A. Laskowski; Janet M. Thornton // Bioinformatics;May2009, Vol. 25 Issue 9, p1192 

    Motivation: Annotation tools help scientists to traverse the gap between characterized and uncharacterized proteins. Tools for the prediction of protein function include those which predict the function of entire proteins or complexes, those annotating functional domains and those which predict...

  • Revealing the hidden functional diversity of an enzyme family. Bastard, Karine; Smith, Adam Alexander Thil; Vergne-Vaxelaire, Carine; Perret, Alain; Zaparucha, Anne; De Melo-Minardi, Raquel; Mariage, Aline; Boutard, Magali; Debard, Adrien; Lechaplais, Christophe; Pelle, Christine; Pellouin, Virginie; Perchat, Nadia; Petit, Jean-Louis; Kreimeyer, Annett; Medigue, Claudine; Weissenbach, Jean; Artiguenave, François; De Berardinis, Véronique; Vallenet, David // Nature Chemical Biology;Jan2014, Vol. 10 Issue 1, p42 

    Millions of protein database entries are not assigned reliable functions, preventing the full understanding of chemical diversity in living organisms. Here, we describe an integrated strategy for the discovery of various enzymatic activities catalyzed within protein families of unknown or little...

  • Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets. Yi-Yuan Chiu; Chun-Yu Lin; Chih-Ta Lin; Kai-Cheng Hsu; Li-Zen Chang; Jinn-Moon Yang // BMC Genomics;2012, Vol. 13 Issue Suppl 7, p1 

    Background: To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential...

  • seeMotif: exploring and visualizing sequence motifs in 3D structures. Chang, Darby Tien-Hao; Chien, Ting-Ying; Chen, Chien-Yu // Nucleic Acids Research;2009, Vol. 37 Issue suppl_2, pW552 

    Sequence motifs are important in the study of molecular biology. Motif discovery tools efficiently deliver many function related signatures of proteins and largely facilitate sequence annotation. As increasing numbers of motifs are detected experimentally or predicted computationally,...

  • High Conservation of Amino Acids with Anomalous Protonation Behavior. Hildebrand, David G. C.; Huyuan Yang; Ondrechen, Mary Jo; Williams, Ronald J. // Current Bioinformatics;Jun2010, Vol. 5 Issue 2, p134 

    The determination of a protein's biochemical function from its 3D structure has proved more difficult than anticipated for structural genomics proteins, most of which are of unknown or uncertain function. Functional annotations typically have been assigned using the closest sequence or structure...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics