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Data Mining Techniques for the Life Sciences

Overview of attention for book
Data Mining Techniques for the Life Sciences
Springer New York

Table of Contents

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    Book Overview
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    Chapter 1 Data Mining Techniques for the Life Sciences
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    Chapter 2 Protein Structure Databases.
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    Chapter 3 The MIntAct Project and Molecular Interaction Databases.
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    Chapter 4 Applications of Protein Thermodynamic Database for Understanding Protein Mutant Stability and Designing Stable Mutants.
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    Chapter 5 Classification and Exploration of 3D Protein Domain Interactions Using Kbdock.
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    Chapter 6 Data Mining of Macromolecular Structures.
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    Chapter 7 Criteria to Extract High-Quality Protein Data Bank Subsets for Structure Users.
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    Chapter 8 Homology-Based Annotation of Large Protein Datasets.
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    Chapter 9 Data Mining Techniques for the Life Sciences
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    Chapter 10 Improving the Accuracy of Fitted Atomic Models in Cryo-EM Density Maps of Protein Assemblies Using Evolutionary Information from Aligned Homologous Proteins.
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    Chapter 11 Systematic Exploration of an Efficient Amino Acid Substitution Matrix: MIQS.
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    Chapter 12 Promises and Pitfalls of High-Throughput Biological Assays.
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    Chapter 13 Data Mining Techniques for the Life Sciences
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    Chapter 14 Predicting Conformational Disorder.
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    Chapter 15 Classification of Protein Kinases Influenced by Conservation of Substrate Binding Residues.
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    Chapter 16 Spectral-Statistical Approach for Revealing Latent Regular Structures in DNA Sequence.
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    Chapter 17 Protein Crystallizability.
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    Chapter 18 Data Mining Techniques for the Life Sciences
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    Chapter 19 Data Mining Techniques for the Life Sciences
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    Chapter 20 Functional Analysis of Metabolomics Data.
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    Chapter 21 Data Mining Techniques for the Life Sciences
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    Chapter 22 A Broad Overview of Computational Methods for Predicting the Pathophysiological Effects of Non-synonymous Variants.
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    Chapter 23 Recommendation Techniques for Drug-Target Interaction Prediction and Drug Repositioning.
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    Chapter 24 Protein Residue Contacts and Prediction Methods.
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    Chapter 25 The Recipe for Protein Sequence-Based Function Prediction and Its Implementation in the ANNOTATOR Software Environment.
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    Chapter 26 Data Mining Techniques for the Life Sciences
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    Chapter 27 Data Mining Techniques for the Life Sciences
Attention for Chapter 6: Data Mining of Macromolecular Structures.
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Chapter title
Data Mining of Macromolecular Structures.
Chapter number 6
Book title
Data Mining Techniques for the Life Sciences
Published in
Methods in molecular biology, January 2016
DOI 10.1007/978-1-4939-3572-7_6
Pubmed ID
Book ISBNs
978-1-4939-3570-3, 978-1-4939-3572-7
Authors

Bart van Beusekom, Anastassis Perrakis, Robbie P. Joosten

Editors

Oliviero Carugo, Frank Eisenhaber

Abstract

The use of macromolecular structures is widespread for a variety of applications, from teaching protein structure principles all the way to ligand optimization in drug development. Applying data mining techniques on these experimentally determined structures requires a highly uniform, standardized structural data source. The Protein Data Bank (PDB) has evolved over the years toward becoming the standard resource for macromolecular structures. However, the process selecting the data most suitable for specific applications is still very much based on personal preferences and understanding of the experimental techniques used to obtain these models. In this chapter, we will first explain the challenges with data standardization, annotation, and uniformity in the PDB entries determined by X-ray crystallography. We then discuss the specific effect that crystallographic data quality and model optimization 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 models for detailed analysis and how to select a set of structure models suitable for data mining.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 20 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Spain 1 5%
Unknown 19 95%

Demographic breakdown

Readers by professional status Count As %
Researcher 6 30%
Student > Ph. D. Student 3 15%
Student > Bachelor 2 10%
Professor > Associate Professor 2 10%
Student > Master 1 5%
Other 3 15%
Unknown 3 15%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 7 35%
Medicine and Dentistry 3 15%
Agricultural and Biological Sciences 2 10%
Chemistry 2 10%
Social Sciences 1 5%
Other 1 5%
Unknown 4 20%