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Discrete restraint‐based protein modeling and the Cα‐trace problem
Author(s) -
DePristo Mark A.,
de Bakker Paul I.W.,
Shetty Reshma P.,
Blundell Tom L.
Publication year - 2003
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.0386903
Subject(s) - dihedral angle , centroid , side chain , trace (psycholinguistics) , protein data bank , discretization , protein structure , chain (unit) , protein data bank (rcsb pdb) , protein structure prediction , atom (system on chip) , algorithm , root mean square , sampling (signal processing) , chemistry , computer science , biological system , crystallography , physics , mathematics , geometry , molecule , stereochemistry , nuclear magnetic resonance , mathematical analysis , biology , filter (signal processing) , quantum mechanics , computer vision , astronomy , hydrogen bond , philosophy , linguistics , embedded system , polymer , organic chemistry
We present a novel de novo method to generate protein models from sparse, discretized restraints on the conformation of the main chain and side chain atoms. We focus on Cα‐trace generation, the problem of constructing an accurate and complete model from approximate knowledge of the positions of the Cα atoms and, in some cases, the side chain centroids. Spatial restraints on the Cα atoms and side chain centroids are supplemented by constraints on main chain geometry, φ/ξ angles, rotameric side chain conformations, and inter‐atomic separations derived from analyses of known protein structures. A novel conformational search algorithm, combining features of tree‐search and genetic algorithms, generates models consistent with these restraints by propensity‐weighted dihedral angle sampling. Models with ideal geometry, good φ/ξ angles, and no inter‐atomic overlaps are produced with 0.8 Å main chain and, with side chain centroid restraints, 1.0 Å all‐atom root‐mean‐square deviation (RMSD) from the crystal structure over a diverse set of target proteins. The mean model derived from 50 independently generated models is closer to the crystal structure than any individual model, with 0.5 Å main chain RMSD under only Cα restraints and 0.7 Å all‐atom RMSD under both Cα and centroid restraints. The method is insensitive to randomly distributed errors of up to 4 Å in the Cα restraints. The conformational search algorithm is efficient, with computational cost increasing linearly with protein size. Issues relating to decoy set generation, experimental structure determination, efficiency of conformational sampling, and homology modeling are discussed.