STRIDER: Steric hindrance estimator

Abstract

AbstractIn silico modeling plays a vital role in the de novo designing and docking of biomacromolecules as well as in exploring their conformational dynamics. Additionally, it has a major role in acquiring the structural insights from the parameters derived from the experimental techniques such as cryo-electron microscopy. Steric hindrance is one of the important measures to validate the accuracy of the constructed model. A web user interface (WUI) namely, STRIDER (steric hindrance estimator) (www.iith.ac.in/strider/) can estimate and report pairwise inter- and intra- molecular steric hindrances using the van der Waals radius of 117 elements through a user interactive interface. STRIDER also identifies and reports the coordination number of 64 metals along with their interacting pattern in an interactive mode. STRIDER can analyze an ensemble of conformers, wherein, multiple conformers are used to circumvent sampling issue in flexible docking, understand protein folding and facilitate structure based virtual screening. Further, it generates a pymol session file that can be used for offline analysis. As STRIDER simply requires the Cartesian coordinates of the given molecule in protein data bank format, any chemical structure can be an input.AvailabilityIt can be freely accessible through: www.iith.ac.in/strider/ without any registration.Theme Of the Concept