ExSer: A standalone tool to mine protein data bank (PDB) for secondary structural elements

Dhandapani, Vignesh; Daniel, Paul; Raja, Natarajan; Balasubramanian, P.; Arul, L.

doi:10.6026/97320630004390

Cited by 2 publications

(1 citation statement)

References 3 publications

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“…It also extracts each chain, α-helix and β- strand sequences in FASTA format. From the extracted secondary structural sequence it identifies the type of helix, the sense of strand with respect to the previous position and the percentage of occurrence from the chain sequence in the header line of FASTA [ 7 ]. The iso‐electric pointcalculator's algorithm is developed based on the expasy pKa values [ 8 ].…”

Section: Methodsmentioning

confidence: 99%

SeqCalc: A portable bioinformatics software for sequence analysis

Dhandapani¹,

Pavlidis²,

Jin³

et al. 2010

Bioinformation

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Rapid genome sequencing enriched biological databases with enormous sequence data. Yet it remains a daunting task to unravel this information. However experimental and computational researchers lead their own way in analyzing sequence information. Here we introduce a standalone portable tool named “SeqCalc” that would assist the research personnel in computational sequence analysis and automated experimental calculations. Although several tools are available online for sequence analysis they serve only for one or two purposes. SeqCalc is a package of offline program, developed using Perl and TCL/Tk scripts that serve ten different applications. This tool would be an initiative to both experimental and computational researchers in their routine research. SeqCalc is executable in all windows operating systems.AvailabilitySeqCalc can be freely downloaded at http://code.google.com/p/seqcalc.

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Section: Methodsmentioning

confidence: 99%

SeqCalc: A portable bioinformatics software for sequence analysis

Dhandapani¹,

Pavlidis²,

Jin³

et al. 2010

Bioinformation

View full text Add to dashboard Cite

show abstract

Exploring the Function of Predicted T‐Cell Epitopes in Enhancing Influenza Virus Vaccine Efficacy

Malviya,

Yadav,

Rathore

et al. 2024

Macromolecular Symposia

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This study investigates the potential utility of predicted T‐cell epitopes derived from the hemagglutinin (HA) sequences of the H1N1 and H5N1 serotypes of the influenza virus. The aim is to contribute to the improvement of a valuable influenza virus vaccine. The influenza virus, a member of the Orthomyxoviridae family, causes the contagious illness commonly known as the “flu.” It contains RNA and exhibits symptoms ranging from mild to severe, including fever, runny nose, sore throat, muscle aches, headaches, coughing, fatigue, and weakness. Each year, the flu epidemic results in a significant number of deaths and cases of severe illness worldwide. The study focuses on the HA protein, which is very useful for entry of virus and host cell strap, and the neuraminidase (NA) enzyme, which facilitates the free of the virus from the host cell. By utilizing computational tools such as Propred 1 and Propred, binding predictions for MHC class I and II are generated and conserved sequences are analyzed. The 3D structures of MHC class I and II human molecules are obtained from the Protein Data Bank (PDB) using the PATCH‐DOCK server. Through patch docking of the analyzed conserved sequences with MHC I and II human molecules, conserved epitopes that hold potential for vaccine development are identified. This research highlights the importance of utilizing predicted T‐cell epitopes in the design of effective influenza virus vaccines. By leveraging computational methods and structural analysis, this approach provides insights into the development of vaccines that target specific influenza virus serotypes. The identified conserved epitopes have the potential to enhance vaccine efficacy and contribute to the ongoing efforts to combat influenza virus infections.

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ExSer: A standalone tool to mine protein data bank (PDB) for secondary structural elements

Cited by 2 publications

References 3 publications

SeqCalc: A portable bioinformatics software for sequence analysis

SeqCalc: A portable bioinformatics software for sequence analysis

Exploring the Function of Predicted T‐Cell Epitopes in Enhancing Influenza Virus Vaccine Efficacy

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