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Exploring Protein Sequence Space Using Knowledge-Based Potentials

Author

Listed:
  • Aderonke Babajide
  • Robert Farber
  • Ivo L. Hofacker
  • Jeff Inman
  • Alan S. Lapedes
  • Peter F. Stadler

Abstract

Knowledge-based potentials can be used to decide whether an amino acid sequence is likely to fold into a prescribed native protein structure. We use this idea to survey the sequence-structure relations in protein space. In particular, we test the following two propositions which were found to be important for efficient evolution: The sequences folding into a particular native fold form extensive neutral networks that percolate through sequence space. The neutral networks of any two native folds approach each other to within a few point mutations. Computer simulations using two very different potential functions, M.Sippl's PROSA pair potential and a neural network based potential, are used to verify these claims. Submitted to Prot.Sci.

Suggested Citation

  • Aderonke Babajide & Robert Farber & Ivo L. Hofacker & Jeff Inman & Alan S. Lapedes & Peter F. Stadler, 1998. "Exploring Protein Sequence Space Using Knowledge-Based Potentials," Working Papers 98-11-103, Santa Fe Institute.
    • Handle: RePEc:wop:safiwp:98-11-103
    as

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