This book covers elements of both the data-driven comparative modeling approach to structure prediction and also recent attempts to simulate folding using explicit or simplified models. Despite the unsolved mystery of how a protein folds, advances are being made in predicting the interactions of proteins with other molecules. Also rapidly advancing are the methods for solving the inverse folding problem, the problem of finding a sequence to fit a structure. This book focuses on the various computational methods for prediction, their successes and their limitations, from the perspective of their most well known practitioners.
Within those four sections, the following topics are covered: Databases and resources that are commonly used for protein structure prediction The structure prediction flagship assessment (CASP) and the protein structure initiative (PSI) ...
This book presents practical computer-based methods using the latest computer modelling algorithms. -
//VTRODUCTIO/V It is now possible to calculate the classical energy of a complex system such as a protein as a function of its coordinates. By making many such calculations for various coordinate values, one can explore multidimensional ...
Volume One of this two-volume sequence focuses on the basic characterization of known protein structures, and structure prediction from protein sequence information.
This volume attempts to present a concise overview of these advances.
Nucleic Acids Res. 26:316-319. Humphrey, W., Dalke, A., and Schulten, K. 1 996. VMD: Visual molecular dynamics. J.Mol. Graph. 14:33-38. Jiang, T., Xu, Y., and Zhang, M. (eds.). 2002. Current Topics in Computational Molecular Biology.
Prediction of Protein Structures, Functions and Interactions presents a comprehensive overview of methods for prediction of protein structure or function, with the emphasis on their availability and possibilities for their combined use.
This text offers in-depth perspectives on every aspect of protein structure identification, assessment, characterization, and utilization, for a clear understanding of the diversity of protein shapes, variations in protein function, and ...
Protein Structure by Distance Analysis
Many methods have been developed for identifying 3D motifs and for searching structures for their occurrence. ... M (2005a) Query3d: a new method for high-throughput analysis of functional residues in protein structures.