Exploring protein sequence space using knowledge-based potentials |
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Authors: | Babajide A Farber R Hofacker I L Inman J Lapedes A S Stadler P F |
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Affiliation: | Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universit?t Wien, W?hringerstrasse 17, A-1090 Vienna, Austria. |
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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. |
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