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Advancement in Gene Delivery
Published in Rishabha Malviya, Pramod Kumar Sharma, Sonali Sundram, Rajesh Kumar Dhanaraj, Balamurugan Balusamy, Bioinformatics Tools and Big Data Analytics for Patient Care, 2023
Shilpa Rawat, Akash Chauhan, Rishabha Malviya, Md. Aftab Alam, Swati Verma, Shivkanya Fuloria
Almost 30 years ago, biophysical chemists and computational biologists were attracted by the topic of protein–protein or protein–ligand docking. A docking technique determines a complex’s 3D shape since the proteins are rotated and translated, producing a huge amount of potential complexes on the computer, and selecting the most favored ones. The PDB is used to put docking techniques to the test on protein–protein complexes, specifically protease–inhibitor and antigen–antibody complexes. CAPRI, a method inspired by Critical Assessment of Structure Prediction (CASP), provided molecular dimensions to the protein components of several target assemblies. When the anticipated interactions were compared to X-ray patterns, they were shown to be particularly effective on several of the targets.
in vitro by electrical and electromagnetic stimulations
Published in Ze Zhang, Mahmoud Rouabhia, Simon E. Moulton, Conductive Polymers, 2018
Convincing and mounting evidence has demonstrated the feasibility of modulating bone cell physiology with EF and EMF. An exogenous field acts on plasma membrane proteins or intracellular compartments, triggering downstream pathways. A wide range of cellular behaviors can be modified, of which some are osteogenic and beneficial for bone repair. However, major challenges must be resolved before EF and EMF could be accepted as standard techniques in a cell culture laboratory and in clinic management. These challenges include knowing the molecular mechanisms of how EF or EMF interacts with the binding sites of plasma membrane receptors, probably with the help of molecular modeling, such as the protein–ligand docking technique. For example, is the weak EF reported in literature able to directly impact the conformation of the active center of a receptor, or does it work together with soluble ions and even water molecules? Do DC EF and EMF act on cells differently, and if they do, how? Another important challenge is to identify specific combinations of ES parameters leading to foreseeable and reproducible cellular consequence. EF and EMF cannot become a standard technique without accuracy. Clinical research must consider the complexity of tissue dielectric properties that vary among individuals and govern the magnitude and distribution of EF in tissue. A conductive scaffold may provide a uniform two- or three-dimensional space of EF for the cells cultured on or in it. However, the feasibility and efficacy of in vivo use of the conductive scaffold remain to be demonstrated.
Synthesis and characterisation of formohydrazide derivatives as potential antimicrobial agents: molecular docking and DFT studies
Published in Molecular Physics, 2022
S. Gunavathi, R. Venkateswaramoorthi, K. Arulvani, S. Bharanidharan
The entire docking calculations were performed using the Auto dock docking module programme. It performs flexible protein–ligand docking and searches for favourable interactions between one typically small ligands molecule and a typically larger protein molecule. Docking process, wherein protein preparation inhibited refinement is carried out with a maximum of 20 poses, wherein the side chains are optimised and refinement of residues takes place if the ligands poses are within 5.0Å. The best docked structure was chosen by docking score and the number of amino acids matches (hydrogen bonds) with the original drug complex.