Evaluating CASP4 predictions with physical energy functions

被引:67
作者
Feig, M [1 ]
Brooks, CL [1 ]
机构
[1] Scripps Res Inst, Dept Mol Biol, La Jolla, CA 92037 USA
关键词
scoring; minimization protocol; implicit solvent;
D O I
10.1002/prot.10217
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Physical energy scoring functions based on implicit solvation models are tested by evaluating predictions from the most recent CASP4 competition. The best performing scoring functions are identified along with the best protocol for preparing structures before energies are evaluated. Ranking of structures with the best scoring functions is compared across CASP4 targets to establish when physical scoring functions can be expected to reliably distinguish structures that are most similar to the native fold in a set of misfolded or unfolded protein conformations. The results are used to interpret previous studies where scoring functions were tested on the standard decoy sets by Park, Levitt, and Baker. We show that the best physical scoring functions can be applied successfully in automated consensus scoring applications where a single best conformation has to be selected from a set of structures from different sources. Finally, the potential for better protein structure scoring functions is discussed with a suggestion for an empirically parameterized linear combination of energy components. (C) 2002 Wiley-Liss, Inc.
引用
收藏
页码:232 / 245
页数:14
相关论文
共 54 条
  • [1] Functional inferences from blind ab initio protein structure predictions
    Bonneau, R
    Tsai, J
    Ruczinski, I
    Baker, D
    [J]. JOURNAL OF STRUCTURAL BIOLOGY, 2001, 134 (2-3) : 186 - 190
  • [2] CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS
    BROOKS, BR
    BRUCCOLERI, RE
    OLAFSON, BD
    STATES, DJ
    SWAMINATHAN, S
    KARPLUS, M
    [J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) : 187 - 217
  • [3] SPIN-GLASSES AND THE STATISTICAL-MECHANICS OF PROTEIN FOLDING
    BRYNGELSON, JD
    WOLYNES, PG
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1987, 84 (21) : 7524 - 7528
  • [4] A 2ND GENERATION FORCE-FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC-ACIDS, AND ORGANIC-MOLECULES
    CORNELL, WD
    CIEPLAK, P
    BAYLY, CI
    GOULD, IR
    MERZ, KM
    FERGUSON, DM
    SPELLMEYER, DC
    FOX, T
    CALDWELL, JW
    KOLLMAN, PA
    [J]. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (19) : 5179 - 5197
  • [5] Development of a generalized born model parametrization for proteins and nucleic acids
    Dominy, BN
    Brooks, CL
    [J]. JOURNAL OF PHYSICAL CHEMISTRY B, 1999, 103 (18): : 3765 - 3773
  • [6] Identifying native-like protein structures using physics-based potentials
    Dominy, BN
    Brooks, CL
    [J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 2002, 23 (01) : 147 - 160
  • [7] BACKBONE-DEPENDENT ROTAMER LIBRARY FOR PROTEINS - APPLICATION TO SIDE-CHAIN PREDICTION
    DUNBRACK, RL
    KARPLUS, M
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1993, 230 (02) : 543 - 574
  • [8] Feig M, 2000, PROTEINS, V41, P86, DOI 10.1002/1097-0134(20001001)41:1<86::AID-PROT110>3.0.CO
  • [9] 2-Y
  • [10] Evaluation of a fast implicit solvent model for molecular dynamics simulations
    Ferrara, P
    Apostolakis, J
    Caflisch, A
    [J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2002, 46 (01) : 24 - 33