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  • 1
    Online Resource
    Online Resource
    CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs
    Oxford University Press (OUP) ; 2011
    In:  Nucleic Acids Research Vol. 39, No. suppl_2 ( 2011-07-01), p. W190-W196
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 39, No. suppl_2 ( 2011-07-01), p. W190-W196
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkr411
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2011
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Bluues server: electrostatic properties of wild-type and mutated protein structures
    Oxford University Press (OUP) ; 2012
    In:  Bioinformatics Vol. 28, No. 16 ( 2012-08-15), p. 2189-2190
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 28, No. 16 ( 2012-08-15), p. 2189-2190
    Abstract: Motivation: Electrostatic calculations are an important tool for deciphering many functional mechanisms in proteins. Generalized Born (GB) models offer a fast and convenient computational approximation over other implicit solvent-based electrostatic models. Here we present a novel GB-based web server, using the program Bluues, to calculate numerous electrostatic features including pKa-values and surface potentials. The output is organized allowing both experts and beginners to rapidly sift the data. A novel feature of the Bluues server is that it explicitly allows to find electrostatic differences between wild-type and mutant structures. Availability: The Bluues server, examples and extensive help files are available for non-commercial use at URL: http://protein.bio.unipd.it/bluues/. Contact:  silvio.tosatto@unipd.it
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/bts343
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2012
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    A CRY FROM THE KRILL
    Informa UK Limited ; 2010
    In:  Chronobiology International Vol. 27, No. 3 ( 2010-04), p. 425-445
    Details
    In: Chronobiology International, Informa UK Limited, Vol. 27, No. 3 ( 2010-04), p. 425-445
    Type of Medium: Online Resource
    ISSN: 0742-0528 , 1525-6073
    URL: Article
    DOI: 10.3109/07420521003697494
    Language: English
    Publisher: Informa UK Limited
    Publication Date: 2010
    detail.hit.zdb_id: 2026725-3
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    ESpritz: accurate and fast prediction of protein disorder
    Oxford University Press (OUP) ; 2012
    In:  Bioinformatics Vol. 28, No. 4 ( 2012-02-15), p. 503-509
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 28, No. 4 ( 2012-02-15), p. 503-509
    Abstract: Motivation: Intrinsically disordered regions are key for the function of numerous proteins, and the scant available experimental annotations suggest the existence of different disorder flavors. While efficient predictions are required to annotate entire genomes, most existing methods require sequence profiles for disorder prediction, making them cumbersome for high-throughput applications. Results: In this work, we present an ensemble of protein disorder predictors called ESpritz. These are based on bidirectional recursive neural networks and trained on three different flavors of disorder, including a novel NMR flexibility predictor. ESpritz can produce fast and accurate sequence-only predictions, annotating entire genomes in the order of hours on a single processor core. Alternatively, a slower but slightly more accurate ESpritz variant using sequence profiles can be used for applications requiring maximum performance. Two levels of prediction confidence allow either to maximize reasonable disorder detection or to limit expected false positives to 5%. ESpritz performs consistently well on the recent CASP9 data, reaching a Sw measure of 54.82 and area under the receiver operator curve of 0.856. The fast predictor is four orders of magnitude faster and remains better than most publicly available CASP9 methods, making it ideal for genomic scale predictions. Conclusions: ESpritz predicts three flavors of disorder at two distinct false positive rates, either with a fast or slower and slightly more accurate approach. Given its state-of-the-art performance, it can be especially useful for high-throughput applications. Availability: Both a web server for high-throughput analysis and a Linux executable version of ESpritz are available from: http://protein.bio.unipd.it/espritz/ Contact:  silvio.tosatto@unipd.it Supplementary information:  Supplementary data are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/btr682
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2012
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    RING: networking interacting residues, evolutionary information and energetics in protein structures
    Oxford University Press (OUP) ; 2011
    In:  Bioinformatics Vol. 27, No. 14 ( 2011-07-15), p. 2003-2005
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 27, No. 14 ( 2011-07-15), p. 2003-2005
    Abstract: Motivation: Residue interaction networks (RINs) have been used in the literature to describe the protein 3D structure as a graph where nodes represent residues and edges physico–chemical interactions, e.g. hydrogen bonds or van-der-Waals contacts. Topological network parameters can be calculated over RINs and have been correlated with various aspects of protein structure and function. Here we present a novel web server, RING, to construct physico–chemically valid RINs interactively from PDB files for subsequent visualization in the Cytoscape platform. The additional structure-based parameters secondary structure, solvent accessibility and experimental uncertainty can be combined with information regarding residue conservation, mutual information and residue-based energy scoring functions. Different visualization styles are provided to facilitate visualization and standard plugins can be used to calculate topological parameters in Cytoscape. A sample use case analyzing the active site of glutathione peroxidase is presented. Availability: The RING server, supplementary methods, examples and tutorials are available for non-commercial use at URL: http://protein.bio.unipd.it/ring/. Contact:  silvio.tosatto@unipd.it
    Type of Medium: Online Resource
    ISSN: 1367-4803 , 1367-4811
