Mathematical Methods for Protein Structure Anaylysis and Design: C.I.M.E. Summer School, Martinal Franca, Italy, July 9-15, 2000 : Advanced Lectures

by Guerra, Concettina; Istrail, Sorin; Guerra, Concettina; Istrail, Sorin

• ISBN13: 9783540401049
• ISBN10: 3540401040
• Format: Paperback
• Copyright: 2003-08-01
• Publisher: Springer Verlag

Summary

The revised lectures presented in this volume are based on a course given by leading scholars at the C.I.M.E. Summer School held in Martina Franca, Italy, in July 2000.The 11 revised chapters presented were carefully revised and cross-reviewed in order to provide competent coverage of mathematical methods for protein structure analysis and design. The topics addressed pinpoint major issues arising in the development and analysis of models, algorithms, and software tools devoted to the structure of proteins, all of which play crucial roles in structural genomics and proteomics.

Table of Contents

Protein Structure Comparison: Algorithms and Applications
Giuseppe Lancia, Sorin Istrail	1	(34)
1 Introduction	1	(3)
2 Preliminaries	4	(2)
3 Applications of Structure Comparisons	6	(5)
4 Software and Algorithms for Structure Comparison	11	(9)
5 Problems Based on Contact Map Representations	20	(10)
6 Acknowledgements	30	(1)
References	30	(5)
Spatial Pattern Detection in Structural Bionformatics
Haim J. Wolfson	35	(22)
1 Introduction	35	(2)
2 Protein Shape Representation	37	(1)
3 Protein Structural Alignment	38	(8)
4 Protein-Protein Docking	46	(6)
5 Summary	52	(1)
References	53	(4)
Geometric Methods for Protein Structure Comparison
Carlo Ferrari, Concettina Guerra	57	(26)
1 Introduction	57	(2)
2 Protein Description	59	(3)
3 Structural Comparison: Problem Formulation	62	(1)
4 Representation of Rigid Transformations	63	(5)
5 Determination of 3D Rigid Transformations	68	(3)
6 Geometric Pattern Matching	71	(2)
7 Indexing Techniques	73	(3)
8 Graph-Theoretic Approaches	76	(1)
9 Integration of Methods for Protein Comparison Using Different Representations	77	(1)
10 Conclusions	78	(1)
11 Acknowledgements	79	(1)
References	79	(4)
Identifying Flat Regions and Slabs in Protein Structures
Mary Ellen Bock, Concettina Guerra	83	(16)
1 Introduction	83	(2)
2 A Geometric Algorithm	85	(2)
3 An Improved Geometric Algorithm	87	(1)
4 Hough Transform	88	(2)
5 Performances of the Two Algorithms	90	(2)
6 Plane Detection in Proteins	92	(3)
7 Acknowledgements	95	(1)
References	96	(3)
OPTIMA: A New Score Function for the Detection of Remote Homologs
Maricel Kann, Richard A. Goldstein	99	(10)
1 Abstract	99	(1)
2 Introduction	99	(1)
3 Methods	100	(7)
References	107	(2)
A Comparison of Methods for Assessing the Structural Similarity of Proteins
Dean C. Adams, Gavin J.P. Naylor	109	(8)
1 Introduction	109	(1)
2 The DALI Algorithm	109	(1)
3 The Root Mean Square Algorithm	110	(1)
4 Geometric Morphometrics	111	(1)
5 Comparison of Methods	111	(2)
6 Discussion	113	(1)
References	114	(3)
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, Garry Lippert, Cle Lund	117	(6)
1 Summary	117	(1)
2 Introduction	117	(1)
3 Methods	118	(1)
4 Results	119	(2)
References	121	(2)
Self-consistent Knowledge-Based Approach to Protein Design
Andrea Rossi, Cristian Micheletti, Flavio Seno, Amos Maritan	123	(8)
1 Introduction	123	(1)
2 The Design Strategy	124	(1)
3 Results and Discussion	125	(2)
4 Summary	127	(1)
References	128	(3)
Protein Structure from Solid-State NMR
John R. Quine, Timothy A. Cross	131	(8)
1 Discrete Curves	131	(2)
2 Tensors and NMR	133	(1)
3 Structure from Orientational Constraints	134	(2)
4 Acknowledgment	136	(1)
References	136	(3)
Learning Effective Amino-Acid Interactions
Flavio Seno, Cristian Micheletti, Amos Maritan, Jayanth R. Banavar	139	(8)
1 Introduction	139	(2)
2 Models and Techniques	141	(1)
3 Results	142	(2)
4 Conclusions	144	(1)
References	144	(3)
Proteinlike Properties of Simple Models
Yves-Henri Sanéjouand, Georges Trinquier	147	(8)
1 The 3x3x3 Cubic Lattice Model	147	(4)
2 N-Soft-Spheres Models	151	(1)
References	152	(3)
List of Participants	155