Linear programming optimization and a double statistical filter for protein threading protocols

Jaroslaw Meller; Ron Elber

doi:10.1002/prot.1145

journal article Sep 21, 2001

Linear programming optimization and a double statistical filter for protein threading protocols

Jaroslaw Meller Ron Elber

Proteins: Structure, Function, and Bioinformatics Vol. 45 No. 3 pp. 241-261 · Wiley

View at Publisher Save 10.1002/prot.1145

Abstract

AbstractThe design of scoring functions (or potentials) for threading, differentiating native‐like from non‐native structures with a limited computational cost, is an active field of research. We revisit two widely used families of threading potentials: the pairwise and profile models. To design optimal scoring functions we use linear programming (LP). The LP protocol makes it possible to measure the difficulty of a particular training set in conjunction with a specific form of the scoring function. Gapless threading demonstrates that pair potentials have larger prediction capacity compared with profile energies. However, alignments with gaps are easier to compute with profile potentials. We therefore search and propose a new profile model with comparable prediction capacity to contact potentials. A protocol to determine optimal energy parameters for gaps, using LP, is also presented. A statistical test, based on a combination of local and globalZ‐scores, is employed to filter out false‐positives. Extensive tests of the new protocol are presented. The new model provides an efficient alternative for threading with pair energies, maintaining comparable accuracy. The code, databases, and a prediction server are available athttp://www.tc.cornell.edu/CBIO/loopp. Proteins 2001;45:241–261. © 2001 Wiley‐Liss, Inc.

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Details

Published: Sep 21, 2001
Vol/Issue: 45(3)
Pages: 241-261
License: View

Authors

J

Jaroslaw Meller

Department of Physical Chemistry, The Hebrew University, Givat Ram, Jerusalem 91904, Israel

R

Ron Elber

Department of Computer Science, Cornell University, Ithaca, New York 14853

Cite This Article

Jaroslaw Meller, Ron Elber (2001). Linear programming optimization and a double statistical filter for protein threading protocols. Proteins: Structure, Function, and Bioinformatics, 45(3), 241-261. https://doi.org/10.1002/prot.1145

Linear programming optimization and a double statistical filter for protein threading protocols

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