Pacific Symposium on Biocomputing 2005 : Hawaii, USA, 4-8 January 2005 / edited by Russ B. Altman ... [et al.].

Format:

Book

Conference/Event

Contributor:

Altman, Russ.

Conference Name:

Pacific Symposium on Biocomputing (10th : 2005 : Hawaii)

Language:

English

Subjects (All):

Biology--Mathematical models--Congresses.

Biology.

Biology--Computer simulation--Congresses.

Molecular biology--Mathematical models--Congresses.

Molecular biology.

Molecular biology--Computer simulation--Congresses.

Physical Description:

1 online resource (565 p.)

Other Title:

Biocomputing 2005

Place of Publication:

Singapore ; Hackensack, NJ : World Scientific, c2005.

Language Note:

English

Summary:

The Pacific Symposium on Biocomputing (PSB 2005) is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. This latest volume in the prestigious conference series contains the contributions of top researchers from the US, the Asia-Pacific region and around the world. Sections are devoted to databases, algorithms, interfaces, visualization, modeling and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology. The book is an essential source of ideas, discoveries and references for academics in biocomputing, bioinformatics researchers and computer scientists.

Contents:

CONTENTS; Preface; BIOGEOMETRY APPLICATIONS OF COMPUTATIONAL GEOMETRY TO MOLECULAR STRUCTURE; Session Introduction A. Tropsha and H. Edelsbrunner; Classification of Non-Coding RNA Using Graph Representations of Secondary Structure Y. Karklin, R.F. Meraz, and S.R. Holbrook; 1. Introduction; 2. An Algorithm for Classification Based on Secondary Structure Topology; 2.1. Labeled Dual Graphs; 2.2. Marginalized Kernels for Labeled Dual Graphs; 3. Methods; 4. Results; 4.1. Single Family SVM; 4.2. Multi-class SVM; 5. Discussion; 6. Conclusion; Acknowledgments; References

An Adaptive Dynamic Programming Algorithm for the Side Chain Placement Problem A. Leaver-Fay, B. Kuhlman, and J. Snoeyink1. Introduction; 2. Methods; 2.1. Interaction Graph Formulation; 2.2. Dynamic Programming; 2.3. The Move Towards Large Rotamer Libraries; 2.4. Stiff Interactions; 2.5. Adaptive Dynamic Programming; 2.6. Irresolvable Collisions; 2.7. Error Analysis; 3. Results; 4. Discussion; 5. Future Work; Acknowledgements; References; Computational Design of Combinatorial Peptide Library for Modulating Protein-Protein Interactions X. Li and J. Liang; 1 Introduction; 2 Model and Methods

3 Results4 Discussion; References; Exploring Protein Folding Trajectories Using Geometric Spanners D. Russel and L. Guibas; 1 Introduction; 2 Representing Proteins Using Spanners; 2.1 Computation; 2.2 Spanners of Proteins; 3. Filtering Noise; 3.1 Matching Spanners; 3.2 Filtering Noise; 3.3 Segmenting Trajectories; 4 Encoding Spanners in One Dimension; 5 Understanding BBA5 Trajectories; 6 Future Work; Acknowledgments; References; ChainTweak: Sampling from the Neighbourhood of a Protein Conformation R. Singh and B. Berger; 1. Introduction; 1.1. Neighbourhood Sampling: The Right Representation?

1.2. Contributions2. Algorithm; 3. Results; 3.1. Performance Analysis; 3.2. Applications; 4. Discussion; References; Coarse and Reliable Geometric Alignment for Protein Docking Y. Wang, P. K. Agarwal, P. Brown, H. Edelsbrunner, and J. Rudolph; 1. Introduction; 2. Methods; 3. Results; 4. Discussion; Acknowledgement.; References; BIOMEDICAL ONTOLOGIES; Session Introduction O. Bodenreider, J.A. Mitchell, and A.T. McCray; Ontology Driven Dynamic Linking of Biology Resources S.K. Bechhofer, R.D. Stevens, and P.W. Lord; 1. Introduction; 2. GO; 3. COHSE; 4. COHSE+GO = GOHSE; 5. Discussion

AcknowledgmentsReferences; Non-Lexical Approaches to Identifying Associative Relations in the Gene Ontology O. Bodenreider, M. Aubry, and A. Burgun; 1. Introduction; 2. Datasets; 3. Methods; 3.1. Similarity in the vector space model; 3.2. Co-occurrence in annotation databases; 3.3. Association rule mining; 3.4. Evaluation; 4. Results; 4.1. Associations identified; 4.2. Overlap; 5. Discussion; Acknowledgments; References; GenesTrace: Phenomic Knowledge Discovery via Structured Terminology M.N. Cantor, I.N. Sarkar, O. Bodenreider, and Y.A. Lussier; 1. Introduction; 2. Methods; 2.1. Materials

2.2. General Steps of the GenesTrace Method

Notes:

Description based upon print version of record.

Includes bibliographical references.

ISBN:

9786611898502

9781281898500

1281898503

9789812702456

9812702458

OCLC:

815746076