Electronic Proceedings for the 1996 Pacific Symposium on Biocomputing

The proceedings should be cited as:

"Biocomputing: Proceedings of the 1996 Pacific Symposium," edited by Lawrence Hunter and Teri Klein, World Scientific Publishing Co, Singapore, 1996.

Session Introductions

R.A. Goldstein and R.B. Altman, The Evolution of Biomolecular Structures and the Structure of Biomolecular Evolution.

Kiyoshi Asai, Tom Head, Katsumi Nitta and Takashi Yokomori, Stochastic Models, Formal Systems and Algorithmic Discovery for Genome Informatics.

Chris Henn and Michael Teschner, Interactive Molecular Visualization.

Steven M. Thompson, Susan J. Johns and A. Keith Dunker, Educational Issues in Biocomputing.

R. Doelz, Internet Tools for Computational Biology.

John S. Conery and Ross Kiester, Population Modelling.

B.R. Brooks, M.J. Field, J. Gao and M.A. Thompson, Hybrid Quantum and Classical Mechanical Methods for Studying Biopolymers in Solution.

Seth Michelson, Control in Biological Systems.

Full papers (peer reviewed)

Tatsuya Akutsu and Hiroshi Tashimo, Protein structure comparison using representation by line segment sequences (abstract)

Kurt Albrect, John Hart, Alex Shaw and A. Keith Dunker, Quaternion Contact Ribbons: a New Tool for Visualizing Intra- and Inter-molecular Interactions in Proteins.

Nickolai N. Alexandrov, Ruth Nussinov and Ralk M. Zimmer, Fast Protein Fold Recognition via Sequence to Structure Alignment and Contact Capacity Potentials.

Russ B. Altman and John Koza, A Programming Course in Bioinformatics for Computer and Information Science Students.

Suchendra M. Bhandarkar, Sridhar Chirravuri, Jonathan Arnord and David Whitmire Massively Parallel Simulated Annealing Algorithms for Chromosome Reconstruction via Clone Ordering.

Erich Bornberg-Bauer, Structure Formation of Biopolymers is Complex, Their Evolution may be Simple.

Michael Brown and Charles Wilson, RNA Pseudoknot Modeling Using Intersections of Stochastic Context Free Grammars with Applications to Database Search.

Su Yun Chung and S. Subbiah, How similar must a template protein be for homology modeling by side-chain packing methods?

Steven A. Corcelli, Joel D. Kress, Lawrence R. Pratt and Gregory Tawa, Mixed Direct-Iterative Methods for Boundary Integral Formulations of Dielectric Solvation Models.

Gordon Crippen and Vladimir Maiorov, All possible protein folds at low resolution.

ErzsŽbet Csuhaj-Varjś, Rudolf Freund, Lila Kari and Gheorghe P‹un, DNA Computing Based on Splicing: Universarity Results.

Ewa Deelman, Thomas Caraco, and Boleslaw K. Szymanski, Parallel Discrete Event Simulation of Lyme Disease

Francisco M. De La Vega, Robert Giegerich and Georg Fuellen, Distance Education through the Internet: The GNA-VSNS Biocomputing Course

T. Gregory Dewey and Bonnie J. Strait, Multfractals, Encoded Walks and the Ergodicity of Protein Sequences.

Reinhard Doelz and Florian Eggenberger, List Update Processing (LUP) - Solving the database update problem

David L. Dowe, Lloyd Allison, Trevor Dix, Lawrence Hunter, Chris S. Wallace and Timothy Edgoose, Circular Clulstering of Protein Dihedral Angles by Minimum Message Length.

Keith Downing, An Object-Oriented Data-Driven Migration Model.

Herbert Edelsbrunner, Michael Facello and Jie Liang, On the Definition and the Construction of Pockets in Macromolecules.

C. Ferretti and S. Kobayashi , DNA Splicing Systems and Post Systems.

Daniel Fischer, Arne Elofsson, Danny Rice and David Eisenberg, Assessing the performance of fold recognition methods by means of a comprehensive benchmark.

Bruno A. Gaeta, Carolyn A. Bucholtz, Rowena Campbell, Camson Huynh, Stephanie Kim, and Alex H. Reisner, Biocomputing Education by the Australian National Genomic Information Service.

K.M. Gernert, L.D. Bergman, B.D. Thomas, J.C. Plurad, J.S. Richardson, D.C. Richardson and L.D. Bergman, Puzzle Pieces Defined: Locating Common Packing Units in Tertiary Protein Contacts

Brad Gulko and David Haussler, Using Multiple Alignments and Phylogenetic Trees to Detect RNA Secondary Structure.

