Cellular and Molecular Life Sciences

, 64:2505

Computational protein function prediction: Are we making progress?

Visions & Reflections (Minireview)

DOI: 10.1007/s00018-007-7211-y

Cite this article as:
Godzik, A., Jambon, M. & Friedberg, I. Cell. Mol. Life Sci. (2007) 64: 2505. doi:10.1007/s00018-007-7211-y


The computational prediction of gene and protein function is rapidly gaining ground as a central undertaking in computational biology. Making sense of the flood of genomic data requires fast and reliable annotation. Many ingenious algorithms have been devised to infer a protein’s function from its amino acid sequence, 3D structure and chromosomal location of the encoding genes. However, there are significant challenges in assessing how well these programs perform. In this article we explore those challenges and review our own attempt at assessing the performance of those programs. We conclude that the task is far from complete and that a critical assessment of the performance of function prediction programs is necessary to make true progress in computational function prediction.


Protein function predictionbioinformaticsCASPAFPaspartate dehydrogenaseaspartate oxidasenon-orthologous replacementNAD synthesis



Directed Acyclic Graph


Critical Assessment of Structure Prediction


Gene Ontology

Copyright information

© Birkhäuser Verlag, Basel 2007

Authors and Affiliations

  1. 1.Burnham Institute for Medical ResearchLa JollaUSA
  2. 2.University of California, San DiegoLa JollaUSA