Genetic algorithms for protein tertiary structure prediction

  • Steffen Schulze-Kremer
Research Papers Genetic Algorithms
Part of the Lecture Notes in Computer Science book series (LNCS, volume 667)


This article describes the application of genetic algorithms to the problem of protein tertiary structure prediction. The genetic algorithm is used to search a set of energetically sub-optimal conformations. A hybrid representation of proteins, three operators MUTATE, SELECT and CROSSOVER and a fitness function, that consists of a simple force field were used. The prototype was applied to the ab initio prediction of Crambin. None of the conformations generated by the genetic algorithm are similar to the native conformation, but all show much lower energy than the native structure on the same force field. This means the genetic algorithm's search was successful but the fitness function was not a good indicator for native structure. In another experiment, the backbone was held constant in the native state and only side chains were allowed to move. For Crambin, this produced an alignment of 1.86 Å r.m.s. from the native structure.


genetic algorithm protein tertiary structure ab initio prediction 


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Copyright information

© Springer-Verlag Berlin Heidelberg 1993

Authors and Affiliations

  • Steffen Schulze-Kremer
    • 1
    • 2
  1. 1.Brainware GmbHBerlin 65
  2. 2.Institute of CrystallographyFree University BerlinBerlin 33Germany

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