A quantum chemical method for rapid optimization of protein structures.
A quantum chemical method for rapid optimization of protein structures is proposed. In this method, a protein structure is treated as an assembly of amino acid units, and the geometry optimization of each unit is performed with taking the effect of its surrounding environment into account. The optimized geometry of a whole protein is obtained by repeated application of such a local optimization procedure over the entire part of the protein. Here, we implemented this method in the MOPAC program and performed geometry optimization for three different sizes of proteins. Consequently, these results demonstrate that the total energies of the proteins are much efficiently minimized compared with the use of conventional optimization methods, including the MOZYME algorithm (a representative linear-scaling method) with the BFGS routine. The proposed method is superior to the conventional methods in both CPU time and memory requirements.
Wada
Mitsuhito
M
Makuhari R&D Center, Celestar Lexico-Sciences, Inc., Makuhari Techno Garden D17, 1-3 Nakase, Mihama-ku, Chiba 261-8501, Japan.
Sakurai
Minoru
M
D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins