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Wednesday, 18th October, 2017, 12:00

Structural Bioinformatics

How to analyze the structure of proteins without using Cryo-EM

Sesiones científicas, CRG Group Leader Seminars; Organizador: PRBB Group Leader Seminar

Speaker: Miguel Beato / Baldo Oliva / Eduard Sabidó / Roni Wright

Room Sala Ramón y Cajal, PRBB

Tuesday, 21th September, 2010, Tue, Sep 21, 2010 11:00 AM - Tue, Sep 21, 2010 12:00 PM

Structural Bioinformatics

ModLink+: improving fold recognition by using protein-protein interactions

MOTIVATION: Several strategies have been developed to predict the fold of a target protein sequence, most of which are based on aligning the target sequence to other sequences of known structure. Previously, we demonstrated that the consideration of protein-protein interactions significantly increases the accuracy of fold assignment compared with PSI-BLAST sequence comparisons. A drawback of our method was the low number of proteins to which a fold could be assigned. Here, we present an improved version of the method that addresses this limitation. We also compare our method to other state-of-the-art fold assignment methodologies. RESULTS: Our approach (ModLink+) has been tested on 3716 proteins with domain folds classified in the Structural Classification Of Proteins (SCOP) as well as known interacting partners in the Database of Interacting Proteins (DIP). For this test set, the ratio of success predictive value (PPV) on fold assignment increases from 75 for PSI-BLAST, 83 for HHSearch and 81 for PRC to >90 for ModLink+at the e-value cutoff of 10(-3). Under this e-value, ModLink+can assign a fold to 30-45 of the proteins in the test set, while our previous method could cover <25. When applied to 6384 proteins with unknown fold in the yeast proteome, ModLink+combined with PSI-BLAST assigns a fold for domains in 3738 proteins, while PSI-BLAST alone covers only 2122 proteins, HHSearch 2969 and PRC 2826 proteins, using a threshold e-value that would represent a PPV >82% for each method in the test set. AVAILABILITY: The ModLink+server is freely accessible in the World Wide Web at http://sbi.imim.es/modlink/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Speaker: Oriol Fornés Crespo, Structural Bioinformatics Lab., IMIM/UPF

Wednesday, 5th May, 2010, Wed, May 5, 2010 3:00 PM - 5:00 PM

Structural Bioinformatics

Biana: a software framework for compiling biological interactions and analyzing networks

The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties. We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php. BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

Speaker: Javier García-García, GRIB (UPF- IMIM)

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