Protein Science
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

Protein Science (2004), 13:400-411. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Zhang, C.
Right arrow Articles by Zhou, Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Zhang, C.
Right arrow Articles by Zhou, Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state

Chi Zhang1, Song Liu1, Hongyi Zhou and Yaoqi Zhou

Howard Hughes Medical Institute (HHMI) Center for Single Molecule Biophysics, Department of Physiology and Biophysics, State University of New York (SUNY) at Buffalo, Buffalo, New York 14214, USA

(RECEIVED July 31, 2003; FINAL REVISION October 29, 2003; ACCEPTED October 31, 2003)



Abstract

Structure prediction on a genomic scale requires a simplified energy function that can efficiently sample the conformational space of polypeptide chains. A good energy function at minimum should discriminate native structures against decoys. Here, we show that a recently developed, residue-specific, all-atom knowledge-based potential (167 atomic types) based on distance-scaled, finite ideal-gas reference state (DFIRE-all-atom) can be substantially simplified to 20 residue types located at side-chain center of mass (DFIRE-SCM) without a significant change in its capability of structure discrimination. Using 96 standard multiple decoy sets, we show that there is only a small reduction (from 80% to 78%) in success rate of ranking native structures as the top 1. The success rate is higher than two previously developed, all-atom distance-dependent statistical pair potentials. Applied to structure selections of 21 docking decoys without modification, the DFIRE-SCM potential is 29% more successful in recognizing native complex structures than an all-atom statistical potential trained by a database of dimeric interfaces. The potential also achieves 92% accuracy in distinguishing true dimeric interfaces from artificial crystal interfaces. In addition, the DFIRE potential with the C{alpha} positions as the interaction centers recognizes 123 native structures out of a comprehensive 125-protein TOUCHSTONE decoy set in which each protein has 24,000 decoys with only C{alpha} positions. Furthermore, the performance by DFIRE-SCM on newly established 25 monomeric and 31 docking Rosetta-decoy sets is comparable to (or better than in the case of monomeric decoy sets) that of a recently developed, all-atom Rosetta energy function enhanced with an orientation-dependent hydrogen bonding potential.

Keywords: Knowledge-based potential; decoy sets; ideal-gas reference state; residue-level potential

Reprint requests to: Yaoqi Zhou, Howard Hughes Medical Institute Center for Single Molecule Biophysics, SUNY Buffalo, 124 Sherman Hall, Buffalo, NY 14214, USA; e-mail: yqzhou{at}buffalo.edu; fax: (716) 829-2344.

1 These two authors contributed equally to this work.

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.03348304.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Protein Sci.Home page
J. E. Fitzgerald, A. K. Jha, A. Colubri, T. R. Sosnick, and K. F. Freed
Reduced Cbeta statistical potentials can outperform all-atom potentials in decoy identification
Protein Sci., October 1, 2007; 16(10): 2123 - 2139.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
H. Zhou and J. Skolnick
Ab Initio Protein Structure Prediction Using Chunk-TASSER
Biophys. J., September 1, 2007; 93(5): 1510 - 1518.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
Y. Wu, M. Lu, M. Chen, J. Li, and J. Ma
OPUS-Ca: A knowledge-based potential function requiring only C{alpha} positions
Protein Sci., July 1, 2007; 16(7): 1449 - 1463.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
J. Cheng, J. Pei, and L. Lai
A Free-Rotating and Self-Avoiding Chain Model for Deriving Statistical Potentials Based on Protein Structures
Biophys. J., June 1, 2007; 92(11): 3868 - 3877.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
H. Zhou, B. Xue, and Y. Zhou
DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile
Protein Sci., May 1, 2007; 16(5): 947 - 955.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
S. O. Yesylevskyy, V. N. Kharkyanen, and A. P. Demchenko
Dynamic Protein Domains: Identification, Interdependence, and Stability
Biophys. J., July 15, 2006; 91(2): 670 - 685.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. Espadaler, R. Aragues, N. Eswar, M. A. Marti-Renom, E. Querol, F. X. Aviles, A. Sali, and B. Oliva
Detecting remotely related proteins by their interactions and sequence similarity
PNAS, May 17, 2005; 102(20): 7151 - 7156.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
F. Fogolari and S. C.E. Tosatto
Application of MM/PBSA colony free energy to loop decoy discrimination: Toward correlation between energy and root mean square deviation
Protein Sci., April 1, 2005; 14(4): 889 - 901.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
B. Ma, Y. Pan, K. Gunasekaran, R. B. Venkataraghavan, A. J. Levine, and R. Nussinov
Comparison of the protein-protein interfaces in the p53-DNA crystal structures: Towards elucidation of the biological interface
PNAS, March 15, 2005; 102(11): 3988 - 3993.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Z. Liu, F. Mao, J.-t. Guo, B. Yan, P. Wang, Y. Qu, and Y. Xu
Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential
Nucleic Acids Res., January 26, 2005; 33(2): 546 - 558.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 2004 by The Protein Society.