Biocomputing '98 : Proceedings of the Pacific Symposium Maui, Hawaii, U. S. A. 4-9 January, 1998

by Altman, Russ B.; Dunker, A. Keith; Hunter, Lawrence; Klein, Teri E.

• ISBN13: 9789810232788
• ISBN10: 9810232780
• Format: Hardcover
• Copyright: 1998-03-01
• Publisher: World Scientific Pub Co Inc

Summary

The Pacific Symposium on Biocomputing brings together key researchers from the international biocomputing community. PSB is designed to be maximally responsive to the need for critical mass in subdisciplines within biocomputing. These proceedings contain peer-reviewed articles in computational biology.

Table of Contents

Preface	v
GENE EXPRESSION AND GENETIC NETWORKS
Session Introduction	3	(3)
B. Bryant
A. Milosavljevic
R. Somogyi
Automated Assay of Gene Expression at Cellular Resolution	6	(12)
D. Kosman
J. Reinitz
D. H. Sharp
REVEAL, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures	18	(12)
S. Liang
S. Fuhrman
R. Somogyi
A Gene Network Approach to Modeling Early Neurogenesis in Drosophila	30	(12)
G. Marnellos
E. Mjolsness
Cluster Analysis and Data Visualization of Large-Scale Gene Expression Data	42	(12)
G. S. Michaels
D. B. Carr
M. Askenazi
S. Fuhrman
X. Wen
R. Somogyi
Rules for the Evolution of Gene Circuitry	54	(12)
M. A. Savageau
Modeling the Normal and Neoplastic Cell Cycle With ``Realistic Boolean Genetic Networks'': Their Application for Understanding Carcinogenesis and Assessing Therapeutic Strategies	66	(11)
Z. Szallasi
S. Liang
Qualitative Analysis of Gene Networks	77	(12)
D. Thieffry
R. Thomas
Genomic Regulation Modeled as a Network with Basins of Attraction	89	(14)
A. Wuensche
MOLECULES TO MAPS: TOOLS FOR VISUALIZATION AND INTERACTION IN COMPUTATIONAL BIOLOGY
Session Introduction	103	(3)
T. E. Ferrin
E. T. Kraemer
DINAMO: A Coupled Sequence Alignment Editor/Molecular Graphics Tool for Interactive Homology Modeling of Proteins	106	(12)
M. Hansen
J. Bentz
A. Baucom
L. Gregoret
A Prototype Molecular Interactive Collaborative Environment (MICE)	118	(12)
P. Bourne
M. Gribskov
G. Johnson
J. Moreland
S. Wavra
H. Weissig
Reusable Graphical Interface to Genome Information Resources	130	(12)
A. Grigoriev
Visualization Based on the Enzyme Commission Nomenclature	142	(11)
I. Shah
L. Hunter
Wavelet-Assisted Volume Ray Casting	153	(12)
T. He
Visualizing Nerve Cells with VolVis	165	(12)
A. Kaufman
A Virtual Laboratory Notebook for Simulation Models	177	(12)
A. J. Winfield
MAVIS: An Interactive Visualization Tool for Computational Chemistry Calculations in a Distributed Networked Environment	189	(12)
C. I. Parkinson
M. D. Cooper
W. T. Hewitt
I. H. Hillier
A High-throughput Graphics Library Designed for a Portable Molecular Structure Viewer	201	(12)
Y. Ueno
K. Asai
GENE STRUCTURE IDENTIFICATION IN LARGE-SCALE GENOMIC SEQUENCE
Session Introduction	213	(4)
E. C. Uberbacher
Y. Xu
An Editing Environment for DNA Sequence Analysis and Annotation	217	(11)
E. C. Uberbacher
Y. Xu
M. B. Shah
V. Olman
M. Parang
R. J. Mural
Recognition of Human Genes by Stochastic Parsing	228	(12)
K. Asai
K. Itou
Y. Ueno
T. Yada
Discrimination Study of Human Core-Promoters	240	(12)
