Bridging the protein sequence-structure gap by structure predictions

Burkhard Rost, Chris Sander

Research output: Contribution to journalReview articlepeer-review

123 Scopus citations

Abstract

The problem of accurately predicting protein three-dimensional structure from sequence has yet to be solved. Recently, several new and promising methods that work in one, two, or three dimensions have invigorated the field. Modeling by homology can yield fairly accurate three-dimensional structures for approximately 25% of the currently known protein sequences. Techniques for cooperatively fitting sequences into known three-dimensional folds, called threading methods, can increase this rate by detecting very remote homologies in favorable cases. Prediction of protein structure in two dimensions, i.e. prediction of interresidue contacts, is in its infancy. Prediction tools that work in one dimension are both mature and generally applicable; they predict secondary structure, residue solvent accessibility, and the location of transmembrane helices with reasonable accuracy. These and other prediction methods have gained immensely from the rapid increase of information in publicly accessible databases. Growing databases will lead to further improvements of prediction methods and, thus, to narrowing the gap between the number of known protein sequences and known protein structures.

Original languageEnglish
Pages (from-to)113-136
Number of pages24
JournalAnnual Review of Biophysics and Biomolecular Structure
Volume25
DOIs
StatePublished - 1996
Externally publishedYes

Keywords

  • homology modeling
  • interresidue contacts
  • knowledge-based mean-force potentials
  • multiple alignments
  • secondary structure
  • solvent accessibility
  • threading
  • transmembrane helices

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