PyPAn: An Automated Graphical User Interface for Protein Sequence and Structure Analyses

Protein sequence and structure analyses have been essential components of bioinformatics and structural biology. They provide a deeper insight into the physicochemical properties, structure, and subsequent functions of a protein. Advanced computational approaches and bioinformatics utilities help so...

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Vydáno v:Protein and peptide letters Ročník 29; číslo 4; s. 306
Hlavní autoři: Mathur, Yash, Mohammad, Taj, Anjum, Farah, Shafie, Alaa, Elasbali, Abdelbaset M, Uversky, Vladimir N, Hassan, Md Imtaiyaz
Médium: Journal Article
Jazyk:angličtina
Vydáno: Netherlands 01.01.2022
Témata:
protein structure analysis
python-based protein analysis
modelling method recommendation
multiple protein sequence alignment
protein sequence analysis
protein analysis GUI
PyPAn
protein model refinement
ISSN:1875-5305, 1875-5305
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Shrnutí:Protein sequence and structure analyses have been essential components of bioinformatics and structural biology. They provide a deeper insight into the physicochemical properties, structure, and subsequent functions of a protein. Advanced computational approaches and bioinformatics utilities help solve several issues related to protein analysis. Still, beginners and non-professional may struggle when encountering a wide variety of computational tools and the sheer number of input parameter variables required by each tool. We introduce a free-to-access graphical user interface (GUI) named PyPAn 'Python-based Protein Analysis' for varieties of protein sequence/structure analyses. PyPAn serves as a universal platform to analyze protein sequences, structure, and their properties. PyPAn facilitates onboard analysis of each task in just a single click. It can be used to calculate the physicochemical properties, including instability index and molar extinction coefficient, for a protein. PyPAn is one of the few computational tools that allow users to generate a Ramachandran plot and calculate solvent accessibility and the radius of gyration (Rg) of proteins at once. In addition, it can refine the protein model along with computation and minimization of its energy. PyPAn can generate a recommendation for an appropriate structure modelling method to employ for a query protein sequence. PyPAn is one of the few, if not the only, Python-based computational GUI tools with an array of options for the user to employ as they see fit. PyPAn aims to unify many successful academically significant proteomic applications and is freely available for academic and industrial research uses at https://hassanlab.org/pypan.
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ISSN:1875-5305
1875-5305
DOI:10.2174/0929866529666220210155421