Mathematical Methods for Protein Structure Analysis and Design

1. Front Matter

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2. Protein Structure Comparison: Algorithms and Applications

   • Giuseppe Lancia, Sorin Istrail

   Pages 1-33

3. Spatial Pattern Detection in Structural Bionformatics

   • Haim J. Wolfson

   Pages 35-56

4. Geometric Methods for Protein Structure Comparison

   • Carlo Ferrari, Concettina Guerra

   Pages 57-82

5. Identifying Flat Regions and Slabs in Protein Structures

   • Mary Ellen Bock, Concettina Guerra

   Pages 83-97

6. OPTIMA: A New Score Function for the Detection of Remote Homologs

   • Maricel Kann, Richard A. Goldstein

   Pages 99-108

7. A Comparison of Methods for Assessing the Structural Similarity of Proteins

   • Dean C. Adams, Gavin J. P. Naylor

   Pages 109-115

8. Prediction of Protein Secondary Structure at High Accuracy Using a Combination of Many Neural Networks

   • Claus Lundegaard, Thomas Nordahl Petersen, Morten Nielsen, Henrik Bohr, Jacob Bohr, Søren Brunak et al.

   Pages 117-122

9. Self-consistent Knowledge-Based Approach to Protein Design

   • Andrea Rossi, Cristian Micheletti, Flavio Seno, Amos Maritan

   Pages 123-129

10. Protein Structure from Solid-State NMR

    • John R. Quine, Timothy A. Cross

    Pages 131-137

11. Learning Effective Amino-Acid Interactions

    • Flavio Seno, Cristian Micheletti, Amos Maritan, Jayanth R. Banavar

    Pages 139-145

12. Proteinlike Properties of Simple Models

    • Yves-Henri Sanejouand, Georges Trinquier

    Pages 147-153

13. Back Matter

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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.

• algorithms
• calculus
• computational biology
• computational molecular biology
• data analysis
• genome
• neural learning
• pattern analysis
• pattern matching
• protein design
• protein informatics
• protein structure analysis
• statistical learning
• structural similarity
• structure prediction
• algorithm analysis and problem complexity

• Topic Chairs,  

  Concettina Guerra

• Center for Molecular Biology and Computer Sciecne Department, Brown University, USA

  Sorin Istrail

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