July 10 – 14 , 1995, Dagstuhl Seminar 9528

Molecular Bioinformatics


D. Gustfield, T. Lengauer, C. Sander

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Dagstuhl-Seminar-Report 120


The seminar was a sequel to the first Dagstuhl Seminar on Molecular Bioinformatics which took place from Sep 7 to Sep 11, 1992 and brought together computer scientists and applied mathematicians with biochemists and molecular biologists in order to discuss possibilities of cooperation in the field of computer-aided design of biomolecular sequences and structures. Since that time, several developments have taken place in Germany and internationally. In Germany, BMBF (the Science Ministry) has funded a program on Molecular Bioinformatics. Within this program, eight large interdisciplinary projects are working on topics such as protein structure prediction, biomolecular docking, genomic databases, and RNA secondary and tertiary structure prediction. Internationally, efforts in computer science applications in molecular biology have increased significantly. Countries such as U. S. and Japan witness lively activity in these fields, albeit somewhat more concentrated on the genome itself than on genomic products such as proteins. Interaction between computer scientists and molecular biologists is intensifying, and a growing number of results are obtained with involvement of computer scientists. The topic of the seminar included research on both the genome and its products, with somewhat of a emphasis on genomic products and on the relationship between those two kinds of research than on the genome itself. As the previous seminar, this seminar concentrated on algorithmic issues and touch issues such as data handling technology, computer graphics etc. only insofar as they relate to algorithmic issues. In addition to the presentations, there was an evening tutorial on protein structures, a round of discussion on traditional and network-based teaching forms for bioinformatics, and a software demonstration. The general feelings of the participants were that after the ground-breaking character of the first seminar, this seminar was marked by an increased understanding and depth of communication between the CS and the molecular biology side. It was clearly evident that the two communities came to understand each other and began to develop a common feeling of identity.
The facilities and procedures at Dagstuhl as well as the unique concept of the Dagstuhl seminars were praised by many participants. The participants expressed the hope that this seminar be succeeded with another seminar on bioinformatics in due time. While a few of the participants expressed the wish to have future workshops more strongly focussed, say, just on alignment of sequences and structures, the majority of the participants welcomed the broadness of the workshop and felt that this width of scope should be maintained of some more time.


Monday, July 10
Tom Lengauer Welcome
Morning Session Chair: Tom Lengauer
John Kececioglu Genome Rearrangements
Gene Myers Developments in DNA Sequencing
Dan Gusfield Parametric Alignment
Afternoon Session Chair: Dan Gusfield
Ralf Zimmer Parametric Alignment
Kevin Karplus Using Simple Markov Models
Tandy Warnow Reconsidering the Construction of Evolutionary Trees
Steve Altschul Aspects of the Statistics of Local Sequence Comparison
Andreas Dress Visualization Procedures Related to Abstract Similarity Analysis, Quasi-Crystals and the Traveling Salesman Problem, Part I: Pictures
Evening Session Chair: Chris Sander
Chris Sander Tutorial on Protein Structures
Tuesday, July 11
Morning Session Chair: Steve Bryant
Andreas Dress Visualization Procedures Related to Abstract Similarity Analysis, Quasi-Crystals and the Traveling Salesman Problem, Part II: Proofs
Volker Brendel Application of Scoring in Sequence Comparison for Evolutionary Studies and Motif Recognition
Dalit Naor Amino-Acid Pair Interchanges at Spatially Conserved Locations
Joachim Selbig Clustering of Protein Structures on the Basis of Hexapeptides
Georg Casari Specific Functional Regions in Protein Families
Afternoon Session Chair: Chris Sander
Russ Altman Probabilistic Representations and Algorithms for Analysis of Structure
Liisa Holm Protein Structure Database Searches
Steve Bryant Finding the Most Surprising Structural Similarities
Ralf Thiele Threading by Recursive Dynamic Programming
Steve Bryant An Alignment Model and Fast Algorithms for Protein Threading
Evening Session Chair: Robert Giegerich
Giegerich, Shamir Teaching Computational Biology
Altman, Karplus -
Vingron, Myers -
Wednesday, July 12
Morning Session Chair: John Kececioglu
Mike Steel Generating New Phylogenetic Information from a Collection of Trees
Ron Shamir Physical Maps and Interval Graphs
Michael Gribskov An Evolutionary Mixture Model for Describing Protein Sequence Families
Ina Koch An Algorithm for Finding All Maximal Common Substructures and Its Application to Protein Structures
Thursday, July 13
Morning Session Chair: Martin Vingron
Norbert Blum On the Prediction of RNA Secondary Structure
Russ Altman Constraint Satisfaction Methods for Modeling the Complete 30S Ribosomal Subunit and its Interaction with Transfer DNA
Robert Giegerich Representing Large RNA Folding Landscapes
Dannie Durand Ultraselfish Genes in Mice
Hans-Peter Lenhof Protein-Protein Docking
Afternoon Session Chair: Dalit Naor
Matthias Rarey Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins
Thomas Seidl A Database System for Protein Docking
John Kececioglu Multiple Sequence Alignment
Gene Myers Rapid Similarity Search
Satoru Miyano BONSAI Garden: Parallel Knowledge Discovery System for Sequences
Matthias Rarey Demonstration: Docking
Friday, July 14
Morning Session Chair: Tandy Warnow
Thure Etzold Integration of Biological Flat File Databanks into an Object-Oriented Retrieval System
Jürgen Kleffe Loglinear Models for Splice Site Recognition
Martin Vingron Sequence Alignment and Phylogeny
Dan Gusfield How to Think About Repetitive Structures
Tom Lengauer Close and Goodbye


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