Protein flexibility modeling using kernel based methods

Proteins play an essential role in nearly all cell functions such as composing cellular structure, promoting chemical reactions, carrying messages from one cell to another and acting as antibodies. The multiplicity of functions that proteins execute is attributed to their 3D conformational structures. Protein flexibility is an important link between protein structure and function. Understanding the conformational changes of a protein molecule is essential in discovering the protein structure and function relationships underlying most biological processes and has underappreciated implications in drug design. However, modeling protein flexibility is a very computationally challenging problem with a large number of degrees of freedom involved. In order to address this important challenge, the paper studies protein dynamics and develop a kernel based computational model to characterize protein conformational changes and to reduce the redundancy in protein conformers.