Mathematical Methods for Protein Structure Analysis and Design, 2003 Advanced Lectures Lecture Notes in Bioinformatics Series

The papers collected in this volume reproduce contributions by leading sch- arstoaninternationalschoolandworkshopwhichwasorganizedandheldwith thegoaloftakinga snapshotofadiscipline undertumultuous growth. Indeed, the area of protein folding, docking and alignment is developing in response to needs for a mix of heterogeneous expertise spanning biology, chemistry, mathematics, computer science, and statistics, among others. Some of the problems encountered in this area are not only important for the scienti?c challenges they pose, but also for the opportunities they disclose intermsofmedicalandindustrialexploitation. Atypicalexampleiso?eredby protein-drug interaction (docking), a problem posing daunting computational problems at the crossroads of geometry, physics and chemistry, and, at the same time, a problem with unimaginable implications for the pharmacopoeia of the future. The schoolfocused on problems posed by the study of the mechanisms - hind protein folding, and explored di?erent ways of attacking these problems under objective evaluations of the methods. Together with a relatively small core of consolidated knowledge and tools, important re?ections were brought to this e?ort by studies in a multitude of directions and approaches. It is obviously impossible to predict which, if any, among these techniques will prove completely successful, but it is precisely the implicit dialectic among them that best conveys the current ?avor of the ?eld. Such unique diversity and richness inspired the format of the meeting, and also explains the slight departure of the present volume from the typical format in this series: the exposition of the current sediment is complemented here by a selection of quali?ed specialized contributions.

Protein Structure Comparison: Algorithms and Applications.- Spatial Pattern Detection in Structural Bionformatics.- Geometric Methods for Protein Structure Comparison.- Identifying Flat Regions and Slabs in Protein Structures.- OPTIMA: A New Score Function for the Detection of Remote Homologs.- A Comparison of Methods for Assessing the Structural Similarity of Proteins.- Prediction of Protein Secondary Structure at High Accuracy Using a Combination of Many Neural Networks.- Self-consistent Knowledge-Based Approach to Protein Design.- Protein Structure from Solid-State NMR.- Learning Effective Amino-Acid Interactions.- Proteinlike Properties of Simple Models.