Docking Flexible Cyclic Peptides with AutoDock CrankPep
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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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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Docking of small molecule compounds into the binding site of a receptor and estimating the binding affinity of the complex is an important part of the structure-based drug design process. For a thorough understanding of the structural principles that determine the strength of a protein/ligand complex both, an accurate and fast docking protocol and the ability to visualize binding geometries and...
متن کاملFlexible docking and design.
Docking and design are the major computational steps toward understanding and affecting receptor-ligand interactions. The flexibility of many ligands makes these calculations difficult and requires the development and use of special methods. The need for such tools is illustrated by two examples: the design of protease inhibitors and the analysis and design of peptide antigens binding to specif...
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ژورنال
عنوان ژورنال: Journal of Chemical Theory and Computation
سال: 2019
ISSN: 1549-9618,1549-9626
DOI: 10.1021/acs.jctc.9b00557