Algorithms for Structure Comparison and Analysis: Homology Modelling of Proteins

Wiltgen, Marco

doi:10.1016/b978-0-12-809633-8.20484-6

Cited by 29 publications

(21 citation statements)

References 82 publications

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“…It is plot visualizes the do-and-not areas in the plane of dihedral angles. The quality of the homolog is poor if many forbidden regions are found (Wiltgen, 2018). Visualization of the results of the Ramachandran plot can be seen in Figure 4.…”

Section: Results and Discussion Homology Modeling Using Swiss Modelmentioning

confidence: 99%

Homology modeling and mutation prediction of ACE2 from COVID-19

et al. 2021

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SARS-CoV-2 has become a pandemic in the world. The virus binds to the Angiotensin-Converting Enzyme 2 (ACE2) receptor, which is found in epithelial cells such as in the lungs, to generate the pathology of COVID-19. It is essential to analyze the characteristics of ACE2 in understanding the development of the disease and study potential new drugs. The analysis was carried out using computer simulations to speed up protein analysis that utilized Artificial Intelligence technology, databases, and big data. Homology modeling is a method to exhibit homologous of protein families, hence the model and arrangement of protein sequences modeled are established. This research aims to determine the possibility of mutations in ACE2 by performing the mutation prediction. The result shows reliable homologous modeling with the score of GA341, MPQS, Z-DOPE, and TSVMod NO35 were 1; 1.28252; -0.47; and 0.793, respectively. Moreover, Gene Ontology (GO) analysis describes that ACE2 has a molecular transport function in cells while there are no mutations found occurred in ACE2 analyzed using SIFT and PROVEAN.

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Section: Results and Discussion Homology Modeling Using Swiss Modelmentioning

confidence: 99%

Homology modeling and mutation prediction of ACE2 from COVID-19

et al. 2021

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“…3a, 4a, 7a, 8a, 9b, S4a, S5a but if Ramachandran plot ( Fig. 5, S6 ) of the computed structures are noticed, it is observed that the residues are lying on proper position related to secondary structures (Wiltgen, Encyclopedia of Bioinformatics and computational Biology, 2019; Laskowski, Swaminathan Comprehensive Medicinal Chemistry II, 2007).…”

Section: Methodsmentioning

confidence: 95%

Optimized structure of monoubiquitinated FANCD2 (human) at Lys 561: a theoretical approach

Mukhopadhyay

Mondal

Reddy

2021

Preprint

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Fanconi anaemia pathway repairs inter-strand cross linking damage (ICL) of the DNA. Monoubiquitination of FANCD2 and FANCI is very crucial for ICL repairing. In this work we have tried to understand the monoubiquitinated FANCD2 structure, which facilitates the FANCD2 for binding the damage part of the chromatin. Crystal structure of the monoubiquitinated FANCD2 alone is not available, therefore we have developed the optimized structure of the human monoubiquitinated (Lys 561) FANCD2. As there is no suitable software or web server we have developed a method for building up monoubiquitinated product and validated on simplest monoubiquitinated protein, diubiquitin. We have predicted the structure of human monoubiquitinated FANCD2 by using our method and studied the interaction with DNA by docking studies. Molecular Dynamics (MD) simulation was used to understand the stability of the structure. Large structural differences have been observed between FANCD2 and monoubiquitinated FANCD2. DNA docking studies suggest that the binding site varies for the FANCD2 and monoubiquitinated FANCD2.

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“…The Ramachandran plot gives information regarding energetically allowed and forbidden regions for the dihedral angles [ 60 ]. The distribution of the Phi/Psi values observed in a protein structure can be used for structure validation [ 61 ].…”

Section: Discussionmentioning

confidence: 99%

“…The distribution of the Phi/Psi values observed in a protein structure can be used for structure validation [ 61 ]. For poor quality homology models, many dihedral angles will be found in the forbidden regions of the Ramachandran plot and such deviations usually indicate problems with the predicted structure [ 60 ]. In this study, the three-dimensional structure predicted for LigA/BCon1-5 protein was highly reliable since only 3.01% were Ramachandran outliers.…”

Section: Discussionmentioning

confidence: 99%

Immunoinformatic Study of Recombinant LigA/BCon1-5 Antigen and Evaluation of Its Diagnostic Potential in Primary and Secondary Binding Tests for Serodiagnosis of Porcine Leptospirosis

et al. 2021

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Leptospirosis is responsible for hampering the productivity of swine husbandry worldwide. The aim of this study was to assess the efficacy of bioinformatics tools in predicting the three-dimensional structure and immunogenicity of recombinant LigBCon1-5 (rLigBCon1-5) antigen. A battery of bioinformatics tools such as I-TASSER, ProSA and SAVES v6.0 were used for the prediction and assessment of the predicted structure of rLigBCon1-5 antigen. Bepipred-2.0, DiscoTope v2.0 and ElliPro servers were used to predict linear and conformational epitopes while T-cell epitopes were predicted using NetMHCpan 4.1 and IEDB recommended 2.22 method for MHC Class I and II peptides respectively. The results obtained using various in silico methods were then compared with wet lab experiments comprising of both primary (IgG Dot ELISA Dipstick test) and secondary-binding assays (Latex Agglutination Test [LAT]) to screen 1153 porcine serum samples. The three-dimensional structure of rLigA/BCon1-5 protein as predicted by I-TASSER was found to be reliable by Ramachandran Plot and ProSA. The ElliPro server suggested 10 and three potential linear and conformational B-cell-epitopes, respectively, on the peptide backbone of the rLigA/BCon1-5 protein. The DiscoTope prediction server suggested 47 amino acid residues to be part of B-cell antigen. Ten of the most efficient peptides for MHC-I and II grooves were predicted by NetMHCpan 4.1 and IEDB recommended 2.22 method, respectively. Of these, three peptides can serve dual functions as it can fit both MHC I and II grooves, thereby eliciting both humoral-and cell-mediated immune responses. The prediction of these computational approaches proved to be reliable since rLigBCon1-5 antigen-based IgG Dot ELISA Dipstick test and LAT gave results in concordance to gold standard test, the Microscopic Agglutination Test (MAT), for serodiagnosis of leptospirosis. Both the IgG Dot ELISA Dipstick test and LAT were serodiagnostic assays ideally suited for peripheral level of animal health care system as “point of care” tests for the detection of porcine leptospirosis.

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Algorithms for Structure Comparison and Analysis: Homology Modelling of Proteins

Cited by 29 publications

References 82 publications

Homology modeling and mutation prediction of ACE2 from COVID-19

Homology modeling and mutation prediction of ACE2 from COVID-19

Optimized structure of monoubiquitinated FANCD2 (human) at Lys 561: a theoretical approach

Immunoinformatic Study of Recombinant LigA/BCon1-5 Antigen and Evaluation of Its Diagnostic Potential in Primary and Secondary Binding Tests for Serodiagnosis of Porcine Leptospirosis

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