M. Q. Zhang
Automatic Extraction of Position Specific Cooccurrence of Transcription Factor Bindings on Promoters	252	(12)
T. Tsunoda
T. Takagi
A. Computational ``Genome Walk'' Technique To Identify Regulatory Interactions in Gene Networks	264	(15)
A. Wagner
Deriving Ribosomal Binding Site (RBS) Statistical Models from Unannotated DNA Sequences and the Use of an RBS Model for N-terminal Prediction	279	(12)
W. S. Hayes
M. Borodovsky
The GAIA Software Framework for Genome Annotation	291	(12)
G. C. Overton
C. Bailey
J. Crabtree
M. Gibson
S. Fischer
J. Schug
MOLECULAR MODELING IN DRUG DESIGN AND BIOTECHNOLOGY
Session Introduction	303	(2)
J. Bajorath
T. E. Klein
T. P. Lybrand
Focus-2D: A New Approach to the Design of Targeted Combinatorial Chemical Libraries	305	(12)
S. J. Cho
W. Zheng
A. Tropsha
Surface Solid Angle-Based Site Points for Molecular Docking	317	(10)
D. K. Hendrix
I. D. Kuntz
Molecular Modeling Information Transfer with VRML: From Small Molecules to Large Systems in Bioscience	327	(12)
G. Moeckel
M. Keil
T. Exner
J. Brickmann
Empirical Free Energy Calculations on Phage 434 Repressor- and cro-DNA Complexes Support the `Indirect Readout' Hypothesis of Specificity	339	(10)
L. M. Brown
R. E. Bruccoleri
J. Novotny
The Object Technology Framework: An Object-Oriented Interface to Molecular Data and its Application to Collagen	349	(13)
C. C. Huang
G. S. Couch
E. F. Pettersen
T. E. Ferrin
A. E. Howard
T. E. Klein
Molecular Anchors with Large Stability Gaps Ensure Linear Binding Free Energy Relationships for Hydrophobic Substituents	362	(12)
P. A. Rejto
G. M. Verkhivker
PROTEIN STRUCTURE PREDICTION
Session Introduction	374	(3)
R. H. Lathrop
Combined Multiple Sequence Reduced Protein Model Approach to Predict the Tertiary Structure of Small Proteins	377	(12)
A. R. Ortiz
A. Kolinski
J. Skolnick
Using Constraint Programming for Lattice Protein Folding	389	(12)
R. Backofen
Are Binding Residues Conserved?	401	(12)
C. Ouzounis
C. Perez-Irratxeta
C. Sander
A. Valencia
Linear Programming Based Approach to the Derivation of a Contact Potential for Protein Threading	413	(12)
T. Akutsu
H. Tashimo
A Protein Conformational Search Space Defined by Secondary Structure Contacts	425	(12)
M. Parisien
F. Major
M. Peitsch
Thousands of Proteins Likely to Have Long Disordered Regions	437	(12)
P. Romero
Z. Obradovic
C. R. Kissinger
J. E. Villafranca
E. Garner
S. Guilliot
A. K. Dunker
Protein Model Determination from Crystallographic Data	449	(12)
K. Edgecombe
A. Ableson
K. Baxter
A. Chiverton
J. Glasgow
S. Fortier
THE RELATIONSHIP BETWEEN PROTEIN STRUCTURE AND FUNCTION, OR HOW HAVE PROTEINS OVER TIME DIVERGED IN FUNCTION?
Session Introduction	461	(2)
P. C. Babbitt
Statistical Significance of Ungapped Sequence Alignments	463	(10)
N. N. Alexandrov
V. V. Solovyev
Protein Disorder and the Evoluation of Molecular Recognition: Theory, Predictions, and Observations	473	(12)
A. K. Dunker
E. Garner
S. Guilliot
P. Romero
K. Albrecht
J. Hart
Z. Obradovic
C. Kissinger
J. E. Villafranca
Function Driven Protein Evolution. A Possible Proto-protein for the RNA-binding Proteins	485	(12)
