Pacific Symposium on Biocomputing '97

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

• ISBN13: 9789810230050
• ISBN10: 9810230052
• Format: Hardcover
• Copyright: 1996-03-01
• Publisher: World Scientific Pub Co Inc

Table of Contents

Preface	v
SESSION INTRODUCTIONS	3	(18)
Distributed and Intelligent Databases	3	(1)
P. Argos
H.-W Mewes
D. Frishman
Modern Concepts in Molecular Modeling	4	(2)
J. Bajorath
T.E. Klein
Extracting Biological Knowledge from DNA Sequences	6	(2)
F.M. De La Vega
D. Thieffry
J. Collado-Vides
Understanding and Predicting Protein Structure	8	(6)
D. Fischer
A. Godzik
S. Chung
S. Subbiah
R. Lathrop
Biopolymer Structures: Where Do They Come From? Where Are They Going? Evolutionary Perspectives on Biopolymer Structure and Function	14	(2)
R.A. Goldstein
E. Bornberg-Bauer
Computing with Biomolecules	16	(2)
T. Head
T. Yokomori
Computation in Biological Pathways	18	(3)
P.D. Karp
M. Riley
REVIEWS	21	(6)
New Challenges in Computational Biochemistry	21	(6)
B. Honig
FULL PAPERS (PEER REVIEWED)	27
Computer Simulations of Prebiotic Evolution	27	(12)
V.I. Abkevich
A.M. Gutin
E.I. Shakhnovich
Ubiquitous Distributed Objects with CORBA	39	(12)
F. Achard
E. Barillot
Towards a Density Functional Treatment of Chemical Reactions in Complex Media	51	(11)
D. Berard
D. Wei
D.R. Salahub
Combinatorial Tools for the Analysis of Transcriptional Regulation	62	(12)
A. Bergeron
E. Gaul
D. Bergeron
The Generalization Method of Relationships Among Nucleotide Sequences Reveals an Order in Assimilation of Amino Acid Codons During the Isoacceptor tRNAs Evolution	74	(11)
M.B. Chaley
E.V. Korotkov
Using Tel for Molecular Visualization and Analysis	85	(12)
A. Dalke
K. Schulten
On Some Operations Suggested by Genome Evolution	97	(12)
J. Dassow
V. Mitrana
The Inverse Protein Folding Problem: Self Consistent Mean Field Optimisation of a Structure Specific Mutation Matrix	109	(13)
M. Delarue
P. Koehl
Theoretical and Algorithmical Optimization of the Dead-End Elimination Theorem	122	(12)
J. Desmet
M. De Maeyer
I. Lasters
Using Views for Retrieving Data from Extremely Heterogeneous Databanks	134	(8)
T. Etzold
G. Verde
Length Scales of Lipid Dynamics and Molecular Dynamics	142	(9)
S.E. Feller
R.W. Pastor
Specific Modelling of Regulatory Units in DNA Sequences	151	(12)
K. Frech
T. Werner
Test Tube Systems with Cutting/Recombination Operations	163	(12)
R. Freund
E. Csuhaj-Varju
F. Wachtler
Organizing and Computing Metabolic Pathway Data in Terms of Binary Relations	175	(12)
S. Goto
H. Bono
H. Ogata
W. Fujibuchi
T. Nishioka
K. Sato
M. Kanehisa
Development of a Cell Signaling Networks Database	187	(11)
T. Igarashi
T. Kaminuma
The Native Sequence Determines Sidechain Packing in a Protein, But Does Optimal Sidechain Packing Determine the Native Sequence?	198	(12)
P. Koehl
M. Delarue
Design of Hydrophobic Core of E. Coli Malate Dehydrogenase Based on the Side-Chain Packing	210	(12)
H. Kono
M. Nishiyama
M. Tanokura
J. Doi
Latent Periodicity of DNA Sequences of Many Genes	222	(10)
E.V. Korotkov
