PSB '97 Papers

Session Introductions

Distributed and Intelligent Databases
P. Argos, H.-W Mewes and D. Frishman

Modern Concepts in Molecular Modeling
J. Bajorath and T.E. Klein

Extracting Biological Knowledge from DNA Sequences
F.M. De La Vega, D. Thieffry and J. Collado-Vides

Understanding and Predicting Protein Structure
D. Fischer, A. Godzik, S. Chung, S. Subbiah and R. Lathrop

Biopolymer Structures: Where Do They Come From? Where Are They Going? Evolutionary Perspectives on Biopolymer Structure and Function
R.A. Goldstein and E. Bornberg-Bauer

Computing with Biomolecules
T. Head and T. Yokomori

Computation in Biological Pathways
P.D. Karp and M. Riley


New Challenges in Computational Biochemistry
B. Honig

Full Papers (peer reviewed)

Computer Simulations of Prebiotic Evolution
V.I. Abkevich, A.M. Gutin and E.I. Shakhnovich

Ubiquitous Distributed Objects with CORBA
F. Achard and E. Barillot

Towards a Density Functional Treatment of Chemical Reactions in Complex Media
D.R. Berard, D. Wei and D.R. Salahub

Combinatorial Tools for the Analysis of Transcriptional Regulation
A. Bergeron, E. Gaul and D. Bergeron

The Generalization Method of Relationships Among Nucleotide Sequences Reveals an Order in Assimilation of Amino Acid Codons During Isoacceptor tRNAs Evolution
M.B. Chaley and E.V. Korotkov

Using Tcl for Molecular Visualization and Analysis
A. Dalke and K Schulten

On Some Operations Suggested by Genome Evolution
J. Dassow and V. Mitrana

The Inverse Protein Folding Problem: Self Consistent Mean Field Optimisation of a Structure Specific Mutation Matrix
M. Delarue and P. Koehl

Theoretical and Algorithmical Optimization of the Dead-End Elimination Theorem
J. Desmet, M. De Maeyer and I. Lasters

Using Views for Retrieving Data from Extremely Heterogeneous Databanks
T. Etzold and G. Verde

Length Scales of Lipid Dynamics and Molecular Dynamics
S.E. Feller and R.W. Pastor

Specific Modelling of Regulatory Units in DNA Sequences
K. Frech and T. Werner

Test Tube Systems with Cutting/Recombination Operations
R. Freund, E. Csuhaj-Varja and F. Wachtler

Organizing and Computing Metabolic Pathway Data in Terms of Binary Relations
S. Goto, H. Bono, H. Ogata, W. Fujibuchi, T. Nishioka, K. Sato and M. Kanehisa

Development of a Cell Signaling Networks Database
T. Igarashi and T. Kaminuma

The Native Sequence Determines Sidechain Packing in a Protein, But Does Optimal Sidechain Packing Determine the Native Sequence?
P. Koehl and M. Delarue

Design of Hydrophobic Core of E. Coli Malate Dehydrogenase Based on the Side-Chain Packing
H. Kono, M. Nishiyama, M. Tanokura and J. Doi

Latent Periodicity of DNA Sequences of Many Genes
E.V. Korotkov and D.A. Phoenix

Integrating Database Homology in a Probabilistic Gene Structure Model
D. Kulp, D. Haussler, M.G. Reese and F.H. Eeckman

Packing as a Structural Basis of Protein Stability: Understanding Mutant Properties from Wildtype Structure
C. Lee and M. Levitt

Facilities for Exploring Molecular Biology Databases on the Web: A Comparative Study
V.M. Markowitz, I-M.A. Chen, A.S. Kosky and E. Szeto

Towards a Bacteriorhodopsin-Silicon Neuromorphic Photosensor
C.H. Martin, Z.P. Chen and R.R. Birge

An Approach to Detection of Protein Structural Motifs Using an Encoding Scheme of Backbone Conformations
H. Matsuda, F. Taniguchi and A. Hashimoto

An Algorithm to Assemble Pathways from Processes
J.E. Mittenthal

Toward a Virtual-Labo-System for Metabolic Engineering: Development of Biochemical Engineering System Analyzing Tool-Kit (BEST-KIT)
M. Okamoto, Y. Morita, D. Tominaga, K. Tanaka, N. Kinoshita, J-I. Ueno, Y. Miura, Y. Maki and Y. Eguchi

Method for Low Resolution Prediction of Small Protein Tertiary Structure
A.R. Ortiz, W.P. Hu, A. Kolinski and J. Skolnick

Multiple Model Approach-Dealing with Alignment Ambiguities in Protein Modeling
K. Pawkowski, K. Jaroszewski, A. Bierzynski and A. Godzik

Search for DNA Conformation Features for Function Sites. Investigation of the TATA Box
M.P. Ponomarenko, J.V. Ponomarenko , A.E. Kel and N.A. Kolchanov

Algorithmic Complexity of Growth Hormone Release in Humans
K. Prank, M. Wagner and G. Brabant

Exploring the Fitness Landscapes of Lattice Proteins
A. Renner and E. Bornberg-Bauer

Accurate Mean-Force Pairwise-Residue Potentials for Discrimination of Protein Folds
B.A. Reva, A.V. Finkelstein, M.F. Sanner and A.J. Olson

Real Time Surface Reconstruction for Moving Molecular Fragments
M.F. Sanner and A.J. Olson

Finding Association Rules on Heterogeneous Genome Data
K. Satou, G. Shibayama, T. Ono, Y. Yamamura, E. Furuichi, S. Kuhara and T. Takagi

Enumerating Suboptimal Alignments of Multiple Biological Sequences Efficiently
T. Shibuya and H. Imai

Redox Properties of Cytochrome C: Novel Linear Response and Hybrid Continuum-Microscopic Methodologies
T. Simonson

Protein Superfamily Members as Targets for Computer Modeling: The Carbohydrate Recognition Domain of a Macrophage Lectin
R.E. Stenkamp, A. Aruffo and J. Bajorath

Definite-Clause Grammars for the Analysis of CIS-Regulatory Regions in E. Coli
D. Thieffry, D.A. Rosenblueth, A.M. Huerta, H. Salgado and J. Collado-Vides

Enumeration of Flux Routes Through Complex Biochemical Reactions
J. Wagg and P. Sellers

Using the Radial Distribution of Physical Features to Compare Amino Acid Environments and Align Amino Acid Sequences
L. Wei, R.B. Altman and J.T. Chang

Transfac Database as a Bridge Between Sequence Data Libraries and Biological Function
E. Wingender, H. Karas and R. Knoppel

A New Approach to Protein Fold Recognition Based on Delaunay Tessellation of Protein Structure
W. Zheng, S.J. Cho, I.I. Vaisman and A. Tropsha