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Human Genome News, May 1994; 6(1)

Computational Molecular Biology Workshop

The third international workshop on Open Problems of Computational Molecular Biology was held July 11-25, 1993, in Telluride, Colorado. The meeting was organized by Andrzej Konopka (BioLingua Research) and Peter Salamon (San Diego State University), with Danielle Konings (University of Colorado, Boulder) as meeting coordinator. The workshop was sponsored by the DOE Human Genome Program, Convex Computer Corporation, and BioLingua Research. Presentations and discussions focused on the four topics highlighted below.

Foundational Issues. Participants identified two logical problems with modeling techniques used in molecular biology. These problems result from lack of methods to (1) judge the formal correctness of sentences that contain ill-defined terms and (2) determine the degree to which a given model corresponds to the modeled phenomenon. This degree of correspondence is generally similar to what logicians call "material adequacy" of a model or definition.

Discussion revealed that the problem of formal correctness is solvable, at least in principle, by employing new mathematical methods (e.g., fuzzy logic) known from the fields of artificial intelligence, system theory, and pattern recognition. Participants were pessimistic, however, about inventing a general methodology for determining material adequacy. Some attendees pointed out that methods of addressing this problem on a case-by-case basis can and should be developed. Others suggested that such techniques should explore situation logic rather than classical, sentence-based logic. Another strategy would require creation of a new information theory based on language pragmatics instead of syntax. How much the two approaches overlap has been hotly debated, but conclusions have not been reached thus far.

Mathematical Modeling. Several discussions and presentations focused on (1)statistical approaches to determine biological significance of sequence and structural patterns in biopolymers, (2) new results concerning local compositional complexity of nucleotide and protein sequences, and (3 new mathematical models of molecular evolution, including classification of evolutionary landscapes and design of algorithms for traversing them.

Computational Issues. A number of new algorithms for sequence analysis, physical mapping of chromosomes, and sequencing by hybridization (SBH) were presented and discussed to facilitate the following.

  • Estimation of protein-coding density in unannotated nucleotide sequences.
  • Technique for determining coordinated changes in protein multiple-sequence alignments.
  • Method to determine distant repeats in protein sequences.
  • Software library for physical mapping of chimeric clones.
  • Vocabulary of elementary RNA structures.
  • Design of a low-redundancy SBH chip that can be miniaturized without sacrificing resolving power.

Structure Predictions. Methods were discussed for predicting protein folding pathways using hydrogen-exchange nuclear magnetic resonance experiments. A new protocol for configuring protein side chains in homology modeling also attracted considerable attention.

Collaborations. As in previous years, the workshop promoted collaborations among scientists from different fields and geographical locations. Topics include local compositional complexity of nucleotide and protein sequences, evolving rugged landscapes, mapping the space of RNA sequences into the space of secondary structures, and correlating surface contraction and expansion waves with differentiation in embryos of some species.

[Andrzej K. Konopka (BioLingua Research) and Peter Salamon (San Diego State University)]

Completed work initiated during the workshop and invited papers have undergone extensive peer review and will be published in the third special issue of Computers and Chemistry [18(3), 1994] devoted to computational molecular biology.

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Human Genome Program, U.S. Department of Energy, Human Genome News (v6n1).

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