Defining a protein: mining the protein structure database
نویسندگان
چکیده
منابع مشابه
Prediction of protein secondary structure by mining structural fragment database.
A new method for predicting protein secondary structure from amino acid sequence has been developed. The method is based on multiple sequence alignment of the query sequence with all other sequences with known structure from the protein data bank (PDB) by using BLAST. The fragments of the alignments belonging to proteins from the PBD are then used for further analysis. We have studied various s...
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The validation, enrichment and organization of the data stored in PDB files is essential for those data to be used accurately and efficiently for modelling, experimental design and the determination of molecular interactions. The Iditis protein structure database has been designed to allow the widest possible range of queries to be performed across all available protein structures. The Iditis d...
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This paper describes the application of machine learning algorithms to the discovery of knowledge in a protein structure database. The problem addressed is the determination of the solvent exposure of each amino acid residue, using different levels of exposed surface to define exposure. First we introduce the baseline classifier which achieves good prediction results despite only taking into ac...
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PrePPI (http://bhapp.c2b2.columbia.edu/PrePPI) is a database that combines predicted and experimentally determined protein-protein interactions (PPIs) using a Bayesian framework. Predicted interactions are assigned probabilities of being correct, which are derived from calculated likelihood ratios (LRs) by combining structural, functional, evolutionary and expression information, with the most ...
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With a large amount of information relating to proteins accumulating in databases widely available online, it is of interest to apply machine learning techniques that, by extracting underlying statistical regularities in the data, make predictions about the functional and evolutionary characteristics of unseen proteins. Such predictions can help in achieving a reduction in the space over which ...
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ژورنال
عنوان ژورنال: Acta Crystallographica Section A Foundations of Crystallography
سال: 2008
ISSN: 0108-7673
DOI: 10.1107/s0108767308079804