Volume one of this two volume sequence focuses on the basic characterization of known protein structures as well as structure prediction from protein sequence information. The 11 chapters provide an overview of the field, covering key topics in modeling, force fields, classification, computational methods, and struture prediction. Each chapter is a self contained review designed to cover (1) definition of the problem and an historical perspective, (2) mathematical or computational formulation of the problem, (3) computational methods and algorithms, (4) performance results, (5) existing software packages, and (6) strengths, pitfalls, challenges, and future research directions.
Key Features
- Addresses a broad interdisciplinary audience in biophysics and biochemistry, molecular and cell biology, computational biology, and bioinformatics
- Provides a comprehensive overview of protein biophysics for both professionals and graduate students
- Presents computational methods for all major aspects of protein structure analysis
- Each chapter offers a self-contained review
Author(s): Ying Xu, Dong Xu, Jie Liang
Series: Biological and Medical Physics, Biomedical Engineering
Publisher: Springer
Year: 2007
Language: English
Pages: 407
Contents......Page 14
Contributors......Page 16
1. A Historical Perspective and Overview of Protein Structure Prediction......Page 20
2. Empirical Force Fields......Page 63
3. Knowledge-Based Energy Functions for Computational Studies of Proteins......Page 88
4. Computational Methods for Domain Partitioning of Protein Structures......Page 141
5. Protein Structure Comparison and Classification......Page 162
6. Computation of Protein Geometry and Its Applications: Packing and Function Prediction......Page 196
7. Local Structure Prediction of Proteins......Page 222
8. Protein Contact Map Prediction......Page 270
9. Modeling Protein Aggregate Assembly and Structure......Page 293
10. Homology-Based Modeling of Protein Structure......Page 332
11. Modeling Protein Structures Based on Density Maps at Intermediate Resolutions......Page 371
C......Page 401
F......Page 402
M......Page 403
P......Page 404
S......Page 405
Y......Page 406
