PMID: 9448278Mar 14, 1998Paper

Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations

Proceedings of the National Academy of Sciences of the United States of America
A R OrtizJ Skolnick

Abstract

By incorporating predicted secondary and tertiary restraints derived from multiple sequence alignments into ab initio folding simulations, it has been possible to assemble native-like tertiary structures for a test set of 19 nonhomologous proteins ranging from 29 to 100 residues in length and representing all secondary structural classes. Secondary structural restraints are provided by the PHD secondary structure prediction algorithm that incorporates multiple sequence information. Multiple sequence alignments also provide predicted tertiary restraints via a two-step process: First, seed side chain contacts are selected from a correlated mutation analysis, and then an inverse folding algorithm expands these seed contacts. The predicted secondary and tertiary restraints are incorporated into a lattice-based, reduced protein model for structure assembly and refinement. The resulting native-like topologies exhibit a coordinate root-mean-square deviation from native for the whole chain between 3.1 and 6.7 A, with values ranging from 2.6 to 4.1 A over approximately 80% of the structure. Overall, this study suggests that the use of restraints derived from multiple sequence alignments combined with a fold assembly algorithm is a promi...Continue Reading

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Citations

Mar 27, 2002·Journal of Computational Chemistry·Keith D BallKen A Dill
Feb 24, 2001·Computers & Chemistry·S G Jacchieri
Dec 11, 2007·Bioinformatics·Angelika FuchsDmitrij Frishman
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Sep 30, 2021·Journal of Chemical Information and Modeling·Jeffrey SkolnickSuresh Singh

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