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.
ErzsZbet Csuhaj-Varjœ, 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. Matsuda, 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
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.