Pacific Symposium on Biocomputing -- Program & Final Announcement

Larry Hunter hunter at work.nlm.nih.gov
Wed Nov 1 19:14:34 EST 1995

		   ****   PSB '96 FINAL ANNOUNCEMENT ****

This is the program of the Pacific Symposium on Biocomputing to be held on
the Big Island of Hawaii, January 3-6, 1996.

For symposium registration information and forms, please see our web site at
http://cgl.ucsf.edu/psb or send email to psb at intsim.com


Minoru Kanehisa, Kyoto University:

   Logical Simulation of Biomolecular Information Pathways

David Weininger, DAYLIGHT Chemical Information Systems. 

   CEX and the Single Chemist 


* Internet Tools for Computational Biology 

* Biocomputing Education: Challenges and Opportunities 

* Interactive Molecular Visualization 

* Stochastic Models, Formal Systems and Algorithmic Discovery for Genome

* The Evolution of Biomolecular Structures and the Structure of Biomolecular
* Discovering, Learning, Analyzing and Predicting Protein Structure 

* Population Modelling 

* Models of Control Systems in Biology 
* Hybrid Quantum and Classical Mechanical Methods for Studying Biopolymers
  in Solution

* Computational Studies on the Design of Protease Inhibitors 


Tatsuya Akutsu and Hiroshi Tashimo, "Protein structure comparison using
representation by line segment sequences"

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

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

Erzsbet Csuhaj-Varj, Rudolf Freund, Lila Kari and Gheorghe Pun,
"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

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

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"

Eugene Kolker and Edward Trifonov, "Sequence Sizes of Eukaryotic Enzymes"

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

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]-" .

Nickolai N. Alexandrov, Ruth Nussinov, and Ralf M. Zimmer, "Fast protein
fold recognition via sequence to structure alignment and contact capacity

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

POSTER PRESENTATIONS (including live poster demonstrations):

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

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 P A tool for interaction exploration of Amino Acid Sequence

GeneQuiz 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

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

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."

Ajay Jain, "Flexible Molecular Docking: Scoring, Site Identification and
Database Searching."

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

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."

Seth Michelson, "Biological control in tumor growth."

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

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

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

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

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."

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."

Lawrence Hunter, PhD.
National Library of Medicine               phone: +1 (301) 496-9300
Bldg. 38A, 9th floor                       fax:   +1 (301) 496-0673
Bethesda. MD 20894 USA                     email: hunter at nlm.nih.gov
PGP 2.62 public key from http://www-swiss.ai.mit.edu/~bal/pks-toplev.html

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