Sampling of Protein Conformations with Computers to Predict the Native Structure

Abstract

Native-structure prediction of proteins only from the aminoacid sequential information, without using information from a sequencestructure database of proteins, has not yet been succeeded. Computer simulation is now popular in protein conformational sampling for the prediction. The sampling is, however, hopelessly difficult when a conventional simulation technique (canonical molecular dynamics simulation) is used, because the conformation is frequently trapped in energy minima in the conformational space. This trapping makes the sampling efficiency considerable poor. I explain an efficient conformational sampling algorithm, multicanonical molecular dynamics simulation, recently developed. Results on the sampling of polypeptide chains showed that the conformation easily overcomes the energy barriers between the energy minima with using this method.