[...]... 9 (Modeling Protein Aggregate Assembly and Structure) describes the basic problem of structure misfolding and implications, experimental approach for data collection in support of computational modeling, computational approaches to prediction of misfolded structures, and related applications Chapter 10 (Homology-Based Modeling of Protein Structure) presents the foundation for homology modeling, computational. .. performance of various tools in CASP is described Chapter 14 (Structure Prediction of Membrane Proteins) covers the methods for prediction of secondary structure and topology of membrane proteins, as well as prediction of their tertiary structure A list of useful resources for membrane protein structure prediction is also provided Chapter 15 (Structure Prediction of Protein Complexes) describes computational. .. faced in improving the prediction of protein structure and new trends for prediction are also discussed 1.2 The Development of Protein Structure Prediction Methodologies 1.2.1 Protein Homology Modeling The methodology for homology modeling (or comparative modeling) , a very successful category of protein structure prediction, is based on our understanding of protein evolution: (1) proteins that have similar... Energy Functions for Computational Studies of Proteins Xiang Li and Jie Liang 1 45 71 4 Computational Methods for Domain Partitioning of Protein Structures 125 Stella Veretnik and Ilya Shindyalov 5 Protein Structure Comparison and Classification 147 Orhan Camo˘ lu and Ambuj K Singh ¸ g 6 Computation of Protein Geometry and Its Applications: Packing and Function Prediction 181... data and evaluation metrics An example of protein structure prediction at genome-wide scale is also given Chapter 18 (Resources and Infrastructure for Structural Bioinformatics) describes tools, databases, and other resources of protein structure analysis and prediction available on the Internet These include the PDB and related databases and servers, structural visualization tools, protein sequence and. .. compatibility between a protein structure and a protein sequence Threading approaches have three distinct applications in protein structure prediction: (1) identifying appropriate protein structure templates for modeling a target protein, (2) identifying protein sequences adopting a known protein fold, and (3) accessing the quality of a protein model 1.2.2.2 3D-profile: Representing Structures by Environmental... Local Structure Prediction of Proteins 207 Victor A Simossis and Jaap Heringa 8 Protein Contact Map Prediction 255 Xin Yuan and Christopher Bystroff 9 Modeling Protein Aggregate Assembly and Structure 279 Jun-tao Guo, Carol K Hall, Ying Xu, and Ronald B Wetzel 10 Homology-Based Modeling of Protein Structure 319 Zhexin Xiang xv SVNY330-Xu-Vol-I November 4, 2006 10:1 xvi Contents 11 Modeling. .. structure of proteins, and protein evolution Appendix 2 (Computer Science for Structural Informatics) discusses computer science concepts that are essential for effective computation for protein structure prediction These include efficient data structure, computational complexity and NP-hardness, various algorithmic techniques, parallel computing, and programming Appendix 3 (Physical and Chemical Basis for Structural... Preface regions, and applications to tertiary structure prediction A number of popular prediction software packages are described Chapter 8 (Protein Contact Maps Prediction) describes the basic principles for residue contact predictions, and computational approaches for prediction of residue– residue contacts Also discussed is the relevance to tertiary structure prediction A number of popular prediction. .. local structures in segment assembly based methods) Doing so improves the efficiency of folding simulation and ab initio methods for protein structure prediction 1.2.3.2 Reduced Models of Proteins and Their Applications Reduced models of proteins are necessary for easy and unambiguous interpretation of computer simulations of proteins and to obtain dramatic reduction (by orders of magnitude) of the computational . Index ii SVNY330-Xu-Vol-I November 4, 2006 10:1 Ying Xu, Dong Xu, and Jie Liang (Eds.) Computational Methods for Protein Structure Prediction and Modeling Volume 1: Basic Characterization iii SVNY330-Xu-Vol-I November. and potential for the future. Chapter 1 (A Historical Perspective and Overview of Protein Structure Prediction) gives a perspective on the methods for the prediction of protein structure and. aspects of protein structure prediction and modeling, it is widely recognized that the field lacks a comprehensive and coherent overview of the science of protein structure prediction and modeling, ” which