The ETH Prediction Group
Dietlind L. Gerloff, Gareth Chelvanayagam, and Steven A. Benner
Department of Chemistry, ETH, CH-8092 Zurich, Switzerland
A Predicted Consensus Structure for the Protein Kinase C2 Homology
(C2H) Domain, the Repeating Unit of Synaptotagmin
A Consensus Prediction of the Secondary Structure for the
6-Phospho-beta-D-Galactosidase Superfamily
The prediction method applies automated heuristics to assign surface,
interior, active site (tertiary structural information), and parsing
residues by analysis of patterns of conservation and variation among
homologous protein sequences in light of evolutionary models that
interpret amino acid substitutions as the consequence of neutral
variation subjected to functional constraints. Secondary structural
elements are assigned from patterns in the tertiary structural
information.
Benner, S. A. Patterns of Divergence in Homologous Proteins as
Indicators of Tertiary and Quaternary Structure. Adv.Enzym.Regulation,
28, 219-236 (1989)
Benner, S. A., and Gerloff, D. L., Patterns of Divergence in Homologous
Proteins as Indicators of Secondary and Tertiary Structure: The
Catalytic Domain of Protein Kinases. Adv. Enzyme Regulat. 31, 121-181
(1991)
Benner, S. A. Predicting de novo the Folded Structure of Proteins.
Curr.Opin.Struct.Biol. 2, 402-412 (1992)
Benner, S. A., Cohen, M. A., Gerloff, D. L., Correct Structure
Prediction? Nature 359, 781 (1992)
Gerloff, D. L., Jenny, T. F., Knecht, L. J., Gonnet, G. H., Benner, S.
A. The Nitrogenase MoFe Protein: A Secondary Structure Prediction. FEBS
Lett. 318, 118-124 (1993)
Benner, S. A., Cohen, M. A., Gerloff, D. L., A Predicted Secondary
Structure for the Src Homology Domain 3. J. Mol. Biol. 229, 295-305
(1993)
Gerloff, D. L., Benner, S. A. Predicting the Conformation of Proteins:
Man versus Machine. FEBS Lett. 325, 29-33 (1993)
Gerloff, D. L., Jenny, T. F., Knecht, L. J., Benner, S. A. A Secondary
Structure Prediction of the Hemorrhagic Metalloprotease Family.
Biochem. Biophys. Res. Comm. 194, 560-565 (1993)
Benner, S. A., I. Badcoe, Cohen, M. A., Gerloff, D. L., De Novo
Prediction of Folded Structures: Assigning Interior and Surface
Residues from Patterns of Variation and Conservation in Homologous
Protein Sequences. J. Mol. Biol. 235, 926-958 (1994)
Benner, S. A. Predicting the Conformation of Proteins from Sequence
Data. in Protein Engineering: A Guide to Design and Production. C. S.
Craik, J. Cleland, editors, in press (1993)
Benner, S. A., Jenny, T. F., Cohen, M. A., Predicting the Conformation
of Proteins from Sequences. Progress and Future Progress. Adv. Enzyme
Regul. 34, 269-353 (1994)
Jenny, T. F., Benner, S. A. Evaluating Predictions of Secondary
Structure in Proteins. Biochem. Biophys. Res. Comm. 200, 149-155
(1994)
Benner, S. A., Gerloff, D. L., T. F. Jenny, G. Chelvanayagam, Knecht,
L. J., Gonnet, G. H. Transparent, bona fide predictions of protein
secondary structure. Nature, Structural Biology submitted(1994)
Jenny, T. F., Benner, S. A. A Prediction of the Secondary Structure of
the Pleckstrin Homology Domain. Proteins: Struct. Funct. Genet. 20, 1-4
(1994)
Benner, S. A., Gerloff, D. L., Jenny, T. F. Predicting Protein Crystal
Structures. Science, 265, 1641-1643 (1994)
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