Based On The Effective Distance Of Protein Hydrophobic Residues Simulated Annealing Method

The prediction of protein folding and protein structure is one of the most challenging researches in bioinformatics and is very important for farther understanding of protein structure and protein function.As an accessorial method,computer simulation could be directly applied to protein design and research.Because of the importance of theory and application,this work is paid more and more attention.When more and more stochastic algorithms being applied,their special advantages on solving protein folding are also discovered.Especially the SA method,which doesn't be influenced by local energy minimum,is attracting growing interest from people.A lot of new SA methods are becoming the main tools of protein folding simulations.In this paper,all work are developed based on HP model(3-dimensional hydrophobic -hydrophilic model).At first,the relations between the hydrophobic residues were discussed and a result,two hydrophobic residues fulfill the relation of |x_i-x_j|+|y_i-y_j|+|z_i-z_j|=|i-j|-2n(n=1,2,3...) if they contri- bute a HH bond,was gained.And then,the valid- correlative-matrix was induced based on above relations.Finally,the valid- distance-matrix was educed from the valid-corre-lative-matrix and the valid-distances were applied as a restriction in the SA-V.At the end of paper,the SA-V were applied in some protein sequence,via analysis of process of SA-V and contrast the results of SA-V and other algorithms mentioned in this paper,astringency of energy of SA-V is better than other algorithms mentioned.At the same time,the tentative conforms of SA-V were more valid than other algorithms mentioned and probability of producing invalid was largely reduced because of introducing restriction of valid-distances.So SA-V can find out lowest energy valid conform,that mean the spending of time is less than other algorithms mentioned in this paper.