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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
To minimize the search space, the initial population generation is not totally random. It follows the Ramachandran plot which was constructed after a huge set of experiments. It illustrates the preferred confirmations (Φ, Ψ) for each of the 20 amino acids found in a number of various experimentally determined protein structures [36, 37, 38, 39, 40, 41, 42, 43]. Output: encoded chromosome.
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 predicted protein structure was validated by using the Ramachandran plot using PROCHECK software that shows the protein molecule contains 1874 in that 1425 amino acid most favored region, 231 amino acid additionally allowed region, and 8 generally allowed and 0 amino acid disallowed. The results are shown in Figure 9.1.
Presence of potent inhibitors of bacterial biofilm associated proteins is the key to Citrus limon’s antibiofilm activity against pathogenic Escherichia coli
Published in Biofouling, 2023
Songeeta Singha, Rajendran Thomas, Abinash Kumar, Devarshi Bharadwaj, Jai N. Vishwakarma, Vivek Kumar Gupta
The Ramachandran plot revealed the dispersion of amino acid residues of the selected protein. The 3D structure of Figure 4i of the selected protein models indicated that 91.2–96.9% of the residues were in the favorable region with 3.1–8.1% of residues in the allowed region (Figure 4ii–iii). No amino acid residues were found in disallowed regions. This study revealed that all compounds from C. limon extract interacted with the active site of target protein receptor in pathogenic E. coli (Figure 5). FabH showed higher binding energy with 5,8-dimethoxycumarin,3-methoxy-5-methylphenol,2,3-dihydrobenzofuran, orotic acid and cyclobarbital compared to the reference antibiotic kanamycin (Table 2 and Figure 6). Orotic acid bonded most effectively with FabH through five conventional hydrogen bonds at positions Asn(193) with a bond length of 2.3 Å, Asn(193) with a bond length of 2 Å, His(85) with a bond length of 2.3 Å, Thr(80) with a bond length of 2.5 Å and Thr(80) with a bond length of 2.1 Å (supplementary Table 3).
Exploring Klebsiella pneumoniae capsule polysaccharide proteins to design multiepitope subunit vaccine to fight against pneumonia
Published in Expert Review of Vaccines, 2022
Jyotirmayee Dey, Soumya Ranjan Mahapatra, S Lata, Shubhransu Patro, Namrata Misra, Mrutyunjay Suar
The three-dimensional structure of the final multi-epitope vaccine was modeled by using the Robetta server. Figure 6 depicts the developed final structure as visualized by the Pymol software. The quality of the predicted 3D model was assessed using various structure validation tools. The calculated Ramachandran plot using PROCHECK revealed that maximum residues fall in allowed regions, 92.2% in the most favored region,7.4% additional allowed region, and 0.4% in the disallowed region, respectively. Further high scoring values in other structure validation tools, such as 85.37% in VERIFY3D and 99.27% in ERRAT, conclusively demonstrated the accuracy and reliability of the three-dimensional structure of the multi epitopic vaccine construct for further studies (Figure 7).
An integrated in silico and in vivo approach to determine the effects of three commonly used surfactants sodium dodecyl sulphate, cetylpyridinium chloride and sodium laureth sulphate on growth rate and hematology in Cyprinus carpio L
Published in Toxicology Mechanisms and Methods, 2022
Ritwick Bhattacharya, Ismail Daoud, Arnab Chatterjee, Soumendranath Chatterjee, Nimai Chandra Saha
The predicted protein structures were refined using 3Drefine. It is an online interactive server enabling computationally efficient protein structure refinement with web-based statistics and graphical analysis capabilities. For effective protein structure refinement, the refinement technique employs repeated optimization of the hydrogen bonding network along with atomic-level energy reduction on the optimized model utilizing a combined physics and knowledge-based force fields (Bhattacharya and Cheng 2013). The structures were further evaluated and validated using PROCHECK by constructing a Ramachandran plot (Laskowski et al. 1993), ERRAT score (Colovos and Yeates 1993) and Levitt-Gerstein (LG) score evaluated using ProQ (Wallner and Elofsson 2003). The Ramachandran plot visualizes the dihedral angles phi and psi of amino acid residues in protein structure and delineates the potential allowed and disallowed configurations of protein structure, whereas the ERRAT interface performs on the statistics of nonbonded atomic interactions and atom allocation (Colovos and Yeates 1993; Laskowski et al. 1993). The LG score is a P-value for structural similarity, and higher values imply better model structural quality (Singh et al. 2018).