title: A novel MHCp binding prediction model.
abstract: Many statistical and molecular mechanics models have been developed and tested for major histocompatibility complex peptide (MHCp) binding predictions during the last decade. The statistical model prediction using pooled peptide sequence data and three-dimensional modeling prediction by molecular mechanics calculations have been assessed for efficiency and human leukocyte antigen diversity coverage. We describe a novel predictive model using information gleaned from 29 human MHCp crystal structures. The validation for the new model is performed using four different sets of data: (1) MHCp crystal structures, (2) peptides with known IC(50) binding values, (3) peptides tested positive by tetramer staining, (4) peptides with known binding information at the MHCBN database. The model produces high prediction efficiencies (average 60 %) with good sensitivity (approximately 50%-73%) and specificity (52%-58%) values. The average positive predictive value of the model is 89%, while the average negative predictive value is only 18%. The efficiency is very high in predicting binders and very low in predicting nonbinders. This model is superior to many existing methods because of its potential application to any given MHC allele whose sequence is clearly defined.
authors: School of Mechanical and Production Engineering, Nanyang Centre for Supercomputing and Visualization, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639 798, Republic of Singapore.
authors: Bing
authors: B
authors: Zhao
authors: Venkatarajan Subramanian
authors: VS
authors: Mathura
authors: Ganapathy
authors: G
authors: Rajaseger
authors: Shabbir
authors: S
authors: Moochhala
authors: Meena Kishore
authors: MK
authors: Sakharkar
authors: Pandjassarame
authors: P
authors: Kangueane
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D006801:Humans; D008285:Major Histocompatibility Complex / Q000502:physiology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D010446:Peptide Fragments