This volume details several important databases and data mining tools. Data Mining Techniques for the Life Sciences, Second Edition guides readers through archives of macromolecular three-dimensional structures, databases of protein-protein interactions, thermodynamics information on protein and mutant stability, "Kbdock" protein domain structure database, PDB_REDO databank, erroneous sequences, substitution matrices, tools to align RNA sequences, interesting procedures for kinase family/subfamily classifications, new tools to predict protein crystallizability, metabolomics data, drug-target interaction predictions, and a recipe for protein-sequence-based function prediction and its implementation in the latest version of the ANNOTATOR software suite. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Data Mining Techniques for the Life Sciences, Second Edition aims to ensure successful results in the further study of this vital field.

This third edition details new and updated methods and protocols on important databases and data mining tools. Chapters guides readers through archives of macromolecular sequences and three-dimensional structures, databases of protein-protein interactions, methods for prediction conformational disorder, mutant thermodynamic stability, aggregation, and drug response. Quality of structural data and their release, soft mechanics applications in biology, and protein flexibility are considered, too, together with pan-genome analyses, rational drug combination screening and Omics Deep Mining. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials, includes step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Data Mining Techniques for the Life Sciences, Third Edition aims to be a practical guide to researches to help further their study in this field.

In this anthology, leading researchers present critical reviews of methods and high-impact applications in computational biology that lead to results that also non-bioinformaticians must know to design efficient experimental research plans. Discovering Biomolecular Mechanisms with Computational Biology also summarizes non-trivial theoretical predictions for regulatory and metabolic networks that have received experimental confirmation. Discovering Biomolecular Mechanisms with Computational Biology is essential reading for life science researchers and higher-level students that work on biomolecular mechanisms and wish to understand the impact of computational biology for their success.

This third edition details new and updated methods and protocols on important databases and data mining tools. Chapters guides readers through archives of macromolecular sequences and three-dimensional structures, databases of protein-protein interactions, methods for prediction conformational disorder, mutant thermodynamic stability, aggregation, and drug response. Quality of structural data and their release, soft mechanics applications in biology, and protein flexibility are considered, too, together with pan-genome analyses, rational drug combination screening and Omics Deep Mining. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials, includes step-by-step, readily reproducible protocols.   Authoritative and cutting-edge, Data Mining Techniques for the Life Sciences, Third Edition aims to be a practical guide to researches to help further their study in this field.

Most life science researchers will agree that biology is not a truly theoretical branch of science. The hype around computational biology and bioinformatics beginning in the nineties of the 20th century was to be short lived (1, 2). When almost no value of practical importance such as the optimal dose of a drug or the three-dimensional structure of an orphan protein can be computed from fundamental principles, it is still more straightforward to determine them experimentally. Thus, experiments and observationsdogeneratetheoverwhelmingpartofinsightsintobiologyandmedicine. The extrapolation depth and the prediction power of the theoretical argument in life sciences still have a long way to go. Yet, two trends have qualitatively changed the way how biological research is done today. The number of researchers has dramatically grown and they, armed with the same protocols, have produced lots of similarly structured data. Finally, high-throu- put technologies such as DNA sequencing or array-based expression profiling have been around for just a decade. Nevertheless, with their high level of uniform data generation, they reach the threshold of totally describing a living organism at the biomolecular level for the first time in human history. Whereas getting exact data about living systems and the sophistication of experimental procedures have primarily absorbed the minds of researchers previously, the weight increasingly shifts to the problem of interpreting accumulated data in terms of biological function and bio- lecular mechanisms.

This volume details several important databases and data mining tools. Data Mining Techniques for the Life Sciences, Second Edition guides readers through archives of macromolecular three-dimensional structures, databases of protein-protein interactions, thermodynamics information on protein and mutant stability, "Kbdock" protein domain structure database, PDB_REDO databank, erroneous sequences, substitution matrices, tools to align RNA sequences, interesting procedures for kinase family/subfamily classifications, new tools to predict protein crystallizability, metabolomics data, drug-target interaction predictions, and a recipe for protein-sequence-based function prediction and its implementation in the latest version of the ANNOTATOR software suite. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Data Mining Techniques for the Life Sciences, Second Edition aims to ensure successful results in the further study of this vital field.

Most life science researchers will agree that biology is not a truly theoretical branch of science. The hype around computational biology and bioinformatics beginning in the nineties of the 20th century was to be short lived (1, 2). When almost no value of practical importance such as the optimal dose of a drug or the three-dimensional structure of an orphan protein can be computed from fundamental principles, it is still more straightforward to determine them experimentally. Thus, experiments and observationsdogeneratetheoverwhelmingpartofinsightsintobiologyandmedicine. The extrapolation depth and the prediction power of the theoretical argument in life sciences still have a long way to go. Yet, two trends have qualitatively changed the way how biological research is done today. The number of researchers has dramatically grown and they, armed with the same protocols, have produced lots of similarly structured data. Finally, high-throu- put technologies such as DNA sequencing or array-based expression profiling have been around for just a decade. Nevertheless, with their high level of uniform data generation, they reach the threshold of totally describing a living organism at the biomolecular level for the first time in human history. Whereas getting exact data about living systems and the sophistication of experimental procedures have primarily absorbed the minds of researchers previously, the weight increasingly shifts to the problem of interpreting accumulated data in terms of biological function and bio- lecular mechanisms.