Computational evolution of a model polymer that folds to a specified target conformation.
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 and pairs that are repulsive have S ij > 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.
Judson
R
R
Center for Computational Engineering, Sandia National Laboratories, Livermore, CA 94551-0969, USA. rsjuds@ca.sandia.gov
D000465:Algorithms; D003198:Computer Simulation; D019143:Evolution, Molecular; D008956:Models, Chemical; D008957:Models, Genetic; D008958:Models, Molecular; D008968:Molecular Conformation; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D011506:Proteins