Research Article
Recognition of coarse-grained protein tertiary structure
Timothy Lezon,
Jayanth R. Banavar,
Amos Maritan,
Corresponding Author
Timothy Lezon
Department of Physics, Pennsylvania State University, University Park, Pennsylvania
Department of Physics, 104 Davey Laboratory, Penn State, University Park, PA 16802===Search for more papers by this authorJayanth R. Banavar
Department of Physics, Pennsylvania State University, University Park, Pennsylvania
Search for more papers by this authorAmos Maritan
Dipartimento di Fisica G. Galileo, Via Marzolos, Italy
Search for more papers by this authorTimothy Lezon,
Jayanth R. Banavar,
Amos Maritan,
Corresponding Author
Timothy Lezon
Department of Physics, Pennsylvania State University, University Park, Pennsylvania
Department of Physics, 104 Davey Laboratory, Penn State, University Park, PA 16802===Search for more papers by this authorJayanth R. Banavar
Department of Physics, Pennsylvania State University, University Park, Pennsylvania
Search for more papers by this authorAmos Maritan
Dipartimento di Fisica G. Galileo, Via Marzolos, Italy
Search for more papers by this authorAbstract
A model of the protein backbone is considered in which each residue is characterized by the location of its Cα atom and one of a discrete set of conformal (ϕ, ψ) states. We investigate the key differences between a description that offers a locally precise fit to known backbone structures and one that provides a globally accurate fit to protein structures. Using a statistical scoring scheme and threading, a protein's local best-fit conformation is highly recognizable, but its global structure cannot be directly determined from an amino acid sequence. The incorporation of information about the conformal states of neighboring residues along the chain allows one to accurately translate the local structure into a global structure. We present a two-step algorithm, which recognizes up to 95% of the tested protein native-state structures to within a 2.5 Å root mean square deviation. Proteins 2004;55:000–000. © 2004 Wiley-Liss, Inc.
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