Data processing: structural design – modeling – simulation – and em – Simulating nonelectrical device or system – Biological or biochemical
Reexamination Certificate
2011-07-19
2011-07-19
Borin, Michael (Department: 1631)
Data processing: structural design, modeling, simulation, and em
Simulating nonelectrical device or system
Biological or biochemical
C702S019000
Reexamination Certificate
active
07983887
ABSTRACT:
The present invention provides a method utilizing primary amino acid sequence of a protein, energy minimization, molecular dynamics and protein vibrational modes to predict three-dimensional structure of a protein. The present invention also determines possible intermediates in the protein folding pathway. The present invention has important applications to the design of novel drugs as well as protein engineering. The present invention predicts the three-dimensional structure of a protein independent of size of the protein, overcoming a significant limitation in the prior art.
REFERENCES:
patent: 4853871 (1989-08-01), Pantoliano
patent: 5241470 (1993-08-01), Lee
patent: 5260882 (1993-11-01), Blanco
patent: 5265030 (1993-11-01), Skolnick
patent: 5436850 (1995-07-01), Eisenberg
patent: 5553004 (1996-09-01), Gronbech-Jensen
patent: 5557535 (1996-09-01), Srinivasan
patent: 5579250 (1996-11-01), Balaji
patent: 5600571 (1997-02-01), Friesner
patent: 5680319 (1997-10-01), Rose
patent: 5740072 (1998-04-01), Still
patent: 5784294 (1998-07-01), Platt
patent: 5842151 (1998-11-01), Noguchi
patent: 5878373 (1999-03-01), Cohen
patent: 5884230 (1999-03-01), Srinivasan
patent: 6178384 (2001-01-01), Kolossvary
patent: 6512981 (2003-01-01), Eisenberg
patent: 6797482 (2004-09-01), Woods
patent: 6832162 (2004-12-01), Floudas
patent: 6882939 (2005-04-01), Homans
patent: 6968275 (2005-11-01), Shackleford
patent: 2002/0137118 (2002-09-01), Inouye
patent: 2002/0150906 (2002-10-01), Debe
patent: 2003/0130797 (2003-07-01), Skolnick
patent: 2003/0135331 (2003-07-01), Hogue
patent: 2003/0158672 (2003-08-01), Ramnarayan
patent: 2004/0083061 (2004-04-01), Hannah
patent: 2004/0096897 (2004-05-01), Zhou
patent: 2004/0215400 (2004-10-01), Slovic
patent: 2004/0219601 (2004-11-01), Xu
patent: 2005/0009735 (2005-01-01), Kim
patent: 2005/0053999 (2005-03-01), Gough
patent: 2005/0069954 (2005-03-01), Sakai
patent: 2005/0090991 (2005-04-01), Dawson
patent: 2005/0112683 (2005-05-01), Reiner
patent: 2006/0019318 (2006-01-01), Lingappa
Higo et al. Protein Engineering vol. 10 No. 4 pp. 373-380, 1997.
Go et al. Proc. Nati Acad. Sci. USA, vol. 80, pp. 3696-3700, Jun. 1983.
Krim et al. Faraday Discuss., 1994,99,181-197.
Tasumi et al. Biopolymers, vol. 21, 711-714, 1982.
Moritsugu et al. Phys. Chem. B, 2005, 109 (24), pp. 12182-12194.
Agarwal, Pratul K., “Enzymes: An Integrated View of Structure, Dynamics and Function”,Microbial Cell Factories, vol. 5, No. 2, pp. 1-12 (2006).
Agarwal et al., “Protein Dynamics and Enzymatic Catalysis: Investigating the Peptidyl-Prolyl Cis-Trans Isomerization Activity of Cyclophilin A”,Biochemistry, vol. 43, No. 33, pp. 10605-10618 (2004).
Carnevali et al., “Fast Protein Structure Prediction Using Monte Carlo Simulations with Modal Moves”,J. Am. Chem. Soc., vol. 125, pp. 14244-14245 (2003).
Chen et al., “A Directed Essential Dynamics Simulation of Peptide Folding”,Biophysical Journal, vol. 88, pp. 3276-3285 (2005).
Delarue et al., “On the Use of Low-Frequency Normal Modes to Enforce Collective Movements in Refining Macromolecular Structural Models”,Proceedings of the National Academy of Sciences of the United States of America, vol. 101, pp. 6957-6962 (2004).
Eisenmesser et al., “Enzyme Dynamics During Catalysis”,Science, vol. 295, pp. 1520-1523 (2002).
Zhang et al., “Molecular Dynamics Simulations of Peptides and Proteins with Amplified Collective Motions”,Biophysical Journal, vol. 84, pp. 3583-3593 (2003).
Zheng et al., “Modeling Protein Conformational Changes by Iterative Fitting of Distance Constraints Using Reoriented Normal Modes”,Biophysical Journal, vol. 90, pp. 4327-4336 (2006).
Zheng et al., “Low-Frequency Normal Modes That Describe Allosteric Transitions in Biological Nanomachines are Robust to Sequence Variations”,Proceedings of the National Academy of Sciences of the United States of America, vol. 103, pp. 7664-7669 (2006).
Borin Michael
Scully , Scott, Murphy & Presser, P.C.
UT-Battelle LLC
LandOfFree
Fast computational methods for predicting protein structure... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Fast computational methods for predicting protein structure..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Fast computational methods for predicting protein structure... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-2723692