Pacific Symposium on Biocomputing 1997

The second Pacific Symposium on Biocomputing (PSB-97) has once again brought together key researchers from the international biocomputing community. The importance of biocomputing is now widely recognized, and a set of critical meetings has emerged providing access to peer-reviewed reports of exciting new techniques and results. The PSB has been designed to be maximally responsive to the need for critical mass in subdisciplines within biocomputing. For that reason, it is the only meeting whose tracks are defined dynamically ( in response to specific proposals) each year, organized by leaders in the emerging subdisciplines, and targeted to provide a forum for publication and discussion of research in biocomputing's "hot areas." In this way, PSB provides an early forum for serious examination of emerging methods and approaches.

As usual, the cultures of biology and computer science clash in the organization of a biocomputing meeting. The desire to have the latest ideas, the biggest names, and the most diverse attendance (typical of biology conferences) causes some to question the utility of providing rigorous peer review of the manuscripts (typical of computer science conferences). The organizers believe that the value of the proceedings to posterity rests on the quality of the review process. This year, every manuscript was examined by at least two anonymous reviewers (as well as the track organizers and meeting chairs), and some manuscripts were examined by as many as five reviewers when significant differences arose. We trust, therefore, that the proceedings will have significant scientific and academic legitimacy.

The session chairs performed admirably in soliciting high quality submissions, and moderating the review process. The organizers wish to thank the invited plenary speaker, Dr. I.D. Kunz, as well as the speakers invited by track organizers for particular track sessions. We would also like to thank Sharon Surles, Kevin Lauderdale, the Stanford Section on Medical Informatics, and the UCSF Computer Graphics Lab for excellent administrative and technical assistance.

The meeting was supported by grants from the National Science Foundation, the Department of Energy and the National Institutes of Health. In addition, corporate sponsors included Molecular Applications Group, Pharmacia & Upjohn. The PSB has now firmly established a tradition of success and excellence, and we look forward to future versions as biocomputing comes to maturity.

Pacific Symposium on Biocomputing, 1997 Co-Chairs:

Russ B. Altman, Section on Medical Informatics, Stanford University

Keith Dunker, Department of Biochemistry/Biophysics, Washington State University

Lawrence Hunter, National Library of Medicine, National Institutes of Health

Teri E. Klein, Department of Pharmaceutical Chemistry, University of California, San Francisco


PSB Proceedings For All Years


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Distributed and Intelligent Databases, P. Argos, H.-W Mewes and D. Frishman; Pacific Symposium on Biocomputing 2:3 (1997).

Modern Concepts in Molecular Modeling, J. Bajorath and T.E. Klein; Pacific Symposium on Biocomputing 2:4-5 (1997).

Extracting Biological Knowledge from DNA Sequences, F.M. De La Vega, D. Thieffry and J. Collado-Vides; Pacific Symposium on Biocomputing 2:6-7 (1997).

Understanding and Predicting Protein Structure, D. Fischer, A. Godzik, S. Chung, S. Subbiah and R. Lathrop; Pacific Symposium on Biocomputing 2:8-13 (1997).

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; Pacific Symposium on Biocomputing 2:14-15 (1997).

Computing with Biomolecules, T. Head and T. Yokomori; Pacific Symposium on Biocomputing 2:16-17 (1997).

Computation in Biological Pathways, P.D. Karp and M. Riley; Pacific Symposium on Biocomputing 2:18 (1997).

Biocomputing Education: Further Challenges, S.J. Johns and S.M. Thompson



New Challenges in Computational Biochemistry, B. Honig; Pacific Symposium on Biocomputing 2:21-24 (1997).



Computer Simulations of Prebiotic Evolution, V.I. Abkevich, A.M. Gutin and E.I. Shakhnovich; Pacific Symposium on Biocomputing 2:27-38 (1997).

Ubiquitous Distributed Objects with CORBA, F. Achard and E. Barillot; Pacific Symposium on Biocomputing 2:39-50 (1997).

Towards a Density Functional Treatment of Chemical Reactions in Complex Media, D.R. Berard, D. Wei and D.R. Salahub; Pacific Symposium on Biocomputing 2:51-61 (1997).

Combinatorial Tools for the Analysis of Transcriptional Regulation, A. Bergeron, E. Gaul and D. Bergeron; Pacific Symposium on Biocomputing 2:62-73 (1997).

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; Pacific Symposium on Biocomputing 2:74-84 (1997).

Using Tcl for Molecular Visualization and Analysis, A. Dalke and K Schulten; Pacific Symposium on Biocomputing 2:85-96 (1997).

On Some Operations Suggested by Genome Evolution, J. Dassow and V. Mitrana; Pacific Symposium on Biocomputing 2:97-108 (1997).

The Inverse Protein Folding Problem: Self Consistent Mean Field Optimisation of a Structure Specific Mutation Matrix, M. Delarue and P. Koehl; Pacific Symposium on Biocomputing 2:109-121 (1997).

Theoretical and Algorithmical Optimization of the Dead-End Elimination Theorum, J. Desmet, M. De Maeyer and I. Lasters; Pacific Symposium on Biocomputing 2:122-133 (1997).

Using Views for Retrieving Data from Extremely Heterogeneous Databanks, T. Etzold and G. Verde; Pacific Symposium on Biocomputing 2:134-141 (1997).

