title: Structure-based functional site recognition for p21-activated kinase 4.
abstract: Recently, many molecular modeling methods are being developed to better understand the principles underlying protein folding. In the present study, fully flexible dinucleotides d(pApA), d(pApC), d(pApG), d(pApT), d(pCpA), d(pCpC), d(pCpG), d(pCpT), d(pGpA), d(pGpC), d(pGpG), d(pGpT), d(pTpA), d(pTpC), d(pTpG) and d(pTpT) were docked onto the surface of p21-activated kinase 4 (PAK4) kinase domain. The results showed that automated docking was a useful tool to identify the functional sites of PAK4 and it may provide a theoretical basis for the interaction data obtained from previous experiments. Therefore, structure-based docking with fully flexible dinucleotide probes might be a good tool to predict and annotate the functional sites of enzymes.
authors.affiliation: Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Gang
authors.initials: G
authors.lastname: Wang
authors.forename: Yu
authors.initials: Y
authors.lastname: Sha
authors.forename: Dong-Mei
authors.initials: DM
authors.lastname: Zhao
authors.forename: Feng
authors.initials: F
authors.lastname: Li
authors.forename: Mao-Sheng
authors.initials: MS
authors.lastname: Cheng
mesh_terms: D001665:Binding Sites / Q000502:physiology; D018360:Crystallography, X-Ray; D062105:Molecular Docking Simulation / Q000379:methods*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship; D054462:p21-Activated Kinases / Q000737:chemistry* / Q000378:metabolism*
chemical_list: C116367:PAK4 protein, human; D054462:p21-Activated Kinases