China
Africa
Explore chapters and articles related to this topic
The Role of Natural Products in COVID-19
Published in Hanadi Talal Ahmedah, Muhammad Riaz, Sagheer Ahmed, Marius Alexandru Moga, The Covid-19 Pandemic, 2023
Iqra Akhtar, Sumera Javad, Tehreema Iftikhar, Amina Tariq, Hammad Majeed, Asma Ahmad, Muhammad Arfan, M. Zia-Ul-Haq
Protein-ligand docking design has been used to predict the role of thymol against COVID-19. Thymol and carvacrol have shown a high docking score for inhibiting receptor-binding domain (RBD) of S protein of COVID-19. This S protein is the main protein which is responsible for viral entry into the human cell. On the basis of such findings, USA Canada have already approved disinfectants for surfaces using thymol extract [185–187].
Computational characterization and integrative analysis of proteins involved in spermatogenesis
Published in C. Yan Cheng, Spermatogenesis, 2018
Pranitha Jenardhanan, Manivel Panneerselvam, Premendu P. Mathur
With the identification of differentially expressed genes/proteins, it becomes necessary to understand their biological significance. Application of bioinformatics finds its place in this step, where several integrated bioinformatics tools are employed. The basic understanding of biological significance aims at understanding different aspects of gene products such as their cellular location, functional classification, structural classification, and analysis of their domain, structures, relationship to biological pathways, and diseases. Several integrated bioinformatics tools like the Database for Annotation, Visualization and Integrated Discovery (DAVID), gene ontology, and Kyoto Encyclopedia of Genes and Genomes (KEGG) are being used for this purpose. DAVID tool performs gene-list-based annotations15,16 that takes gene list as the input and identifies data related to gene ontology17 and metabolic pathway analysis from KEGG.18 With identification of protein targets it becomes essential to understand their interaction partners, which can be achieved using web-based protein-protein interaction databases such as String.19 Later, structural analysis of predicted targets is achieved by three-dimensional structure prediction of proteins by the MODELLER suite20 and the Rosetta suite.21 With analysis of individual protein structures it becomes essential to understand how selected protein interacts with its targets using protein-protein docking software such as HADDOCK22 and protein-ligand docking such as Schrodinger Glide.23 Finally, the conformational changes induced by complex formation are evaluated using molecular dynamics simulation studies that use software such as the Gromacs suite.24
Advances in the discovery of new chemotypes through ultra-large library docking
Published in Expert Opinion on Drug Discovery, 2023
Felix Potlitz, Andreas Link, Lukas Schulig
There are two general approaches for docking small molecules. Either the conformations of the ligands are calculated in advance (rigid docking) or on the fly during the docking process (flexible docking). Rigid body docking is particularly useful for those substances that either have a very large conformational space (e.g. highly flexible ligands, proteins) or when the constitution of the molecule highly restricts the conformation (e.g. macrocyclic compounds) [28]. In contrast, flexible docking is usually used to study small molecules since the calculated conformations in solution or vacuum are often significantly different from the bound conformation in the host-guest complex [29]. Since the binding of a ligand to its target usually affects not only its own conformation but also the target structure, the target’s flexibility must be considered (induced fit docking). The extent to which the structure of the target changes upon binding of a ligand must be studied individually and is one of the major challenges for protein-ligand docking. Molecular dynamics simulations can further optimize the obtained host-guest complex from docking to provide more accurate information about the conformations and interactions in the complex.
Is high performance computing a requirement for novel drug discovery and how will this impact academic efforts?
Published in Expert Opinion on Drug Discovery, 2020
Savíns Puertas-Martín, Antonio J. Banegas-Luna, María Paredes-Ramos, Juana L. Redondo, Pilar M. Ortigosa, Ol’ha O. Brovarets', Horacio Pérez-Sánchez
Some HPC based VS techniques are more accurate/advanced than others. The usual compound databases are so large that current VS methods cannot perform exhaustive searches. Instead, they mainly rely on local optimizers than can get easily stuck in local optima. Thus, they may discard promising compounds or even return erroneous recommendations. As an example we can consider rigid protein-ligand docking versus fully flexible Molecular Dynamics.
Development of stable emulsified formulations of Terminalia arjuna for topical application: evaluation of antioxidant activity of final product and molecular docking study
Published in Drug Development and Industrial Pharmacy, 2019
Dinanath Gaikwad, Namdeo Jadhav
GRIP (flexible and accurate protein-ligand docking methodology) type of docking was performed where favored geometry for protein–ligand interaction was obtained by changing internal torsions of ligand into the active sites while receptor remains fixed in which rotation angle was kept at 10°, a number of placements were 30, the ligand was kept nonflexible, and ligand wise 10 results (poses) were selected.