STRIDER: Steric hindrance and metal coordination identifier

Patro, L.P.P. and Rathinavelan, Thenmalarchelvi (2022) STRIDER: Steric hindrance and metal coordination identifier. Computational Biology and Chemistry, 98. pp. 1-7. ISSN 1476-9271

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Abstract

Biomolecular structural knowledge is important to understand the biological processes and the mechanisms underlying human diseases. In silico modeling plays a vital role in de novo design and docking of biomacromolecules as well as in exploring their conformational dynamics. Additionally, it has a major role in acquiring the structural insights using the parameters derived from experimental techniques such as cryo-electron microscopy. Steric hindrance is one of the important measures to validate the accuracy of the modeled biomolecular structures. A web user interface (WUI), namely, STRIDER (steric hindrance and metal coordination identifier) (www.iith.ac.in/strider/) estimates and reports pairwise inter- and intra- molecular steric hindrances using the van der Waals radius of 117 elements. STRIDER identifies and reports the coordination pattern of 64 metals in an interactive mode. It can provide conformer wise interaction pattern(s) of an ensemble of conformers which is needed in circumventing sampling issue in flexible docking, protein folding and structure based virtual screening. Further, it generates a pymol session file which highlights the aforementioned interaction for an offline analysis. Since STRIDER simply requires the Cartesian coordinates of a molecule in PDB format, any chemical structure can be given as an input. Functionality of STRIDER is illustrated here by considering several examples. © 2022 Elsevier Ltd

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IITH Creators:
IITH CreatorsORCiD
Rathinavelan, Thenmalarchelvihttp://orcid.org/0000-0002-1142-0583
Item Type: Article
Additional Information: The work was supported by BIRAC-SRISTI GYTI award (PMU_2017_010), BIRAC-SRISTI GYTI award (2019) and Indian Insti- tute of Technology Hyderabad (IITH). LPPP is supported by the Ministry of Education fellowship. CDAC India is acknowledged for the compu- tational support
Uncontrolled Keywords: Ensemble of conformers, Metal coordination, Steric hindrance, van der Waals radius, Web interface
Subjects: Others > Biotechnology
Divisions: Department of Biotechnology
Depositing User: . LibTrainee 2021
Date Deposited: 24 Jun 2022 04:39
Last Modified: 30 Jun 2022 07:30
URI: http://raiith.iith.ac.in/id/eprint/9371
Publisher URL: https://doi.org/10.1016/j.compbiolchem.2022.107686
OA policy: https://v2.sherpa.ac.uk/id/publication/11156
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