Analysis of Physico-Chemical Properties of Protein Docking Decoys Generated by Rigid-Body Docking
نویسندگان
چکیده
منابع مشابه
Scoring docked conformations generated by rigid-body protein-protein docking.
Rigid-body methods, particularly Fourier correlation techniques, are very efficient for docking bound (co-crystallized) protein conformations using measures of surface complementarity as the target function. However, when docking unbound (separately crystallized) conformations, the method generally yields hundreds of false positive structures with good scores but high root mean square deviation...
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Molecular docking is widely used to predict novel lead compounds for drug discovery. Success depends on the quality of the docking scoring function, among other factors. An imperfect scoring function can mislead by predicting incorrect ligand geometries or by selecting nonbinding molecules over true ligands. These false-positive hits may be considered "decoys". Although these decoys are frustra...
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We present a simple and effective algorithm RDOCK for refining unbound predictions generated by a rigid-body docking algorithm ZDOCK, which has been developed earlier by our group. The main component of RDOCK is a three-stage energy minimization scheme, followed by the evaluation of electrostatic and desolvation energies. Ionic side chains are kept neutral in the first two stages of minimizatio...
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1. Rajamani D, Thiel S, Vajda S, Camacho C. Anchor residues in protein-protein interactions. PNAS 2004;101(31):1128711292 2. Kussie, P. H.; Gorina, S.; Marechal, V.; Elenbaas, B.; Moreau, J.; Levine, A. J.; Pavletich, N. P. Science 1996, 274, 948-953. 3. Ding K, Lu Y, Nikolovska-Coleska Z, Wang G, Qiu S, Shangary S, Gao W, Qin D, Stuckey J, Krajewski K, Roller PP, Wang S. Structure-based design...
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Since protein complex crystallization is expensive and time-consuming, computational docking tools provide a valuable method to investigate protein interactions. While the sampling of possible docked conformers of two proteins can be performed efficiently by Fast Fourier Transform (FFT) methods, the selection of near-native decoys from the pool of thousands of possible decoys is still far from ...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2016
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2015.11.1759