Pacific Symposium on Biocomputing '96: Hawaii, USA 3-6 January 1996

by Hunter, Lawrence; Klein, T. E. D.

• ISBN13: 9789810225780
• ISBN10: 9810225784
• Format: Hardcover
• Copyright: 1996-03-01
• Publisher: World Scientific Pub Co Inc

Table of Contents

Introduction
The Evolution of Biomolecular Structures and the Structure of Biomolecular Evolution	p. 3
Discovering, Learning, Analyzing and Predicting Protein Structure	p. 5
Stochastic Models, Formal Systems and Algorithmic Discovery for Genome Informatics	p. 9
Interactive Molecular Visualization	p. 11
Educational Issues in Biocomputing	p. 12
Internet Tools for Computational Biology	p. 14
Population Modelling	p. 16
Hybrid Quantum and Classical Mechanical Methods for Studying Biopolymers in Solution	p. 18
Control in Biological Systems	p. 20
Protein Structure Comparison using Representation by Line Segment Sequences	p. 25
Quaternion Contact Ribbons: A New Tool for Visualizing Intra- and Inter-molecular Interactions in Proteins	p. 41
Fast Protein Fold Recognition via Sequence to Structure Alignment and Contact Capacity Potentials	p. 53
A Programming Course in Bioinformatics for Computer and Information Science Students	p. 73
Massively Parallel Algorithms for Chromosome Reconstruction	p. 85
Structure Formation of Biopolymers is Complex, Their Evolution May be Simple	p. 97
RNA Pseudoknot Modeling Using Intersections of Stochastic Context Free Grammars with Applications to Database Search	p. 109
How Similar Must a Template Protein be for Homology Modeling by Side-Chain Packing Methods?	p. 126
Mixed Direct-Iterative Methods for Boundary Integral Formulations of Dielectric Solvation Models	p. 142
All Possible Protein Folds at Low Resolution	p. 160
DNA Computing Based on Splicing: Universarity Results	p. 179
Parallel Discrete Event Simulation of Lyme Disease	p. 191
Distance Education through the Internet: The GNA-VSNS Biocomputing Course	p. 203
Multfractals, Encoded Walks and the Ergodicity of Protein Sequences	p. 216
List Update Processing (LUP) - Solving the Database Update Problem	p. 230
Circular Clustering of Protein Dihedral Angles by Minimum Message Length	p. 242
An Object-Oriented Data-Driven Migration Model	p. 256
On the Definition and the Construction of Pockets in Macromolecules	p. 272
DNA Splicing Systems and Post Systems	p. 288
Assessing the Performance of Fold Recognition Methods by Means of a Comprehensive Benchmark	p. 300
Biocomputing Education by the Australian National Genomic Information Service	p. 319
Puzzle Pieces Defined: Locating Common Packing Units in Tertiary Protein Contacts	p. 331
Using Multiple Alignments and Phylogenetic Trees to Detect RNA Secondary Structure	p. 350
A Branch and Bound Algorithm for Local Multiple Alignment	p. 368
Beyond the Hyperactive Molecule: Search, Salvage and Visualization of Chemical Information from the Internet	p. 384
An Introductory Course in Computational Molecular Biology: Rationale, History, Observations and Course Description	p. 396
Visualisation in the SPROUT Molecular Design Program	p. 408
Computational Evolution of a Model Polymer that Folds to a Specified Target Conformation	p. 423
A Protocol for Maintaining Multidatabase Referential Integrity	p. 438
An Algorithm for Prediction of Structural Elements in Small Proteins	p. 446
Sequence Sizes of Eukaryotic Enzymes	p. 461
A High Performance System for Molecular Dynamics Simulations of Biomolecules Using a Special-Purpose Computer	p. 472
Correlating Structure-Dependent Mutation Matrices with Physical-Chemical Properties	p. 488
A Case Study Where Biology Inspired a Solution to a Computer Science Problem	p. 500
Protein Phylogenetic Inference using Maximum Likelihood with a Genetic Algorithm	p. 512
Ab Initio Calculations of Free Energy Barriers for Chemical Reactions in Solution: Proton Transfer in [FHF]-	p. 524
Mixed Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution and in Enzymes by the Classical Trajectory Mapping Approach	p. 539