Paul Horton, A Branch and Bound Algorithm for Local Multiple Alignment

Wolf-Dietrich Ihlenfeldt and Johann Gasteiger, Beyond the Hyperactive Molecule: Search, Salvage and Visualization of Chemical Information from the Internet.

Susan J. Johns, Steve M. Thompson, and A.Keith Dunker, An Introductory Course in Computational Molecular Biology: Rationale, History, Observations and Course Description.

A. Peter Johnson and Zsolt Zsoldos, Visualisation in the SPROUT molecular design program.

Richard Judson, Computational Evolution of a Model Polymer that Folds to a Specified Target Conformation

Peter Karp, A Protocol for Maintaining Multidatabase Referential Integrity

Andrzej Kolinski, Jeffrey Skolnick and Adam Godzik, An algorithm for prediction of structural elements in small proteins

Y. Komeiji, H. Yokoyama, M. Uebayasi, M. Taiji, T. Fukushige, D. Sugimoto, R.Takata, A Shimizu and K. Itsukashi, A high performance system for molecular dynamics simulations of biomolecules using a special-purpose computer

J. M. Koshi and R. A. Goldstein, Correlating Mutation Matrices with Physical-Chemical Properties

John R. Koza and David Andre, A Case Study Where Biology Inspired a Solution to a Computer Science Problem.

H. Matsua, Protein Phylogenetic Inference using Maximum Likelihood with a Genetic Algorithm

Richard P. Muller and Arieh Warshel, Ab Initio Calculations of Free Energy Barriers for Chemical Reactions in Solution: Proton Transfer in [FHF]- .

Jiann-Jong Pan and Jenn-Kang Hwang, Mixed Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution and in Enzymes by the Classical Trajectory Mapping Approach .

Andrew Pohorille, Christophe Chipot, Michael H. New, and Michael A. Wilson, Molecular Modeling of Protocellular Functions

Stephen D. Rufino, Luis E. Donate, Luc Canard, and Tom L. Blundell, Analysis, clustering and prediction of the conformation of short and medium size loops connecting regular secondary structure

Junko Shimura, Satoru Miyazaki, Sachiko Hirose, Toshikazu Shirai and Hideaki SugawaraSomatic mutations in immunoglobulin V gene determine the structure and function of the protein -- evidence from homology modelling

E. Swanson and T. P. Lybrand, Computational Biology Instruction at the University of Washington Center for Bioengineering

Erika Tateishi and Satoru Miyano, A Greedy Strategy for Finding Motifs from Yes-No Examples

A. Tropsha, R. K. Singh, I. I. Vaisman and W. Zheng, Statistical Geometry Analysis of Proteins: Implications for inverted structure prediction

David Van Der Spoel and Herman J.C. Berendsen, Determination of Proton Transfer Rate Constants Using Ab Initio, Molecular Dynamics and Density Matrix Evolution Calculations

Gennady Verkhivker, 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

Michal Vieth, Andrzej Kolinski, Charles L. Brooks, III, and Jeffrey Skolnick, Prediction of the quaternary structure of coiled coils: GCN4 leucine zipper and its mutants

H. Vollhardt and J. Brickmann, 3D Molecular Graphics on the World Wide Web

Cathy H. Wu, Hsi-Lien Chen, Chin-Ju Lo and Jerry W. McLarty, Motif Identification Neural Design for Rapid and Sensitive Protein Family Search

Tetsushi Yada, Masato Ishikawa, Hidetoshi Tanaka and Kiyoshi Asai, Extraction of Hidden Markov Model Representations of Signal Patterns in DNA Sequences

Short Abstracts

Tatsuya Akutsu, A Simple Alignment Algorithm for Three-dimensional Protein Structures.

Russ B. Altman and Steven C. Bagley, Conserved biochemical features among four protease molecules with not structural or sequential homology.

Russ B. Altman, Robert Schmidt and Mark Gerstein, A library of low-variance cores for protein families.

Paul Bieganski, John Riedl, John Carlis and Ernest F. Retzel, Motif Explorer: A tool for interaction exploration of Amino Acid Sequence Motifs.

Ondine Harris Callan, On-Yee So and David C. Swinney, A New Mathematical Model of Slow-Binding Enzyme Inhibition

Georg Casari, Christos Ouzounis, Alfonso Valencia and Chris SanderGeneQuiz II: Automatic Function Asignment for Genome Sequence Analysis.

