Method and system for protein modeling

Details Method and system for protein modeling Method and system for protein modeling

1996-06-14

1999-03-16

Feisee, Lila

Data processing: measuring, calibrating, or testing

Measurement system in a specific environment

Chemical analysis

702 19, 702 27, 530300, 530350, G06F 1900, C07K 500, C07K 1400

Patent

active

058842306

ABSTRACT:
A method in a computer system for modeling a three-dimensional structure of a model protein is provided. In one embodiment, the modeling is based upon a three-dimensional structure of a template protein and an amino acid sequence alignment of the model protein and the template protein. For each amino acid in the model protein, when the template protein has an amino acid aligned with the amino acid of the model protein, the position of the backbone atom of the amino acid of the model protein is established based on the position of a topologically equivalent backbone atom in the aligned amino acid of the template protein. In another embodiment, the modeling of a variable region of the model protein is based on a collection of .psi. and .phi. angle values for amino acid pairs in a family of proteins. In a further embodiment, these .psi. and .phi. angle values are classified according to a tetramer of adjacent amino acids and filtered based on a most probable conformation of portions of the variable region of the model protein.

REFERENCES:
patent: 4881175 (1989-11-01), Ladner
patent: 4908773 (1990-03-01), Pantoliano et al.
patent: 5025388 (1991-06-01), Cramer, III et al.
patent: 5241470 (1993-08-01), Lee et al.
patent: 5260882 (1993-11-01), Blanco et al.
patent: 5307287 (1994-04-01), Cramer, III et al.
patent: 5420805 (1995-05-01), Still et al.
patent: 5436850 (1995-07-01), Eisenberg et al.
patent: 5557535 (1996-09-01), Srinivasan et al.
J. Moult and M.N.G. James. Proteins: Structure, Function and Genetics. 1:146-163 (1986), Dec. 1986.
W.R. Taylor. J. Mol. Biol. 188 233-258, 1986.
B.R. Brooks et al. Journal of Computational Chemistry vol. 4, No. 2, 187-217 (1983).
New Riverside University Dictionary, A.H. Soukhanov (Editor), The Riverside Publishing Company 1988.
Brooks et al., "CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations," Journal of Computational Chemistry, vol. 4, No. 2, 1983, pp. 187-217.
Srinivasan, Subhashini et al., "Multistep Modeling of Protein Structure: Application to Bungarotoxin," International Journal of Quantum Chemistry: Quantum Biology Symposium 13, 1986, pp. 167-174.
Havel, Timothy and Mark E. Snow, "A New Method For Building Protein Conformations From Sequence Alignments With Homologues of Known Structure," J. Mol. Biol., 1991, pp. 1-7.
Srinivasan et al., "An Evaluation of the Performance of an Automated Procedure For Comparative Modeling of Protein Tertiary Structure," Protein Engineering, vol. 6, No. 5, pp. 501-512, 1993.
Baldi et al, "Hidden Markov Models of Biological Primary Sequence Information," Proceeding of the National Academy of Science, vol. 91, pp. 1059-1063, 1994.

Affiliated with

Also associated with

Rating

Method and system for protein modeling does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Method and system for protein modeling, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Method and system for protein modeling will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFUS-PAI-O-826982