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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

  1. Altmetric Badge
    Book Overview
  2. Altmetric Badge
    Chapter 1 Data Mining Techniques for the Life Sciences
  3. Altmetric Badge
    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.
  16. Altmetric Badge
    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.
  19. Altmetric Badge
    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
  23. Altmetric Badge
    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.
  27. Altmetric Badge
    Chapter 26 Data Mining Techniques for the Life Sciences
  28. Altmetric Badge
    Chapter 27 Data Mining Techniques for the Life Sciences
Attention for Chapter 24: Protein Residue Contacts and Prediction Methods.
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Chapter title
Protein Residue Contacts and Prediction Methods.
Chapter number 24
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_24
Pubmed ID
Book ISBNs
978-1-4939-3570-3, 978-1-4939-3572-7
Authors

Badri Adhikari, Jianlin Cheng

Editors

Oliviero Carugo, Frank Eisenhaber

Abstract

In the field of computational structural proteomics, contact predictions have shown new prospects of solving the longstanding problem of ab initio protein structure prediction. In the last few years, application of deep learning algorithms and availability of large protein sequence databases, combined with improvement in methods that derive contacts from multiple sequence alignments, have shown a huge increase in the precision of contact prediction. In addition, these predicted contacts have also been used to build three-dimensional models from scratch.In this chapter, we briefly discuss many elements of protein residue-residue contacts and the methods available for prediction, focusing on a state-of-the-art contact prediction tool, DNcon. Illustrating with a case study, we describe how DNcon can be used to make ab initio contact predictions for a given protein sequence and discuss how the predicted contacts may be analyzed and evaluated.

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X Demographics

The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 83 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Canada 1 1%
Unknown 82 99%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 25 30%
Researcher 10 12%
Student > Master 10 12%
Student > Bachelor 7 8%
Student > Doctoral Student 4 5%
Other 11 13%
Unknown 16 19%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 28 34%
Computer Science 14 17%
Agricultural and Biological Sciences 7 8%
Pharmacology, Toxicology and Pharmaceutical Science 4 5%
Chemistry 4 5%
Other 5 6%
Unknown 21 25%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 11 December 2020.
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#18,463,662
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Outputs from Methods in molecular biology
#7,924
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#284,559
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Outputs of similar age from Methods in molecular biology
#845
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