Length Scales of Lipid Dynamics and Molecular Dynamics, S.E. Feller and R.W. Pastor; Pacific Symposium on Biocomputing 2:142-150 (1997).

Specific Modelling of Regulatory Units in DNA Sequences, K. Frech and T. Werner; Pacific Symposium on Biocomputing 2:151-162 (1997).

Test Tube Systems with Cutting/Recombination Operations, R. Freund, E. Csuhaj-Varjú and F. Wachtler; Pacific Symposium on Biocomputing 2:163-174 (1997).

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; Pacific Symposium on Biocomputing 2:175-186 (1997).

Development of a Cell Signaling Networks Database, T. Igarashi and T. Kaminuma; Pacific Symposium on Biocomputing 2:187-197 (1997).

The Native Sequence Determines Sidechain Packing in a Protein, But Does Optimal Sidechain Packing Determine the Native Sequence?, P. Koehl and M. Delarue; Pacific Symposium on Biocomputing 2:198-209 (1997).

Design of Hydrophobic Core of E. Coli Malate Dehydrogenase Based on the Side-Chain Packing, H. Kono, M. Nishiyama, M. Tanokura and J. Doi;Pacific Symposium on Biocomputing 2:210-221 (1997).

Latent Periodicity of DNA Sequences of Many Genes, E.V. Korotkov and D.A. Phoenix;Pacific Symposium on Biocomputing 2:222-231 (1997).

Integrating Database Homology in a Probabilistic Gene Structure Model, D. Kulp, D. Haussler, M.G. Reese and F.H. Eeckman;Pacific Symposium on Biocomputing 2:232-244 (1997).

Packing as a Structural Basis of Protein Stability: Understanding Mutant Properties from Wildtype Structure, C. Lee and M. Levitt;Pacific Symposium on Biocomputing 2:245-255 (1997).

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;Pacific Symposium on Biocomputing 2:256-267 (1997).

Towards a Bacteriorhodopsin-Silicon Neuromorphic Photosensor, C.H. Martin, Z.P. Chen and R.R. Birge;Pacific Symposium on Biocomputing 2:268-279 (1997).

An Approach to Detection of Protein Structural Motifs Using an Encoding Scheme of Backbone Conformations, H. Matsuda, F. Taniguchi and A. Hashimoto;Pacific Symposium on Biocomputing 2:280-291 (1997).

An Algorithm to Assemble Pathways from Processes, J.E. Mittenthal;Pacific Symposium on Biocomputing 2:292-303 (1997).

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;Pacific Symposium on Biocomputing 2:304-315 (1997).

Method for Low Resolution Prediction of Small Protein Tertiary Structure, A.R. Ortiz, W.P. Hu, A. Kolinski and J. Skolnick;Pacific Symposium on Biocomputing 2:316-327 (1997).

Multiple Model Approach--Dealing with Alignment Ambiguities in Protein Modeling, K. Pawlowski, Jaroszewski, A. Bierzynski and A. Godzik;Pacific Symposium on Biocomputing 2:328-339 (1997).

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;Pacific Symposium on Biocomputing 2:340-351 (1997).

Algorithmic Complexity of Growth Hormone Release in Humans, K. Prank, M. Wagner and G. Brabant;Pacific Symposium on Biocomputing 2:352=360 (1997).

Exploring the Fitness Landscapes of Lattice Proteins, A. Renner and E. Bornberg-Bauer;Pacific Symposium on Biocomputing 2:361-372 (1997).

Accurate Mean-Force Pairwise-Residue Potentials for Discrimination of Protein Folds, B.A. Reva, A.V. Finkelstein, M.F. Sanner and A.J. Olson;Pacific Symposium on Biocomputing 2:373-384 (1997).

Real Time Surface Reconstruction for Moving Molecular Fragments, M.F. Sanner and A.J. Olson;Pacific Symposium on Biocomputing 2:385-396 (1997).

Finding Association Rules on Heterogeneous Genome Data, K. Satou, G. Shibayama, T. Ono, Y. Yamamura, E. Furuichi, S. Kuhara and T. Takagi;Pacific Symposium on Biocomputing 2:397-408 (1997).

Enumerating Suboptimal Alignments of Multiple Biological Sequences Efficiently, T. Shibuya and H. Imai;Pacific Symposium on Biocomputing 2:409-420 (1997).

Redox Properties of Cytochrome C: Novel Linear Response and Hybrid Continuum-Microscopic Methodologies, T. Simonson;Pacific Symposium on Biocomputing 2:421-431 (1997).

Protein Superfamily Members as Targets for Computer Modeling: The Carbohydrate Recognition Domain of a Macrophage Lectin, R.E. Stenkamp, A. Aruffo and J. Bajorath;Pacific Symposium on Biocomputing 2:432-440 (1997).

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;Pacific Symposium on Biocomputing 2:441-452 (1997).

Enumeration of Flux Routes Through Complex Biochemical Reactions, J. Wagg and P. Sellers;Pacific Symposium on Biocomputing 2:453-464 (1997).

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;Pacific Symposium on Biocomputing 2:465-476 (1997).

Transfac Database as a Bridge Between Sequence Data Libraries and Biological Function, E. Wingender, H. Karas and R. Knuppel;Pacific Symposium on Biocomputing 2:477-485 (1997).

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;Pacific Symposium on Biocomputing 2:486-497 (1997).