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. Â© 2022 Elsevier Ltd

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IITH Creators:

IITH Creators	ORCiD
Rathinavelan, Thenmalarchelvi	http://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