Data processing: structural design – modeling – simulation – and em – Simulating nonelectrical device or system – Biological or biochemical
Reexamination Certificate
2011-03-08
2011-03-08
DeJong, Eric S. (Department: 1631)
Data processing: structural design, modeling, simulation, and em
Simulating nonelectrical device or system
Biological or biochemical
C702S019000, C703S012000
Reexamination Certificate
active
07904283
ABSTRACT:
The present invention provides for the first time a quantum mechanics-based method for scoring protein-ligand interactions and binding affinity predictions, using quantum mechanical Hamiltonians and/or a combined quantum mechanical/molecular mechanical approach, and Poisson-Boltzmann (PB)-based solvation methods. Also provided is a method for using quantum mechanics to describe the enthalpic and solvation effects of binding. The method comprises comparing the calculated binding affinities to experimental values in order to measure the success of the method. The methods disclosed herein may further be used to score protein and drug or protein and inhibitor interactions. The present method can predict the free energy of binding of protein-ligand complexes with high accuracy so as to enable lead optimization, thus serving as a powerful tool in computational drug design.
REFERENCES:
patent: 5612894 (1997-03-01), Wertz
patent: 5726014 (1998-03-01), Edwards et al.
patent: 5995908 (1999-11-01), Pullen
patent: 6178334 (2001-01-01), Kolossvary
patent: 6185548 (2001-02-01), Schwartz et al.
Beck et al. “Some Biological Applications of Semiempirical MO Theory” Perspectives in Drug Discovery and Design (1998) pp. 131-159.
Massova et al. “Combined molecular mechanical and continuum solvent approach to (MM-PBSA/GBSA) to predict ligand binding” Perspectives in Drug discovery and Design (2000) vol. 18, pp. 113-135.
Pang et al. “EUDOC: A Computer Program for Identification of Drug Interaction Sites in Macromolecules and Drug Leads from Chemical Databases” Journal of Computational Chemistry (2001) vol. 22, pp. 750-1771.
Vincent et al. “Parallel implementation of a divide and conquer semiemperical algorithm” Theoretical Chemistry Accounts (1998) vol. 99, pp. 220-223.
Gao, J. The hydration and solvent polarization effects of nucleotide bases. Biophysical Chemistry. 1994, vol. 51, pp. 253-261.
Khandogin et al. Quantum Mechanical Characterization of Nucleic Acids in Solution: A Linear-Scaling Study of Charge Fluctuations in DNA and RNA. J. Phys. Chem. 2002, vol. 106, pp. 7693-7703.
Zheing et al. Statistical Survey of Transition States and Conformational Substrates of the Sperm Whale Myoglobin—CO Reaction System. J. Chem. Soc. 1996, vol. 118, pp. 2818-2824.
Merz, Jr. Kenneth M.
Raha Kaushik
DeJong Eric S.
Johnson, Esq. Barbara E.
The Penn State Research Foundation
LandOfFree
Quantum mechanics based method for scoring protein-ligand... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Quantum mechanics based method for scoring protein-ligand..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Quantum mechanics based method for scoring protein-ligand... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-2669391