IBM and NeSC workshop on Protein Science
National e-Science Centre, Edinburgh, March
15-16 2002
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Accurate Quantum-Chemical Modeling of Ultra-large Protein Systems. Victor M. Anisimov, Nikolai Anikine, Vladislav Bugaenko, Vladimir Bobrikov, Alexey Andreyev. Quantum Biochemistry Group, Krakow, Poland. Traditional drug design is based on structure-activity relationship prediction derived mainly from molecular structure of small drug candidates. This approach leaves uncovered complex questions regarding reaction mechanisms, multiple reaction steps, and structure and property of produced intermediates. The latter to be mentioned may have chemical properties very different from the properties of the initial molecule. Accurate investigation of reaction mechanisms requires enormous computer power as conventional semiempirical methods give unsatisfactory accuracy and therefore non-empirical calculations have to be involved. In response to this challenge our group has developed Advanced Lagrange Multiplier method, as a core technique for very fast semiempirical calculations, and FSP Hamiltonian, a protein optimized semiempirical functional, providing accuracy in prediction of electrostatic molecular properties near to quality of correlated non-empirical calculations. With this in total we demonstrate calculation of 1 000 000 atom model linear polypeptide system built from randomly ordered aminoacids. The calculation time of a molecular wavefunction for a frozen geometry took 12 hours on a single CPU IBM compatible personal computer under Microsoft Windows operating system, opening thus new perspectives for quantum chemical modeling of real life viruses and their interactions with live cells. |
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