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Protein-carbohydrate complexes: Binding site analysis, prediction, binding affinity and molecular dynamics simulations
Date Issued
01-01-2020
Author(s)
Veluraja, K.
Shanmugam, N. R.Siva
Blessy, J. Jino
Jeyaram, R. A.
Lalithamaheswari, B.
Indian Institute of Technology, Madras
Abstract
Carbohydrates are considered the molecules of molecular recognition because of their influential roles in interacting with viruses, toxins and cell-cell adhesion phenomena. The recognition phenomena are due to the diversified sequences and three-dimensional structures of carbohydrates and their conformational dynamics, binding site residues of proteins and noncovalent interactions between them. This review provides (1) different databases of carbohydrates, which have vital roles in studying protein-carbohydrate interactions, (2) the role of molecular dynamics (MD) simulations for deducing conformational models of carbohydrates as well as studying the interactions between proteins and carbohydrates and (3) design of inhibitors to avoid pathogenic interactions.