2013
DOI: 10.4236/ojgen.2013.33021
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Correctness and accuracy of template-based modeled single chain fragment variable (scFv) protein anti-breast cancer cell line (MCF-7)

Abstract: Multiple sequence alignments can be used in the template-based modelling of protein structures to build fragment-based assembly models. Therefore, useful functional information on the 3D structure of the anti-MCF-7 scFv protein can be obtained using available bioinformatics tools. This paper utilises several commonly-used bioinformatics tools and databases, including BLAST (Basic Local Alignment Search Tool), GenBank, PDB (Protein Data Bank), KABAT numbering and SWISS-MODEL, to gain specific functional insight… Show more

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Cited by 9 publications
(7 citation statements)
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“…The programme shows the sterio-chemistry of the main-chain torsion angles Phi, Psi (φ, ψ) of a good protein model. The Ramachandran plot displays the polypeptide chain of a protein structure using the φ, ψ angles pair (Laskowski et al, 1993;Mahgoub and Bolad, 2013;Ramachandran et al, 1963). Figure 4 and Table 1 indicate that up to 91.6% of the residues fall within the most favoured regions, 6.8% in the allowed regions whereas only 1.6% residues are in the outlier regions, further confirming that the predicted model is of good quality.…”
Section: Model Of the ∆9-fatty Acid Desaturasementioning
confidence: 65%
“…The programme shows the sterio-chemistry of the main-chain torsion angles Phi, Psi (φ, ψ) of a good protein model. The Ramachandran plot displays the polypeptide chain of a protein structure using the φ, ψ angles pair (Laskowski et al, 1993;Mahgoub and Bolad, 2013;Ramachandran et al, 1963). Figure 4 and Table 1 indicate that up to 91.6% of the residues fall within the most favoured regions, 6.8% in the allowed regions whereas only 1.6% residues are in the outlier regions, further confirming that the predicted model is of good quality.…”
Section: Model Of the ∆9-fatty Acid Desaturasementioning
confidence: 65%
“…These structures have been validated via objective function, ERRAT, and Verify3D. The analyses have inferred that model 1 which is allocated the parameter values with the minimum objective function 44 , the quality factor above 70% of ERRAT, and the model quality score of 97.81% with Verify3D with an average scoring above 0.3 45 , 46 is the best one among the suggested models (Table 1 , Supplementary Figs S3 , S4 ).…”
Section: Resultsmentioning
confidence: 99%
“…The programme shows the sterio-chemistry of the main-chain torsion angles Phi, Psi ( φ , ψ ) of a good protein model. The Ramachandran plot displays the polypeptide chain of a protein structure using the φ , ψ angles pair ( Laskowski, Moss & Thornton, 1993 ; Mahgoub & Bolad, 2013 ; Ramachandran, Ramakrishnan & Sasisekharan, 1963 ). Figure 4 and Table 1 indicate that up to 91.6% of the residues fall within the most favoured regions, 6.8% in the allowed regions whereas only 1.6% residues are in the outlier regions, further confirming that the predicted model is of good quality.…”
Section: Resultsmentioning
confidence: 99%