NDLI: Side-chain flexibility in protein docking

Content Provider	IEEE Xplore Digital Library
Author	Liu Hui Lin Feng Yang Jianli Liu Xiu-Ling
Copyright Year	2015
Description	Author affiliation: Sch. of Comput. Eng., Nanyang Technol. Univ., Singapore, Singapore (Liu Hui; Lin Feng) \|\| Sch. of Electron. & Inf. Eng., Hebei Univ., Baoding, China (Yang Jianli; Liu Xiu-Ling)
Abstract	Conventional protein docking methods use rigid docking algorithms but the results have been unsatisfactory, because protein structures are flexible in live environments. In this study, the side-chain flexibility is introduced into protein docking. First, the Morse theory is applied to curvature labelling and region-growing for segmenting the protein surface into smaller patches. The surface critical points are then extracted for each surface region which has been obtained in the segmentation, and a list of more precise and smaller surface patches can be obtained. Secondly, based on the segmented surface, we propose to describe the protein with an ensemble of conformations which incorporate the flexibility of interface side-chains by sampling their conformations using rotamers. We define a 3D rotation invariant shape descriptor based on the Spherical Harmonics Descriptor to deal with the flexible protein surface patches. The signature for each surface patch can be more accurately described and easily compared for the similarity between the signatures. The pairwise complementarity matching is needed only between the convex patches of the ligand with concave patches of the receptor and vice versa, thus the computational cost is greatly reduced. Finally, we are able to use the iterative closest point (ICP) algorithm, thanks to the advantage of our matching method that is able to pre-compute and store the transformation invariant, fast Fourier transform (FFT) docking correlation based representation of each flexible surface patch. Compared with the global geometric matching algorithm and other methods, our FlexDock system generates much less false positive docking candidates, it shows promising advantages in identification of the complementary candidates.
Starting Page	1
Ending Page	8
File Size	680618
Page Count	8
File Format	PDF
e-ISBN	9781479969265
DOI	10.1109/CIBCB.2015.7300315
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2015-08-12
Publisher Place	Canada
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Three-dimensional displays Harmonic analysis Surface fitting Surface treatment Power harmonic filters Libraries interaction sites protein docking side-chain rotamer Morse theory
Content Type	Text
Resource Type	Article

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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