J. S. Fetrow
A. Godzik
Recognizing Protein Binding Sites Using Statistical Descriptions of their 3D Environments	497	(12)
L. Wei
R. B. Altman
Modeling and Superposition of Multiple Protein Structures Using Affine Transformations: Analysis of the Globins	509	(12)
T. D. Wu
S. C. Schmidler
T. Hastie
D. L. Brutlag
COMPUTING WITH BIOMOLECULES
Session Introduction	521	(2)
P. Clote
M. Hagiya
T. Head
Color Recognition with Bacteriorhodopsin	523	(12)
M. Frydrych
P. Silfsten
S. Parkkinen
J. Parkkinen
T. Jaaskelainen
Bidirectional Sticker Systems	535	(12)
R. Freund
G. Paun
G. Rozenberg
A. Salomaa
Finite H-Systems with 3 Test Tubes are not Predictable	547	(12)
L. Priese
Y. Rogojine
M. Margenstern
COMPLEXITY AND INFORMATION-THEORETIC APPROACHES TO BIOLOGY
Session Introduction	559	(2)
D. L. Dowe
K. Prank
An Information Theoretic View of Gapped and Other Alignments	561	(12)
J. P. Schmidt
Application of a Novel and Fast Information-Theoretic Method to the Discovery of Higher-Order Correlations in Protein Databases	573	(12)
E. W. Steeg
H. Pham
An MML Classification of Protein Structure that Knows about Angles and Sequence	585	(12)
T. Edgoose
L. Allison
D. L. Dowe
Discovering Simple DNA Sequences by Compression	597	(12)
D. R. Powell
D. L. Dowe
L. Allison
T. I. Dix
Self-Assembling Automata: A Model of Conformational Self-Assembly	609	(12)
K. Saitou
On the Application of Information Theory to Neural Spike Trains	621	(12)
S. P. Strong
R. R. de Ruyter van Steveninck
W. Bialek
R. Koberle
Coding of Time-Varying Hormonal Signals in Intracellular Calcium Spike Trains	633	(12)
K. Prank
C. Schofl
L. Laer
M. Wagner
A. von Zur Muhlen
G. Brabant
F. Gabbiani
Coarse-Grained Entropy Rates Quantify Fast CA2+ Dynamics Modulated by Pharmacological Stimulation	645	(12)
M. Palus
C. Schofl
A. von Zur Muhlen
G. Brabant
K. Prank
Is the Hippocampus a Kalman Filter?	657	(12)
O. Bousquet
K. Balakrishnan
V. Honavar
Maximum A Posteriori Classification of DNA Structure from Sequence Information	669	(12)
D. M. Loewenstern
H. M. Berman
H. Hirsh
DISTRIBUTED AND INTELLIGENT DATABASES
Session Introduction	681	(2)
D. Frishman
DBGET/LinkDB: an Integrated Database Retrieval System	683	(12)
W. Fujibuchi
S. Goto
H. Migimatsu
I. Uchiyama
A. Ogiwara
Y. Akiyama
M. Kanehisa
Ontologies for Molecular Biology	695	(12)
S. Schulze-Kremer
Toward Information Extraction: Identifying Protein Names from Biological Papers	707	(12)
K. Fukuda
A. Tamura
T. Tsunoda
T. Takagi
ProClass Protein Family Database: New Version with Motif Alignments	719	(14)
C. H. Wu
S. Shivakumar
BUILDING BIOINFORMATION INFRASTRUCTURE IN THE PACIFIC RIM
Session Introduction	733	(2)
T. W. Tan
S. Subbiah
Development of Software Tools at Bioinformatics Centre (BIC) at the National University of Singapore (NUS)	735	(12)
P. R. Kolatkar
M. K. Sakharkar
C. R. Tse
B. K. Kiong
L. Wong
T. W. Tan
S. Subbiah
From Sequence to Structure to Literature: The Protocol Approach to Bioinformation	747	(12)
O. P. Wu
K. T. Seow
L. Wong
S. Y. Chung
S. Subbiah
Towards the Asia-Pacific Bioinformatics Network	759
H. Sugawara
S. Miyazaki