Titlebook: Data Mining Techniques for the Life Sciences; Oliviero Carugo,Frank Eisenhaber Book 2022Latest edition The Editor(s) (if applicable) and T

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Profiles of Natural and Designed Protein-Like Sequences Effectively Bridge Protein Sequence Gaps: Im protein families. Powerful profile-based sequence search methods rely on a sequence space continuum to identify non-trivial relationships through homology detection. The computational design of protein-like sequences that serve as “artificial linkers” is useful in identifying relationships between

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Turning Failures into Applications: The Problem of Protein ΔΔ, Predictiondiction upon variations, we now realize that all the approaches are poorly performing when tested on specific cases and that there is large space for improvement. Why this is so? Is it wrong the underlying assumption that experimental protein thermodynamics in solution reflects the thermodynamics of

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Extracting the Dynamic Motion of Proteins Using Normal Mode Analysis results similar to those produced by principal components analysis of a molecular dynamics simulation, but with only a fraction of the computational effort. Here, we provide a brief overview of the theory and describe three methods for carrying out NMA, including the use of one of the on-line servi

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Uses and Abuses of the Atomic Displacement Parameters in Structural Biologyies in biological macromolecules. In this chapter, the most recent studies and applications of B-factors in protein engineering and structural biology are briefly summarized. Particular emphasis is given to the limitations in using B-factors, in order to prevent inappropriate applications. It is eve

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Optimizing the Parametrization of Homologue Classification in the Pan-Genome Computation for a Bactel sequence diversity within organism populations, strain collections, clades, etc. A single genome is no longer sufficient to describe bacteria of interest, but instead, the genomic repertoire of all existing strains is the key to the metabolic, evolutionary, or pathogenic potential of a species. Th

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Computational Pipeline for Rational Drug Combination Screening in Patient-Derived Cellstherapies as next-line regimens. However, due to a massive number of possible drug combinations to test, there is a need for systematic and rational approaches to finding safe and effective drug combinations for each individual patient. This protocol describes an ecosystem of computational methods t