Optimizing strategies research on the later stage of protein structure model

Homology modeling is the most widely used and fully developed method for protein structure prediction. Researchers of this field paid great attention to either improvement of modeling method or update of modeling algorithm in the past while ignoring the fact that different structure optimizing methods could contribute to the accuracy of the final structure as well. Lip8 was chosen as an example to find out the influences of different optimizing methods. After a initial Lip8 model was built by the method of homology modeling, four ways were applied to optimize the model based on two different strategies called 'grade unpacking' and 'fitting together'. Each of these ways was considered under two different conditions: with periodic bounded cubic (PBC) water surrounded or without, which resulted in 8 optimized structures all together. Procheck, Errat, Profile 3D and Ramachandran plot were used to evaluate each final model. From the results, we found that 'grade unpacking' strategy combining with molecular dynamics optimization under explicit water could get a better model.