The Research On Ligand-Protein Interaction Using Molecular Docking

The research of the interactions and the identification process between the protein and small molecule is now become a hot spot, and bioinformatics-based molecular docking technology is an effective means to the research of this issue. Molecular docking is to find the lowest energy conformation by the combination of the ligand and the receptor in their active area.There are two basic problems need to be solved in molecular docking method: The one is the evaluation of the compact combination degree between ligand and receptor ,and this problem can be solved by the evaluation function. The other is to find all the possible optimal combination ways between the ligands and receptors, this could be solved by optimization algorithm. In essence, molecular docking is a minimum value solving process using evaluation function as the objective function through the optimal algorithm.In this paper, firstly, introduced the interaction between the protein and the small molecule, elaborated the knowledge on the relevance of molecular docking theoretical, and then making the detailed comparison and evaluation of their advantages and disadvantages of the evaluation function and optimal algorithm in molecule docking process.Secondly, introduced Particle Swarm Optimization Algorithm (PSO) and Quantum-behaved Particle Swarm Optimization Algorithm (QPSO) in detail. After analysis of their advantages and disadvantages, proposed an improved algorithm which is merged QPSO and local search QPSO-LS and making the test by test function. The results show that the QPSO-LS is efficiency of PSO and QPSO.Thirdly, introduce the QPSO-LS into molecular docking as conformation research algorithm, and format the molecular docking program called QLDOCK. By a large number of the crystal structure of protein compound recovery tests, proved that QLDOCK had great search power in conformation space which is used QPSO-LS search algorithm. The accuracy of molecular docking is available over the existing protein and small molecule docking software-SODOCK.Finally, take QLDOCK as a tool, on the premise of the successful verification of the activity of lipase 1LGY using molecular docking method, researcher and analyzed the interaction between 1LGY and different chain length fatty acid ester, furthermore making the conclusion of the substrate specificity of the different chain length fatty acid ester by 1LGY.