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STRIDER: Steric hindrance and metal coordination identifier
Published in Elsevier Ltd
2022
PMID: 35512549
Volume: 98
   
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
About the journal
JournalData powered by TypesetComputational Biology and Chemistry
PublisherData powered by TypesetElsevier Ltd
ISSN14769271