Patrice Koehl
Department of Computer Science
Genome Center
Room 4319, Genome Center, GBSF
451 East Health Sciences Drive
University of California
Davis, CA 95616
Phone: (530) 754 5121

Computational Structural Biology: Winter 2024

What is Computational Biology?

"Is there a danger, in molecular biology, that the accumulation of data
will get so far ahead of its assimilation into a conceptual framework
that the data will eventually prove an encumbrance ?"
John Maddox, 1988

Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. The field is broadly defined and includes foundations in biology, applied mathematics, statistics, biochemistry, chemistry, biophysics, molecular biology, genetics, genomics, computer science and evolution.

Computational biology is different from biological computation, which is a subfield of computer science and computer engineering using bioengineering and biology to build computers, but is similar to bioinformatics, which is an interdisciplinary science using computers to store and process biological data.

The top 10 challenges in Bioinformatics

  1. Precise models of where and when transcription will occur in a genome (initiation and termination)
    ability to predict where and when transcription will occur in genome
  2. Precise, predictive models of alternative RNA splicing.
    ability to predict the splicing pattern of any primary transcript in any tissue
  3. Precise models of signal transduction pathways
    ability to predict cellular responses to external stimuli
  4. Determining protein:DNA, protein:RNA, protein:protein recognition codes
  5. Accurate ab-initio protein structure prediction
  6. Rational design of small molecule inhibitors of proteins
  7. Mechanistic understanding of protein evolution
    understanding exactly how new protein functions evolve
  8. Mechanistic understanding of speciation
    molecular details of how speciation occurs
  9. Development of effective gene ontologies
    systematic ways to describe gene and protein functions
  10. Education: development of bioinformatics curricula

Lecture Notes

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Further Reading

  Page last modified 19 February 2024