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Proteins: Structure, Function and Evolution

Pacific Symposium on Biocomputing 2002
January 3-7, 2002
Kauai Marriott Resort and Beach Club


Problems related with the protein structure determination problem have dominated work in computational biology, from the very inception of this field. New computational advances, such as that currently underway with IBM's Blue Gene supercomputer (projected completion in 2005), as well as advances in the understanding of energy potentials and development of statistical methods for recognition of specific folds or protein classes, together promise better methods for protein structure prediction. Indeed, we have recently witnessed enormous progress in the field of protein folding, including successful approaches to computational structure prediction as documented in recent CASP competitions.

On a different front, advances in evolutionary genomics have led to efforts to mine the evolutionary history of proteins, in order to better understand the structure and function of proteins. Indeed, in developing methods for optimal extraction of structure and functional prediction from multiple sequences, there is a growing realization that proper evolutionary analysis is an essential component. Extensions of neutral evolution theory have led to the development of more complex models for the adaptive landscape of protein mutation and selection, leading to interactive efforts, where model predictions of computational biologists can be tested in the laboratory by molecular biologists.

The prediction of protein structure has been a major focus of biophysical research over the last two decades, There is a growing realization that the historical information, the sequence diversity available in databanks, is extremely useful in solving the protein folding problem. Even neural network methods perform better when multiple and diverse sequences are included in the analysis. The patterns of variation and conservation throughout a homologous sequence set provide signals indicating the underlying shared structure. Analyzing the presence of co-evolving sites in proteins is beginning to make important contributions to the solution as analytical methods improve, as are more refined estimates of the tendencies of different secondary structures and hydrophobic environments to have different substitution rates. Sophisticated methods for detecting amino acid residues under diversifying selective pressure across closely related species are generating interesting hypotheses about the structure and function of the protein, which can be tested in the laboratory. The methods and accuracy of phylogenetic inference have also been improving, and with that has come a better understanding of the effect of phylogenetic inference (and sequence alignment) on inferences of substitutional and coevolutionary patterns. We now have the ability to recreate ancestral proteins, and thus test general trends in protein function and hypothetical correlated functional relationships. In vitro evolution, both random and directed, can attempt to replicate the historical patterns, and further elucidate the details of the adaptive landscape.

Topics in the CALL FOR PAPERS


The organizers are P. Clote, G. Naylor, E. Shakhnovich and Z. Yang. You can contact each of the organizers below for more details.

Submission Information

Submissions are due: 16 July 2001
Decisions are announced: 20 August 2001
Camera ready copy due: 24 September 2001
Poster abstracts due: 5 November 2001
Further general information

All papers must be submitted to in electronic format. The file formats we accept are: postscript (*.ps), adobe acrobat (*.pdf) and Microsoft Word documents (*.doc). Attached files should be named with the last name of the first author (e.g., altman.pdf, or altman.doc).

Hardcopy submissions or unprocessed TEX or LATEX files will be rejected without review.

Each paper must be accompanied by a cover letter. The cover letter must state the following:

  • The email address of the corresponding author
  • The specific PSB session that should review the paper or abstract
  • The submitted paper contains original, unpublished results, and is not currently under consideration elsewhere.
  • All co-authors concur with the contents of the paper.

Submitted papers are limited to twelve (12) pages in our publication format. Please format your paper according to instructions found at If figures can not be easily resised and placed precisely in the text, then it should be clear that with appropriate modifications, the total manuscript length would be within the page limit.