Prediction Of Protein Structure Based On Van Der Waals Potential Energy

The genetic information of organisms is stored in DNA and expressed through proteins whose functions are determined by their structures.Solving the problem of how the amino acid sequence of a protein determines its spatial structure will theoretically help people better understand the whole process of genetic information from DNA to protein,thus deepen the understanding of the life process and promote the development of life science.In practical application,it will help people understand the mechanism of genetic diseases and infectious diseases,so as to design drugs with specific therapeutic functions to tackle various diseases,and help people design proteins with specific biological functions according to their own needs.Therefore,the prediction of protein structure is one of the core problems in the neighborhood of bioinformatics.Van der Waals force is the mutual attraction or repulsion force between molecules.Different from covalent bonds and ionic bonds,Van der Waals force is caused by polarization coupling between close molecules and atoms.Proteins in natural state have compact internal structure,and Van der Waals force plays an irreplaceable role in short-range effect.Therefore,in order to predict protein structure more accurately and truly,a mathematical optimization model based on Van der Waals force potential energy is established in this paper.Therefore,protein structure prediction is transformed into a mathematical optimization problem.Through further analysis of mathematical optimization model,it is found that this problem is a NP-hard problem,so heuristic algorithm is considered to solve it.Genetic algorithm is an adaptive global search algorithm,which has the advantage of not depending on the problem model and has better search ability,so it has the advantage that other optimization algorithms can not have,but the traditional GA also has the disadvantage of easily falling into local optimum.In this paper,a new crossover probability and mutation probability were constructed to solve the problem that the traditional genetic algorithm is easy to fall into local optimum.In addition,in order to improve the efficiency of protein structure prediction,the concept of adjusting operator was introduced and the genetic algorithm was further improved.In this paper,the improved genetic algorithm was used to solve the protein structure in two-dimensional three-direction,two-dimensional four-direction and three-dimensional six-direction respectively.By comparing the optimal protein structure with the optimal protein structure calculated by HP model,it can be seen that it is feasible to use Van der Waals force potential energy function as a mathematical model,and genetic algorithm has great potential in protein structure prediction.