Prediction of side-chain conformations on protein surfaces.

Prediction of side-chain conformations on protein surfaces. Research Abstract Details 

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Prediction of side-chain conformations on protein surfaces. Abstract Text:

Zhexin Xiang,Peter J Steinbach,Matthew P Jacobson,Richard A Friesner,Barry Honig,

An approach is described that improves the prediction of the conformations of surface side chains in crystal structures, given the main-chain conformation of a protein. A key element of the methodology involves the use of the colony energy. This phenomenological term favors conformations found in frequently sampled regions, thereby approximating entropic effects and serving to smooth the potential energy surface. Use of the colony energy significantly improves prediction accuracy for surface side chains with little additional computational cost. Prediction accuracy was quantified as the percentage of side-chain dihedral angles predicted to be within 40 degrees of the angles measured by X-ray diffraction. Use of the colony energy in predictions for single side chains improved the prediction accuracy for chi(1) and chi(1+2) from 65 and 40% to 74 and 59%, respectively. Several other factors that affect prediction of surface side-chain conformations were also analyzed, including the extent of conformational sampling, details of the rotamer library employed, and accounting for the crystallographic environment. The prediction of conformations for polar residues on the surface was generally found to be more difficult than those for hydrophobic residues, except for polar residues participating in hydrogen bonds with other protein groups. For surface residues with hydrogen-bonded side chains, the prediction accuracy of chi(1) and chi(1+2) was 79 and 63%, respectively. For surface polar residues, in general (all side-chain prediction), the accuracy of chi(1) and chi(1+2) was only 73 and 56%, respectively. The most accurate results were obtained using the colony energy and an all-atom description that includes neighboring molecules in the crystal (protein chains and hetero atoms). Here, the accuracy of chi(1) and chi(1+2) predictions for surface side chains was 82 and 73%, respectively. The root mean square deviations obtained for hydrogen-bonding surface side chains were 1.64 and 1.81 A, with and without consideration of crystal packing effects, respectively.

Prediction of side-chain conformations on protein surfaces. Publishing Authors By Initials

Z Xiang,PJ Steinbach,MP Jacobson,RA Friesner,B Honig,

For similar proteins research abstracts see: proteins research

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Prediction of side-chain conformations on protein surfaces. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Proteins

VOLUME: 66

Page Numbers: 814-23

Journal Abbreviation: Proteins

ISSN: 1097-0134

DAY: 1

MONTH: Mar

YEAR: 2007

Prediction of side-chain conformations on protein surfaces. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 8700181

Prediction of side-chain conformations on protein surfaces. Keywords Mesh Terms:

KEYWORDS: Proteins

MESH TERMS: genetics

Chemical & Substance for Abstract: Prediction of side-chain conformations on protein surfaces. Information

Substance Name: Proteins

Registry Number: 0

Grant and Affiliation Information for Prediction of side-chain conformations on protein surfaces.

AFFILIATION: Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892-5624, USA. xiangz@mail.nih.gov

Country: United States

AGENCY: United States NIGMS

GRANT: GM-30518

ACRONYM: GM

MEDLINETA: Proteins

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