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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