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Biochemistry apps as enabler of compound and DNA computational: next-generation computing technology
Published in A. K. Haghi, Lionello Pogliani, Eduardo A. Castro, Devrim Balköse, Omari V. Mukbaniani, Chin Hua Chia, Applied Chemistry and Chemical Engineering, 2017
To be able to completely understand the protein function, knowledge of protein structure and molecular interaction and mechanism must be understood thoroughly. The PDB is the worldwide repository of experimentally classified protein structures, nucleic acids, and complex assemblies, including drug-target complexes.5 The PDB was created in Brookhaven National Laboratories in 1971. It mainly contains information on molecular structure of macromolecules from x-ray crystallography and nuclear magnetic resonance (NMR) method. Currently, Research Collaboratory for Structural Bioinformatics plays a huge role in maintaining PDB. One of the features of PDB is that it mainly allows user to display and present data either in plain text or through a molecular viewer using JMOL.
Informatics For Sciences: A Novel Approach
Published in Alexander V. Vakhrushev, Omari V. Mukbaniani, Heru Susanto, Chemical Technology and Informatics in Chemistry with Applications, 2019
Heru Susanto, Ching Kang Chen, Teuku Beuna Bardant
To completely understand the protein function, knowledge of protein structure and molecular interaction and mechanism is must. The PDB is the worldwide repository of experiments which classified the protein structure, nucleic acids, and complex assemblies, including drug-target complexes. The PDB was created in Brookhaven National Laboratories during 1971. It mainly contained information on the molecular structure of macromolecules obtained from X-ray crystallography and NMR method. Currently, Research Collaboratory for Structural Bioinformatics plays huge role in maintaining PDB. One of the main features of PDB is that it allows the user to display and present data either in plain text or through a molecular viewer using JMOL.
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.
Quantitative assessment of LPS-HBsAg interaction by introducing a novel application of immunoaffinity chromatography
Published in Preparative Biochemistry & Biotechnology, 2023
Alireza Kavianpour, Mohsen Ashjari, Seyed Nezamedin Hosseini, Maryam Khatami
The positions of the HBsAg-LPS binding sites were predicted on the analogy of the lipopolysaccharide-binding protein (LBP) binding sites. LBP is a particular protein of the immune system against LPS, consisting of 467 amino acids, 20.6% of which are in the form of the helix. The structural data of the protein is available in the protein data bank (PDB) with a 4M4D code.[41] The three-dimensional structure of LBP (Figure 4) revealed that the ligand sites are located in the space between special helixes of the protein. In the potential area of interaction, there is a fluctuation of accessibility to the water (or solvent) environment due to the repeating pattern of hydrophobic-hydrophilic amino acids on the highlighted helixes.