D.A. Phoenix
Integrating Database Homology in a Probabilistic Gene Structure Model	232	(13)
D. Kulp
D. Haussler
M.G. Reese
F.H. Eeckman
Packing as a Structural Basis of Protein Stability: Understanding Mutant Properties from Wildtype Structure	245	(11)
C. Lee
M. Levitt
Facilities for Exploring Molecular Biology Databases on the Web: A Comparative Study	256	(12)
V.M. Markowitz
I.-M.A. Chen
A.S. Kosky
E. Szeto
Towards a Bacteriorhodopsin-Silicon Neuromorphic Photosensor	268	(12)
C.H. Martin
Z.P. Chen
R.R. Birge
An Approach to Detection of Protein Structural Motifs Using an Encoding Scheme of Backbone Conformations	280	(12)
H. Matsuda
F. Taniguchi
A. Hashimoto
An Algorithm to Assemble Pathways from Processes	292	(12)
J.E. Mittenthal
Toward a Virtual-Labo-System for Metabolic Engineering: Development of Biochemical Engineering System Analyzing Tool-Kit (BEST-KIT)	304	(12)
M. Okamoto
Y. Morita
D. Tominaga
K. Tanaka
N. Kinoshita
J.-I. Ueno
Y. Miura
Y. Maki
Y. Eguchi
Method for Low Resolution Prediction of Small Protein Tertiary Structure	316	(12)
A.R. Ortiz
W.P. Hu
A. Kolinski
J. Skolnick
Multiple Model Approach--Dealing with Alignment Ambiguities in Protein Modeling	328	(12)
K. Pawlowski
L. Jaroszewski
A. Bierzynski
A. Godzik
Search for DNA Conformational Features for Functional Sites. Investigation of the TATA Box	340	(12)
M.P. Ponomarenko
J.V. Ponomarenko
A.E. Kel
N.A. Kolchanov
Algorithmic Complexity of Growth Hormone Release in Humans	352	(9)
K. Prank
M. Wagner
G. Brabant
Exploring the Fitness Landscapes of Lattice Proteins	361	(12)
A. Renner
E. Bornberg-Bauer
Accurate Mean-Force Pairwise-Residue Potentials for Discrimination of Protein Folds	373	(12)
B.A. Reva
A.V. Finkelstein
M.F. Sanner
A.J. Olson
Real Time Surface Reconstruction for Moving Molecular Fragments	385	(12)
M.F. Sanner
A.J. Olson
Finding Association Rules on Heterogeneous Genome Data	397	(12)
K. Satou
G. Shibayama
T. Ono
Y. Yamamura
E. Furuichi
S. Kuhara
T. Takagi
Enumerating Suboptimal Alignments of Multiple Biological Sequences Efficiently	409	(12)
T. Shibuya
H. Imai
Redox Properties of Cytochrome C: Novel Linear Response and Hybrid Continuum-Microscopic Methodologies	421	(11)
T. Simonson
Protein Superfamily Members as Targets for Computer Modeling: The Carbohydrate Recognition Domain of a Macrophage Lectin	432	(9)
R.E. Stenkamp
A. Aruffo
J. Bajorath
Definite-Clause Grammars for the Analysis of CIS-Regulatory Regions in E. Coli	441	(12)
D. Thieffry
D.A. Rosenblueth
A.M. Huerta
H. Salgado
J. Collado-Vides
Enumeration of Flux Routes Through Complex Biochemical Reactions	453	(12)
J. Wagg
P. Sellers
Using the Radial Distribution of Physical Features to Compare Amino Acid Environments and Align Amino Acid Sequences	465	(12)
L. Wei
R.B. Altman
J.T. Chang
Transfac Database as a Bridge Between Sequence Data Libraries and Biological Function	477	(9)
E. Wingender
H. Karas
R. Knuppel
A New Approach to Protein Fold Recognition Based on Delaunay Tessellation of Protein Structure	486
W. Zheng
S.J. Cho
I.I. Vaisman
A. Tropsha