Decoys ‘R’ Us: A database of incorrect conformations to improve protein structure prediction

RAM SAMUDRALA; MICHAEL LEVITT

doi:10.1110/ps.9.7.1399

Abstract

The development of an energy or scoring function for protein structure prediction is greatly enhanced by testing the function on a set of computer-generated conformations (decoys) to determine whether it can readily distinguish native-like conformations from nonnative ones. We have created “Decoys ‘R’ Us,” a database containing many such sets of conformations, to provide a resource that allows scoring functions to be improved.

Crossref Citations

This article has been cited by the following publications. This list is generated based on data provided by Crossref.

Mizejewski, Gerald J 2001. Peptides as receptor ligand drugs and their relationship to G-coupled signal transduction. Expert Opinion on Investigational Drugs, Vol. 10, Issue. 6, p. 1063.

Carugo, Oliviero and Pongor, Sándor 2002. The evolution of structural databases. Trends in Biotechnology, Vol. 20, Issue. 12, p. 498.

Gan, Hin Hark and Schlick, Tamar 2002. Computational Methods for Macromolecules: Challenges and Applications. Vol. 24, Issue. , p. 3.

Liu, Yongxing and Beveridge, D. L. 2002. Exploratory studies of ab initio protein structure prediction: Multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model. Proteins: Structure, Function, and Bioinformatics, Vol. 46, Issue. 1, p. 128.

Felts, Anthony K. Gallicchio, Emilio Wallqvist, Anders and Levy, Ronald M. 2002. Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all‐atom force field and the surface generalized born solvent model. Proteins: Structure, Function, and Bioinformatics, Vol. 48, Issue. 2, p. 404.

Samudrala, Ram and Levitt, Michael 2002. A comprehensive analysis of 40 blind protein structure predictions. BMC Structural Biology, Vol. 2, Issue. 1,

Fain, Boris Xia, Yu and Levitt, Michael 2002. Design of an optimal Chebyshev‐expanded discrimination function for globular proteins. Protein Science, Vol. 11, Issue. 8, p. 2010.

Dominy, Brian N. and Brooks,, Charles L. 2002. Identifying native‐like protein structures using physics‐based potentials. Journal of Computational Chemistry, Vol. 23, Issue. 1, p. 147.

Forrest, Lucy R. and Woolf, Thomas B. 2003. Discrimination of native loop conformations in membrane proteins: Decoy library design and evaluation of effective energy scoring functions. Proteins: Structure, Function, and Bioinformatics, Vol. 52, Issue. 4, p. 492.

DePristo, Mark A. de Bakker, Paul I. W. Lovell, Simon C. and Blundell, Tom L. 2003. Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles. Proteins: Structure, Function, and Bioinformatics, Vol. 51, Issue. 1, p. 41.

Zhu, Jiang Zhu, Qianqian Shi, Yunyu and Liu, Haiyan 2003. How well can we predict native contacts in proteins based on decoy structures and their energies?. Proteins: Structure, Function, and Bioinformatics, Vol. 52, Issue. 4, p. 598.

Betancourt, Marcos R. 2003. A reduced protein model with accurate native‐structure identification ability. Proteins: Structure, Function, and Bioinformatics, Vol. 53, Issue. 4, p. 889.

de Bakker, Paul I. W. DePristo, Mark A. Burke, David F. and Blundell, Tom L. 2003. Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all‐atom statistical potential and the AMBER force field with the Generalized Born solvation model. Proteins: Structure, Function, and Bioinformatics, Vol. 51, Issue. 1, p. 21.

DePristo, Mark A. de Bakker, Paul I.W. Shetty, Reshma P. and Blundell, Tom L. 2003. Discrete restraint‐based protein modeling and the Cα‐trace problem. Protein Science, Vol. 12, Issue. 9, p. 2032.

Wallner, Björn and Elofsson, Arne 2003. Can correct protein models be identified?. Protein Science, Vol. 12, Issue. 5, p. 1073.

Buchete, N.-V. Straub, J. E. and Thirumalai, D. 2003. Anisotropic coarse-grained statistical potentials improve the ability to identify nativelike protein structures. The Journal of Chemical Physics, Vol. 118, Issue. 16, p. 7658.

Seok, Chaok Rosen, J. B. Chodera, John D. and Dill, Ken A. 2003. MOPED: Method for optimizing physical energy parameters using decoys. Journal of Computational Chemistry, Vol. 24, Issue. 1, p. 89.

Li, Xiang Hu, Changyu and Liang, Jie 2003. Simplicial edge representation of protein structures and alpha contact potential with confidence measure. Proteins: Structure, Function, and Bioinformatics, Vol. 53, Issue. 4, p. 792.

Hsieh, Meng‐Juei and Luo, Ray 2004. Physical scoring function based on AMBER force field and Poisson–Boltzmann implicit solvent for protein structure prediction. Proteins: Structure, Function, and Bioinformatics, Vol. 56, Issue. 3, p. 475.

Buchete, Nicolae‐Viorel Straub, John E. and Thirumalai, Devarajan 2004. Orientational potentials extracted from protein structures improve native fold recognition. Protein Science, Vol. 13, Issue. 4, p. 862.

Download full list

Article contents

Decoys ‘R’ Us: A database of incorrect conformations to improve protein structure prediction

Abstract

Keywords

Access options

This article has been cited by the following publications. This list is generated based on data provided by Crossref.

Article contents

Decoys ‘R’ Us: A database of incorrect conformations to improve protein structure prediction

Abstract

Keywords

Access options

Save article to Kindle

Save article to Dropbox

Save article to Google Drive

Reply to: Submit a response

Your details

You have entered the maximum number of contributors

Conflicting interests