Titlebook: Data Mining Techniques for the Life Sciences; Oliviero Carugo,Frank Eisenhaber Book 2016Latest edition Springer Science+Business Media New

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Systematic Exploration of an Efficient Amino Acid Substitution Matrix: MIQSd function. In this study, we improve amino acid substitution matrices to identify distantly related proteins. We systematically sampled and benchmarked substitution matrices generated from the principal component analysis (PCA) subspace based on a set of typical existing matrices. Based on the benc

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Promises and Pitfalls of High-Throughput Biological Assaystrategies and guidelines that researchers should follow when undertaking such studies. We discuss common errors in experimental design and data analysis that lead to irreproducible and non-replicable research and provide some guidelines to avoid these common mistakes so that researchers may have con

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Predicting Conformational Disordersordered proteins are ubiquitous proteins that fulfill essential biological functions while lacking a stable 3D structure. Their conformational heterogeneity is encoded at the amino acid sequence level, thereby allowing intrinsically disordered proteins or regions to be recognized based on their seq

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Classification of Protein Kinases Influenced by Conservation of Substrate Binding Residues kinases are generally classified into different subfamilies based on their sequence similarity with members of known subfamilies of kinases. A functional association is then defined to the kinase based on the subfamily to which it has been characterized. However, one of the key factors that give id

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Spectral–Statistical Approach for Revealing Latent Regular Structures in DNA Sequenceis in the HeteroGenome database which collects the sequences similar to approximate tandem repeats in the genomes of model organisms are adduced. In consequence of further developing of the spectral–statistical approach, the techniques for recognizing latent profile periodicity are considered. These

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Data Mining of Macromolecular Structuresptimization methods have on structural models and how validation tools can be used to make informed choices. We also discuss specific advantages of using the PDB_REDO databank as a resource for structural data. Finally, we will provide guidelines on how to select the most suitable protein structure

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Criteria to Extract High-Quality Protein Data Bank Subsets for Structure Userse incessant growth of the Protein Data Bank and especially of the number of high-resolution structures is allowing the use of more stringent selection criteria, with a consequent improvement of the quality of the subsets of the Protein Data Bank.

PALSY

Promises and Pitfalls of High-Throughput Biological Assaysta, and methods to correct for it are presented, as well as approaches to detect and correct for experimental biases and batch effects, which often plague high-throughput assays. We highlight the importance of sharing data and analysis code to facilitate reproducibility and present tools and softwar