title: The dataset for protein-RNA binding affinity.
abstract: We have developed a non-redundant protein-RNA binding benchmark dataset derived from the available protein-RNA structures in the Protein Database Bank. It consists of 73 complexes with measured binding affinity. The experimental conditions (pH and temperature) for binding affinity measurements are also listed in our dataset. This binding affinity dataset can be used to compare and develop protein-RNA scoring functions. The predicted binding free energy of the 73 complexes from three available scoring functions for protein-RNA docking has a low correlation with the binding Gibbs free energy calculated from Kd.
authors.affiliation: Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
authors.forename: Xiufeng
authors.initials: X
authors.lastname: Yang
authors.forename: Haotian
authors.initials: H
authors.lastname: Li
authors.forename: Yangyu
authors.initials: Y
authors.lastname: Huang
authors.forename: Shiyong
authors.initials: S
authors.lastname: Liu
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D003625:Data Collection; D030562:Databases, Protein; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D040901:Proteomics; D012313:RNA / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D011506:Proteins; D016601:RNA-Binding Proteins; D012313:RNA
keywords: binding affinity benchmark; binding free energy; protein-RNA docking; scoring function