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This paper describes a novel approach to ligand-based virtual screening, which includes various current standard approaches and novelties such as flexible 3D alignment of ligands, and a fast similarity search strategy for three dimensional molecular structures. This method identifies the top ranking of molecules based on their 3D structures. Furthermore, we introduce here two methods (‘Shape’ and ‘Match’ algorithms), that are available in Screen3D, to compare molecules according to their three dimensional structure.
Screen software suite includes tools for similarity searching with a variety of different fingerprints (ChemAxon’s chemical fingerprint, Pharmacophore fingerprint, ECFP, FCFP) as well as several different dissimilarity metrics and metrics optimization methods. Screen3D opens a way to find bio-equivalent molecules in the presence or absence of crystallographic information, while JKlustor integrates numerous clustering methods that are applicable even for large data-sets. A fast lowest energy 3D conformation, conformer generator is also available.
From the case studies, we will demonstrate that Screen3D provides a consistently accurate similarity screening method toward identifying true active compounds. The Match algorithm uses the atomic distance histogram which can be generated from structures regardless of original conformations. This eliminates the preparation of 3D conformation sampling prior to the 3D alignment. From the evaluation result, it will also be shown that Screen3D is also significantly faster than other virtual screening methods. All these features make Screen3D an excellent tool for reliable and rapid virtual screening.
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