Fancisco M. De La Vega, Carlos Cerpa, Gabriel Guarneros and Robert M. Farber, A Mutal Information Analysis of tRNA seqeuence and modification patterns distinctive of species and phylogentic domain.

P. De Rijk and R. De Wachter, tkDCSE, The dedicated comparitive sequence editor.

Christopher Dubay and William Hersh Creating a curriculum for a Masters of Science program in Medical Informatics that develops biomedical computing skills.

Christopher J. Dubay, David Zimmerman and Bradley Popovich Protocol Modeling in a Laboratory Information Management System

Yukiko Fujiwara, Minoru Asogawa and Akihiko Konagaya, Motif extraction using an improved iterative duplication method for HMM topology learning.

K.M. Gernert, J.S. Richardson and D.C. Richardson, MAGE as a teaching tool.

Andrei Grigoriev, Richard Mott and Hans Lehrach, Handling experimental noise and integrating different types of data in genomic mapping.

X. Guan and E. Uberbacher, A fast lookup algorithm for detecting repetitive DNA sequences.

Chris Henn and Michael Teschner, Molecular Inventor: Discovering novel compounds in a collaborative environment.

C. N. Hodge, Z.W. Wasserman, P.F.W. Stouten, B.A. Luty and C. Liang, Fitting Flexible ligands into flexible active sites.

Conrad C. Huang, Gregory S. Couch, Eric F. Pettersen and Thomas E. Ferrin, Chimera: An extensible molecular modelling application constructed using standard components.

Peter D. Karp and Suzanne M. Paley, Retrofitting existing applications and authoring new applications for the World Wide Web.

F. Lebon, Strategy for de novo computational drug design of HIV-1 PR inhibitors.

J.E. Marstaller and M. D. Zorn, An electronic laboratory notebook based on the World Wide Web.

H. Matsuda, F. Taniguchi and A. Hashimoto, A notation of amino acid conformations for exploring similar protein structures.

Kenneth M. Merz Jr.Development and Application of Quantum Mechanical/Molecular Mechanical Coupled Potentials

Seth Michelson, Biological control in tumor growth.

Yoshihiko Nishibata, Chiaki Fukushima, Momi Murase and Toshikazu Miyagishima A New Approach to Peptide Ligand Design Based on Atom-by-atom de novo Design

Arthur J. Olson and Bruce S. Duncan, Protein-protein docking using parametric surface representations.

Matthias Rarey, Bernd Kramer, Christoph Bernd, and Thomas Lengauer Time-Efficient Docking of Similar Flexible Ligands

Martin G. Reese, Nomi L. Harris and Frank H. Eeckman, Large scale sequencing specific neural networks for promotor and splice site recognition.

B. A. Reva, A. V. Finkelstein, D. S. Rykunov and A. J. Olson, Building of self-avoidingt lattice models of proteins using a SCF-optimization

Michel F. Sanner, Boris A. Reva, Alexei V. Finkelstein and Arthur J. Olson, Increasing accuracy of energy calculations of lattice models by adjusting the potentials.

R. K. Singh, D. L. Hoffman and A. Tropsha, Rapid comparison and classification of protein 3D structures using one-dimensional structure profiles.

Wayne E. Steinmetz, Steve Cotton and Cynthia D. Selassie, A CoMFA analysis of the elastase catalyzed hydrolysis of glycine esters.

Hideaki Sugawara, Junko Shimura, Satoru Miyazaki, Yoshihiro Masuda and Yasuhiro Ishitobi, Application of a new data model and visualization to systematics.

Barnabas Takacs, A parallel computational model of attention and saccade generation in the human visual system.

Hidetoshi Tanaka, An automatic configuration algorithm of discrete hidden Markov models for amino acid sequences.

Holly Tao, Zhen Tao Chu and Arieh Warshel, Quantitative studies of ligand-receptor interactions: A rapid evaluation of binding free energies of endothiapepsin to its inhibitors.

Mark A. Thompson and Gregory K, Schenter, Excited states of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis: A QM/MM study that includes MM polarization.

Iosif I. Vaisman, Virtual communities at interdisciplinary boundaries.

V.A. Vavilin, S.V. Rytov and L.Ya. LokshinaSimulation Model and User-friendly Computer Program METHANE as a Tool for Effective Biogas Production During Anaerobic Conversion of Complex Organic Matter

Please send additions and corrections to: