Docking Decoys for Modeled Proteins
نویسندگان
چکیده
منابع مشابه
Decoys for docking.
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...
متن کاملDetecting near-native docking decoys by Monte Carlo stability analysis.
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 ...
متن کاملDARS (Decoys As the Reference State) potentials for protein-protein docking.
Decoys As the Reference State (DARS) is a simple and natural approach to the construction of structure-based intermolecular potentials. The idea is generating a large set of docked conformations with good shape complementarity but without accounting for atom types, and using the frequency of interactions extracted from these decoys as the reference state. In principle, the resulting potential i...
متن کاملUsing correlated parameters for improved ranking of protein-protein docking decoys
A successful protein-protein docking study culminates in identification of decoys at top ranks with near-native quaternary structures. However, this task remains enigmatic because no generalized scoring functions exist that effectively infer decoys according to the similarity to near-native quaternary structures. Difficulties arise because of the highly irregular nature of the protein surface a...
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Protein structure-based molecular design using the computational techniques of protein structure prediction, ligand docking, and virtual screening is an integral part of drug discovery for limiting the application of the structure-based approach to target proteins such as G-protein-coupled receptors (GPCRs). GPCRs play an important role in living organisms and are of major interest to the pharm...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2020
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2019.11.1729