Computational evolution of a model polymer that folds to a specified target conformation.
Richard Judson · PubMed · 1996
A method is described for folding polymers to specific target conformations. The approach uses a fast but approximate dynamics algorithm, coupled with a genetic algorithm that is used to evolve the large number of free parameters needed. The dynamics algorithm uses a state transition matrix approach. At each time step, the distances between pairs of atoms are adjusted by shifting them from Dij to Dij + Sij where Sij is an element of the state transition matrix S. Atom pairs that are attractive have Sij 0. The atomic movement is carried out by gradient minimizing the molecular mechanics energy of the molecule subject to harmonic distance constraints. The method is applied to a simple test case, a 19 atom 2-D polymer. The paper also show that the S matrices can correctly fold a limited variety of initial conformations that differ from the one used during the evolution phase.