Protein Domain Boundary Prediction APBioNET蛋白质结构域边界预测 APBioNet.pptVIP

Protein Domain Boundary Prediction Which model is best? What is Protein Domain? Domains can be seen as distinct functional and/or structural units of a protein. Independent folding unit of a polypeptide chain also carries specific function. Domains are often identified as recurring (sequence or structure) units, which may exist in various contexts. 1IGR: First three domain protein / 1998 Domain 1: L domain (Magenta) Domain 2: Growth factor receptor domain (Brown) Domain 3: L domain (Green) PDB: 1IGR Introduction Domains provide one of the most valuable information for the prediction of protein structure, function, evolution and design. Since Anfinsen’s (1973) seminal work, many have proposed various structure prediction models from amino acid sequence only. This study, - Provides an overview of the modeling methods for protein domain boundary prediction. - Proposes an new semi-parametric model that can show superior performance to the existing models. Motivation Accurate prediction of domain boundaries forms a basis of many types of protein research. - New proteins such as chimeric proteins can be created as they are composed of multifunctional domains (Suyama Ohara, 2003). - The search method for templates used in comparative modeling can also be optimized by the delineation of domain boundaries (Contreras-Moreira Bates, 2002). - As for threading methods, the domain boundary prediction can improve its performance by enhancing the signal-to-noise ratio (Wheelan et al., 2000). - Accurate identification of domain boundaries for homologous domains plays a key role for reliable multiple sequence alignment (Gracy Argos, 1998). Problem Statement Limitations of experimental tools X-ray crystallography Nuclear Magnetic Resonance (NMR) Costly, time consuming, laborious and inefficient 3D coordinates to 1D amino acids Assumption: a domain has relatively more contacts within itself than with residues in the remainder of the structure