    URL: Article
    DOI: 10.1093/bioinformatics/btr191
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2011
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    RAPHAEL: recognition, periodicity and insertion assignment of solenoid protein structures
    Oxford University Press (OUP) ; 2012
    In:  Bioinformatics Vol. 28, No. 24 ( 2012-12-01), p. 3257-3264
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 28, No. 24 ( 2012-12-01), p. 3257-3264
    Abstract: Motivation: Repeat proteins form a distinct class of structures where folding is greatly simplified. Several classes have been defined, with solenoid repeats of periodicity between ca. 5 and 40 being the most challenging to detect. Such proteins evolve quickly and their periodicity may be rapidly hidden at sequence level. From a structural point of view, finding solenoids may be complicated by the presence of insertions or multiple domains. To the best of our knowledge, no automated methods are available to characterize solenoid repeats from structure. Results: Here we introduce RAPHAEL, a novel method for the detection of solenoids in protein structures. It reliably solves three problems of increasing difficulty: (1) recognition of solenoid domains, (2) determination of their periodicity and (3) assignment of insertions. RAPHAEL uses a geometric approach mimicking manual classification, producing several numeric parameters that are optimized for maximum performance. The resulting method is very accurate, with 89.5% of solenoid proteins and 97.2% of non-solenoid proteins correctly classified. RAPHAEL periodicities have a Spearman correlation coefficient of 0.877 against the manually established ones. A baseline algorithm for insertion detection in identified solenoids has a Q2 value of 79.8%, suggesting room for further improvement. RAPHAEL finds 1931 highly confident repeat structures not previously annotated as solenoids in the Protein Data Bank records. Availability: The RAPHAEL web server is available with additional data at http://protein.bio.unipd.it/raphael/ Contact:  silvio.tosatto@unipd.it Supplementary information:  Supplementary data are available at Bioinformatics online
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/bts550
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2012
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 7
    Online Resource
    Online Resource
    MOBI: a web server to define and visualize structural mobility in NMR protein ensembles
    Oxford University Press (OUP) ; 2010
    In:  Bioinformatics Vol. 26, No. 22 ( 2010-11-15), p. 2916-2917
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 26, No. 22 ( 2010-11-15), p. 2916-2917
    Abstract: Motivation: MOBI is a web server for the identification of structurally mobile regions in NMR protein ensembles. It provides a binary mobility definition that is analogous to the commonly used definition of intrinsic disorder in X-ray crystallographic structures. At least three different use cases can be envisaged: (i) visualization of NMR mobility for structural analysis; (ii) definition of regions for reliable comparative modelling in protein structure prediction and (iii) definition of mobility in analogy to intrinsic disorder. MOBI uses structural superposition and local conformational differences to derive a robust binary mobility definition that is in excellent agreement with the manually curated definition used in the CASP8 experiment for intrinsic disorder in NMR structure. The output includes mobility-coloured PDB files, mobility plots and a FASTA formatted sequence file summarizing the mobility results. Availability: The MOBI server and supplementary methods are available for non-commercial use at URL: http://protein.bio.unipd.it/mobi/ Contact:  silvio.tosatto@unipd.it Supplementary information:  Supplementary data are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/btq537
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2010
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Fly cryptochrome and the visual system
    Proceedings of the National Academy of Sciences ; 2013
    In:  Proceedings of the National Academy of Sciences Vol. 110, No. 15 ( 2013-04-09), p. 6163-6168
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 110, No. 15 ( 2013-04-09), p. 6163-6168
    Abstract: Cryptochromes are flavoproteins, structurally and evolutionarily related to photolyases, that are involved in the development, magnetoreception, and temporal organization of a variety of organisms. Drosophila CRYPTOCHROME (dCRY) is involved in light synchronization of the master circadian clock, and its C terminus plays an important role in modulating light sensitivity and activity of the protein. The activation of dCRY by light requires a conformational change, but it has been suggested that activation could be mediated also by specific “regulators” that bind the C terminus of the protein. This C-terminal region harbors several protein–protein interaction motifs, likely relevant for signal transduction regulation. Here, we show that some functional linear motifs are evolutionarily conserved in the C terminus of cryptochromes and that class III PDZ-binding sites are selectively maintained in animals. A coimmunoprecipitation assay followed by mass spectrometry analysis revealed that dCRY interacts with Retinal Degeneration A (RDGA) and with Neither Inactivation Nor Afterpotential C (NINAC) proteins. Both proteins belong to a multiprotein complex (the Signalplex) that includes visual-signaling molecules. Using bioinformatic and molecular approaches, dCRY was found to interact with Neither Inactivation Nor Afterpotential C through Inactivation No Afterpotential D (INAD) in a light-dependent manner and that the CRY–Inactivation No Afterpotential D interaction is mediated by specific domains of the two proteins and involves the CRY C terminus. Moreover, an impairment of the visual behavior was observed in fly mutants for dCRY, indicative of a role, direct or indirect, for this photoreceptor in fly vision.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1212317110
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2013
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
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