Protein Bioinformatics From Sequence to Function 1st Edition by Michael Gromiha 8131222977 9788131222973

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ISBN 10: 8131222977

ISBN 13: 9788131222973

Author: M. Michael Gromiha

One of the most pressing tasks in biotechnology today is to unlock the function of each of the thousands of new genes identified every day. Scientists do this by analyzing and interpreting proteins, which are considered the task force of a gene. This single source reference covers all aspects of proteins, explaining fundamentals, synthesizing the latest literature, and demonstrating the most important bioinformatics tools available today for protein analysis, interpretation and prediction. Students and researchers of biotechnology, bioinformatics, proteomics, protein engineering, biophysics, computational biology, molecular modeling, and drug design will find this a ready reference for staying current and productive in this fast evolving interdisciplinary field.

Explains all aspects of proteins including sequence and structure analysis, prediction of protein structures, protein folding, protein stability, and protein interactions

Teaches readers how to analyze their own datasets using available online databases, software tools, and web servers, which are listed and updated on the book’s web companion page.

 Presents a cohesive and accessible overview of the field, using illustrations to explain key concepts and detailed exercises for students.

Protein Bioinformatics From Sequence to Function 1st Table of contents:

Chapter 1: Proteins

1.1 Building blocks

1.2 Hierarchical representation of proteins

1.3 Structural classification of proteins

1.4 Databases for protein sequences

1.5 Protein structure databases

1.6 Literature databases

1.7 Exercises

References

Chapter 2: Protein Sequence Analysis

2.1 Sequence alignment

2.2 Programs for aligning sequences

2.3 Amino acid properties

2.4 Amphipathic character of α-helices and β-strands

2.5 Amino acid properties for sequence analysis

2.6 Exercises

References

Chapter 3: Protein Structure Analysis

3.1 Assignment of secondary structures

3.2 Computation of solvent accessibility

3.3 Representation of solvent accessibility

3.4 Residue–residue contacts

3.5 Amino acid clusters in protein structures

3.6 Contact potentials

3.7 Cation-π interactions in protein structures

3.8 Noncanonical interactions

3.9 Free energy calculations

3.10 Amino acid properties derived from protein structural data

3.11 Parameters for proteins

3.12 Protein structure comparison

3.13 Exercises

References

Chapter 4: Protein Folding Kinetics

4.1 Ф-value analysis

4.2 Folding nuclei and Ф-values

4.3 Relationship between amino acid properties and Ф-values

4.4 Ф-value analysis with hydrophobic clusters and long-range contact networks

4.5 Kinetic database for proteins

4.6 Prediction of protein folding rates

4.7 Relationship between Ф-values and folding rates

4.8 Exercises

References

Chapter 5: Protein Structure Prediction

5.1 Protein structural class

5.2 Secondary structure content

5.3 Secondary structural regions

5.4 Discrimination of transmembrane helical proteins and predicting their membrane-spanning segments

5.5 Discrimination of transmembrane strand proteins

5.6 Identification of membrane-spanning β-strand segments

5.7 Discrimination of disordered proteins and domains

5.8 Solvent accessibility

5.9 Inter-residue contact prediction

5.10 Protein tertiary structure prediction

5.11 Exercises

References

Chapter 6: Protein Stability

6.1 Determination of protein stability

6.2 Thermodynamic database for proteins and mutants

6.3 Relative contribution of noncovalent interactions to protein stability

6.4 Stability of thermophilic proteins

6.5 Analysis and prediction of protein mutant stability

6.6 Exercises

References

Chapter 7: Protein Interactions

7.1 Protein–protein interactions

7.2 Protein–DNA interactions

7.3 Protein–RNA interactions

7.4 Protein–ligand interactions

7.5 Quantitative structure activity relationship in protein–ligand interactions

7.6 Exercises

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