Building Protein Folds Using Distance Geometry: Towards a General Modeling and Prediction Method
A known protein structure can be modified and manipulated to produce a model for another protein with which it shares some sequence similarity. Typical changes involve the substitution and reorientation of side chains and the remodeling of the main chain to accommodate possible insertions and deletions of sequences. Where the two sequences are clearly related (say, more than 50%), such changes are relatively minor and a model can easily be constructed automatically.
KeywordsSecondary Structure Distance Matrix Hydrophobic Residue Globular Protein Distance Constraint
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- Aszódi A, Taylor WR (1994): Secondary structure formation in model polypeptide chains. Prot Engng (Submitted)Google Scholar
- Cohen FE, Richmond TJ, Richards FM (1979): Protein folding: Evaluation of some simple rules for the assembly of helices into tertiary structures with myoglobin as as example. J Mol Biol 132Google Scholar
- Creighton TE (1983): Proteins: Structures and Molecular Properties. New York: FreemanGoogle Scholar
- Crippen GM, Havel TF (1988): Distance Geometry and Molecular Conformation. Chemometrics Research Studies PressGoogle Scholar
- Dayhoff MO, Schwartz RM, Orcutt BC (1978): A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure. Dayhoff MO, ed. Washington, DC: Nat Biomed Res Foundation, Vol. 5, Suppl. 3, pp. 345–352Google Scholar
- Flory PJ (1969): Statistical Mechanics of Chain Molecules. New York: Wiley-InterscienceGoogle Scholar
- MacKay AL (1983): The numerical geometry of biological structures. In Computing in Biological Science. Geisow MJ, Barrett AN, eds. Amsterdam: Elsevier Biomedical, pp 349–392Google Scholar
- Press WH, Flannery BP, Teukolsky SA, Vetterling WT (1986): Numerical Recipes: The Art of Scientific Computing. Cambridge: Cambridge University PressGoogle Scholar
- Taylor WR (1993): Protein fold refinement: Building models from idealised folds using motif constraints and multiple sequence data. Prot Engng 6Google Scholar
- Taylor WR, Jones DT, Green NM (1994): A method for α-helical integral membrane protein fold prediction. Prot Struct Funct Genet (In press)Google Scholar
- Taylor WR, Jones DT, Segal AW (1993): A structural model for the nucleotide binding domain of the cytochrome b -245 β-chain. Protein Science Google Scholar