AutoDock CrankPep: combining folding and docking to predict protein–peptide complexes
نویسندگان
چکیده
منابع مشابه
AutoDock-based incremental docking protocol improves docking of large ligands
It is well known that computer-aided docking of large ligands, with many rotatable bonds, is extremely difficult. AutoDock is a widely used docking program that can dock small ligands, with upto 5 or 6 rotatable bonds, accurately and quickly. Docking of larger ligands, however, is not very accurate and is computationally expensive. In this paper we present an AutoDock-based incremental docking ...
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BACKGROUND Cross-docking is an approach to find the best holo structures among multiple structures available for a target protein. RESULTS CrossDocker significantly decreases the time needed for setting parameters and inputs for performing multiple dockings, data collection and subsequent analysis. CONCLUSION CrossDocker was written in Python language and is available as executable binary f...
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{Global optimization approaches are proposed for addressing both the protein folding and peptide docking problems. In the protein folding problem, the ultimate goal involves predicting the native protein conformation. A common approach, based on the thermodynamic hypothesis, assumes that this conformation corresponds to the structure exhibiting the global minimum free energy. However, molecular...
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The molecular docking tools Autodock and Surflex accurately reproduce the crystallographic structures of a collection of small molecule ligands that have been shown to bind nucleic acids. Docking studies were performed with the intercalators daunorubicin and ellipticine and the minor groove binders distamycin and pentamidine. Autodock and Surflex dock daunorubicin and distamycin to their nuclei...
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MOTIVATION AutoGrid/AutoDock is one of the most popular software packages for docking, but its automation is not trivial for tasks such as (1) the virtual screening of a library of ligands against a set of possible receptors; (2) the use of receptor flexibility and (3) making a blind-docking experiment with the whole receptor surface. This is an obstacle for research teams in the fields of Chem...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2019
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btz459