Application of Numerical Optimization Methods to Perform Molecular Docking on Graphics Processing Units

Abstract

An analysis of numerical optimization methods for solving a problem of molecular docking has been performed. Some additional requirements for optimization methods according to GPU architecture features were specified. A promising method for implementation on GPU was selected. Its implementation was described and performance and accuracy tests were performed.

Keywords

• gpgpu
• cuda
• molecular docking
• virtual screening
• ligand-protein docking