Molecular Modeling of Protocellular Functions	p. 550
Analysis, Clustering and Prediction of the Conformation of Short and Medium Size Loops Connecting Regular Secondary Structure	p. 570
Computational Biology Instruction at the University of Washington Center for Bioengineering	p. 590
A Greedy Strategy for Finding Motifs from Yes-No Examples	p. 599
Statistical Geometry Analysis of Proteins: Implications for Inverted Structure Prediction	p. 614
Determination of Proton Transfer Rate Constants Using Ab Initio, Molecular Dynamics and Density Matrix Evolution Calculations	p. 624
Empirical Free Energy Calculations of Human Immunodeficiency Virus Type 1 Protease Crystallographic Complexes. II. Knowledge-Based Ligand-Protein Interaction Potentials Applied to the Thermodynamic Analysis of Hydrophobic Mutations	p. 638
Prediction of the Quaternary Structure of Coiled Coils: GCN4 Leucine Zipper and its Mutants	p. 653
3D Molecular Graphics on the World Wide Web	p. 663
Motif Identification Neural Design for Rapid and Sensitive Protein Family Search	p. 674
Extraction of Hidden Markov Model Representations of Signal Patterns in DNA Sequences	p. 686
A Simple Alignment Algorithm for Three-dimensional Protein Structures	p. 699
Conserved Biochemical Features Among Four Protease Molecules with no Structural or Sequential Homology	p. 701
A Library of Low-Variance Cores for Protein Families	p. 703
Motif Explorer - A tool for Interaction Exploration of Amino Acid Sequence Motifs	p. 705
GeneQuiz II: Automatic Function Assignment for Genome Sequence Analysis	p. 707
A Mutal Information Analysis of tRNA Sequence and Modification Patterns Distinctive of Species and Phylogenetic Domain	p. 710
tkDCSE, The Dedicated Comparitive Sequence Editor	p. 712
Motif Extraction Using an Improved Iterative Duplication Method for HMM Topology Learning	p. 713
MAGE as a Teaching Tool	p. 715
Handling Experimental Noise and Integrating Different Types of Data in Genomic Mapping	p. 717
A Fast Look-Up Algorithm for Detecting Repetitive DNA Sequences	p. 718
Molecular Inventor: Discovering Novel Compounds in a Collaborative Environment	p. 720
Fitting Flexible Ligands into Flexible Active Sites	p. 722
Chimera: An Extensible Molecular Modeling Application Constructed Using Standard Components	p. 724
Retrofitting Existing Applications and Authoring New Applications for the World Wide Web	p. 725
Strategy for de novo Computational Drug Design of HIV-1 PR Inhibitor	p. 728
An Electronic Laboratory Notebook Based on the World Wide Web	p. 730
A Notation of Amino Acid Conformations for Exploring Similar Protein Structures	p. 732
Biological Control in Tumor Growth	p. 734
Protein-Protein Docking Using Parametric Surface Representations	p. 736
Large Scale Sequencing Specific Neural Networks for Promotor and Splice Site Recognition	p. 737
Building of Self-Avoiding Lattice Models of Proteins Using a SCF-Optimization	p. 739
Increasing Accuracy of Energy Calculations of Lattice Models by Adjusting the Potentials	p. 741
Rapid Comparison and Classification of Protein 3D Structures Using One-Dimensional Structure Profiles	p. 743
A CoMFA Analysis of the Elastase Catalyzed Hydrolysis of Glycine Esters	p. 745
Application of a New Data Model and Visualization to Systematics	p. 746
A Parallel Computational Model of Attention and Saccade Generation in the Human Visual System	p. 748
An Automatic Configuration Algorithm of Discrete Hidden Markov Models for Amino Acid Sequences	p. 750
Quantitative Studies of Ligand-Receptor Interactions: A Rapid Evaluation of Binding Free Energies of Endothiapepsin to its Inhibitors	p. 752
Excited States of the Chromophores of the Photosynthetic Reaction Center from Rhodopseudomonas viridis: A QM/MM Study That Includes MM Polarization	p. 754
Virtual Communities at Interdisciplinary Boundaries	p. 756
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