Abstract
The important functions that CDKs perform in cell division and cell cycle regulation made central protein kinase of Saccharomyces cerevisiae CDC28 a target model for structural and functional analysis. The 3D models of CDC28 protein kinase using molecular modeling techniques will enlarge our understanding of the phosphorylation mechanism and the structural changes of mutant kinases. The structural template for S. cerevisiae CDC28 was identified from PDB (Protein Databank) using BLASTP (basic local alignment search tool for proteins). Template-target alignments were generated for homology modeling and checked manually for errors. The models were then generated using MODELLER and validated using PROCHECK followed by energy minimization and molecular dynamics calculations in AMBER force field.
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Selwyne, R.A., Kholmurodov, K.T. & Koltovaya, N.A. Homology modeling of yeast cyclin-dependent protein kinase. Phys. Part. Nuclei Lett. 4, 339–342 (2007). https://doi.org/10.1134/S1547477107040085
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DOI: https://doi.org/10.1134/S1547477107040085