Computational methods to study intrinsically disordered proteins

Kumar, Prateek; Bhardwaj, Aparna; Uversky, Vladimir N.; Tripathi, Timir; Giri, Rajanish

doi:10.1016/b978-0-323-90264-9.00030-1

Cited by 5 publications

(2 citation statements)

References 71 publications

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“…MoRFs are small binding regions within proteins around 5–25 residues in length, located inside disordered regions (Kumar, Bhardwaj, Uversky, & Tripathi, 2022). Our study used three servers to predict MoRFs in spike endodomains, including MorfCHiBi_Web (Malhis et al, 2015), Anchor2 (Mészáros et al, 2018), and Disopred 3 (Jones & Cozzetto, 2015).…”

Section: Methodsmentioning

confidence: 99%

Coronaviruses spike glycoprotein endodomains: The sequence and structure‐based comprehensive study

Kumar,

Bhardwaj,

Mukherjee

et al. 2023

Protein Science

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Any protein's flexibility or region makes it available to interact with many biomolecules in the cell. Specifically, such interactions in viruses help them to perform more functions despite having a smaller genome. Therefore, these flexible regions can be exciting and essential targets to be explored for their role in pathogenicity and therapeutic developments as they achieve essential interactions. In the continuation with our previous study on disordered analysis of SARS‐CoV‐2 spike protein's cytoplasmic tail (CTR), or endodomain, here we have explored the endodomain's disordered potential of six other coronaviruses using multiple bioinformatics approaches and molecular dynamics simulations. Based on the comprehensive analysis of its sequence and structural composition, we report the varying disorder propensity in endodomains of spike proteins of coronaviruses. The observations of this study may help to understand the importance of spike glycoprotein endodomain and creating therapeutic interventions against them.

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Section: Methodsmentioning

confidence: 99%

Coronaviruses spike glycoprotein endodomains: The sequence and structure‐based comprehensive study

Kumar,

Bhardwaj,

Mukherjee

et al. 2023

Protein Science

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“…Molecular recognition features (MoRFs) are small binding regions within proteins around residues in length, located inside disordered regions 52 . Our study used three servers to predict MoRFs in spike endodomains, including MorfCHiBi_Web 53 , Anchor2 49 , and Disopred 3 54 .…”

Section: ‫ܦܫܲܲ‬ ൌ ‫ݎܾ݁݉ݑܰ‬ ‫݂‬ ‫݀݁ݎ݁݀ݎݏ݅݀‬ ‫ݏ݁ݑ݀݅ݏ݁ݎ‬ ‫݈ܽݐܶ‬ ‫ݏ݁ݑ݀݅ݏ݁...mentioning

confidence: 99%

Coronaviruses Spike glycoprotein endodomains: the sequence and structure-based comprehensive study

Kumar,

Bhardwaj,

Mukherjee

et al. 2023

Preprint

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The flexibility of proteins makes them available to interact with many biomolecules in the cell. Specifically, such interactions in viruses help them to perform more functions despite having a smaller genome. Therefore, these flexible regions can be exciting and essential targets to be explored for their role in pathogenicity and therapeutic developments as they achieve essential interactions. In the continuation with our previous study on disordered analysis of SARS-CoV-2 spike cytoplasmic tail (CTR), or endodomain, here we have explored the disordered potential endodomains of six other coronaviruses using multiple bioinformatics approaches and molecular dynamics simulations. Based on the comprehensive analysis of its sequence and structural composition, we report the varying disorder propensity in endodomains of spike proteins of coronaviruses. The observations of this study may help to understand the importance of spike glycoprotein endodomain and creating therapeutic interventions against them.

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Targeting Intrinsically Disordered Proteins (IDPs) in Drug Discovery

Vemulapalli

2024

Computational Methods for Rational Drug Design

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Computational methods to study intrinsically disordered proteins

Cited by 5 publications

References 71 publications

Coronaviruses spike glycoprotein endodomains: The sequence and structure‐based comprehensive study

Coronaviruses spike glycoprotein endodomains: The sequence and structure‐based comprehensive study

Coronaviruses Spike glycoprotein endodomains: the sequence and structure-based comprehensive study

Targeting Intrinsically Disordered Proteins (IDPs) in Drug Discovery

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