title: Predicting binding sites by analyzing allosteric effects.
abstract: This chapter describes a method for analyzing the allosteric influence of molecular interactions on protein conformational distributions. The method, called Dynamics Perturbation Analysis (DPA), generally yields insights into allosteric effects in proteins and is especially useful for predicting ligand-binding sites. The use of DPA for binding site prediction is motivated by the following allosteric regulation hypothesis: interactions in native binding sites cause a large change in protein conformational distributions. Here, we review the reasoning behind this hypothesis, describe the math behind the method, and present a recipe for predicting binding sites using DPA.
authors: Department of Physiology and Biophysics, School of Life Science, Fudan University, Shanghai, China.
authors: Dengming
authors: D
authors: Ming
authors: Michael E
authors: ME
authors: Wall
mesh_terms: D000465:Algorithms; D000494:Allosteric Regulation / Q000502:physiology; D001665:Binding Sites; D008962:Models, Theoretical; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D011506:Proteins