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Orders Norzivirales and Timlovirales
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
After successful cloning of the full-length A1 gene of the phage Qβ in E. coli (Kozlovska et al. 1993), Tatyana Kozlovska et al. (1996, 1997) recognized the 195-aa-residues long readthrough extension of the phage Qβ coat as a promising site for foreign insertions by the generation of the mosaic Qβ VLP particles. The readthrough A1 extension was proposed to contain elements that could protrude as the spike-like structures on the Qβ VLP surface. This assumption was achieved by the sensitive homology programs elaborated at that time by Indulis Gusārs from the Grēns team. He detected some unexpected similarities when the readthrough Qβ A1 extension was compared with the protruding preS part of the hepatitis B virus surface antigen (Kozlovska et al. 1996). The real 3D structure of the Qβ A1 readthrough domain was revealed at high resolution by x-ray crystallography after 15 years (Rumnieks and Tars 2011). The fold was found unique among all proteins in the protein data bank. However, the real fold of the protruding hepatitis B virus preS1 region remains still unresolved.
An Efficient Protein Structure Prediction Using Genetic Algorithm
Published in Abdel-Badeeh M. Salem, Innovative Smart Healthcare and Bio-Medical Systems, 2020
Mohamad Yousef, Tamer Abdelkader, Khaled El-Bahnasy
It is a web-based server for protein homology detection and structure prediction. Input to HHpred can be amino acid sequence or a multiple sequence alignment. It uses a novel approach that conducts a pair-wise alignments of profile hidden Markov models (HMMs). It also uses a variety of databases like SCOP (Structural Classification of Proteins), Pfam, and PDB (Protein Data Bank). HHpred performs fast and well for single domain and for multi-domain query sequences and can be used to predict functional information of a protein from homolog proteins using various sequence-based search tools like BLAST, FASTA, or PSI-BLAST [11, 12, 13].
Preliminary Phytochemical Screening and Identification of Bioactive Compounds from Banana Inflorescence and to Find the Interactions on Molecular Docking for PCOS
Published in Parimelazhagan Thangaraj, Phytomedicine, 2020
M. C. Kamaraj, Suman Thamburaj, R. Akshaya, V. Bhanu Deepthi
The PDB is the database that contains information about the 3D structure of biomacromolecules and their complexes as determined by X-ray crystallography, NMR spectroscopy, and includes more than a few Nobel Prize winning structures. Polycystic ovarian syndrome protein (CYP17A) was retrieved from the protein data bank with the specific resolution, and the PDB ID is 3RUK.
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
A generally accepted workflow of three phases has been established when performing docking calculations (Figure 1)[43]. Since the success of the calculated binding pose strongly depends on the characteristics of the respective target or ligands, careful preparation as the initial step in the process is essential [44]. The experimental target structures are usually available via the Protein Data Bank (PDB), established as an open-access database in 1971. Before these structures can be used for docking, it is often necessary to replace missing amino acid side chains or flexible loops, add hydrogen atoms, and determine bond orders. After the basic preparation, the hydrogen bond assignment should be optimized, followed by a restrained minimization to eliminate potential clashes [45]. Alternatively, the target structures can be predicted based on their sequence via homology modeling and more recent tools such as AlphaFold2 [46] or RoseTTAFold [47].
Dietary Diindolylmethane Enhances the Therapeutic Effect of Centchroman in Breast Cancer by Inhibiting Neoangiogenesis
Published in Nutrition and Cancer, 2023
Dhanamjai Penta, Jagadish Natesh, Priya Mondal, Syed Musthapa Meeran
The three-dimensional structure of DIM (PubChem ID: 3071), CC (PubChem ID: 154413), and standard VEGFR2 kinase inhibitor drug sorafenib (PubChem ID: 216239) was retrieved from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/) [35]. These ligand molecules were converted into Protein Data Bank format using Open Babel software and were prepared for docking analysis using AutoDock Tools (The Open Babel Package, version 2.3.1; http://openbabel.org) [36, 37]. The three-dimensional structure of VEGFR2 (PDB ID: 4ASD, Resolution: 2.03 Å) was obtained from the RCSB PDB web portal [38]. The molecular docking investigation was executed using AutoDock Vina [39]. The grid box was created using ADT around the standard drug sorafenib binding site, with a grid resolution of 1 Å. The binding energy for each ligand with VEGFR2 docked complexes was acquired, and three-dimensional stereo figures were drawn as described previously [40, 41].
β-Caryophyllene promotes oxidative stress and apoptosis in KB cells through activation of mitochondrial-mediated pathway – An in-vitro and in-silico study
Published in Archives of Physiology and Biochemistry, 2022
Duraisamy Ramachandhiran, Chandrasekaran Sankaranarayanan, Raju Murali, Sukumar Babukumar, Veerasamy Vinothkumar
The protein data bank (PDB) web contains a collection of 3 D structure of large biological molecules including proteins and nucleic acids (Parasuraman 2012). The docking analysis was performed by auto dockvina, 3 D structure was visualised by Discover Studio Version 4.5 (Biovia Dassault system, Inc. USA). The structural information of the macromolecules determined by X-ray crystallographic and nuclear magnetic resonance (NMR) methods is available in the PDB. To remove the water, interacting heavy atoms, metal ions from the protein structure and added with hydrogen atoms before the docking analysis. X-ray crystallographic structures of NFҡB (PDB ID: 1IKN) resolution: 2.3 Å; R-Value Free: 0.277; R-Value Work: 0.223, PI3K (PDB ID: 5XGI) Resolution: 2.56 Å, R-Value Free: 0.290, R-Value Work: 0.239 and AKT (PDB ID: 6BUU) Resolution: 2.4 Å, R-Value Free: 0.230, R-Value Work: 0.183 were retrieved from PDB.