STRIDER: Steric hindrance estimator

Abstract

In 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.

Molecular Docking Study of Active Compunds in Ginger as Inhibitor Against Covid-19

“…However, the combined docking score results have not shown better results than the individual docking scores. This shows that the interaction between the combination of 4 active compounds in ginger has a constructive bond with protein, as evidenced by more van der Waals bonds, but there is a destructive interaction as evidenced by more unfavorable bump bonds [23], [24]. Studies on the arrangement and coordination of the four active compounds in ginger against 7a49 protein are needed in the future to provide more representative results.…”

“…The four compounds interacted with van der Waals binding with protein 7a49 of the SARS CoV-2 spike. All four of them also have an unfavorable bump which is an interaction that occurs due to the steric effect of the compound [22], [23]. Alpha-Curcumene has an unfavorable bump bond with THR315 and a van der Waals bond with five amino acids, namely THR302, GLU298, ASN317, GLN314, and SER316., as well as alpha-Farnesene and beta-Sesquiphelandrene, which interact with the same amino acid as alpha-Curcumene.…”