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Data Mining Techniques for the Life Sciences

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Cover of 'Data Mining Techniques for the Life Sciences'

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 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 title
Improving the Accuracy of Fitted Atomic Models in Cryo-EM Density Maps of Protein Assemblies Using Evolutionary Information from Aligned Homologous Proteins.
Chapter number 10
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_10
Pubmed ID
Book ISBNs
978-1-4939-3570-3, 978-1-4939-3572-7
Authors

Ramachandran Rakesh, Narayanaswamy Srinivasan

Editors

Oliviero Carugo, Frank Eisenhaber

Abstract

Cryo-Electron Microscopy (cryo-EM) has become an important technique to obtain structural insights into large macromolecular assemblies. However the resolution of the density maps do not allow for its interpretation at atomic level. Hence they are combined with high resolution structures along with information from other experimental or bioinformatics techniques to obtain pseudo-atomic models. Here, we describe the use of evolutionary conservation of residues as obtained from protein structures and alignments of homologous proteins to detect errors in the fitting of atomic structures as well as improve accuracy of the protein-protein interfacial regions in the cryo-EM density maps.

Mendeley readers

The data shown below were compiled from readership statistics for 48 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
New Zealand 1 2%
Unknown 47 98%

Demographic breakdown

Readers by professional status Count As %
Researcher 15 31%
Student > Ph. D. Student 13 27%
Student > Doctoral Student 3 6%
Student > Bachelor 2 4%
Professor 2 4%
Other 4 8%
Unknown 9 19%
Readers by discipline Count As %
Agricultural and Biological Sciences 18 38%
Biochemistry, Genetics and Molecular Biology 12 25%
Chemistry 3 6%
Medicine and Dentistry 2 4%
Psychology 1 2%
Other 3 6%
Unknown 9 19%