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Online biophysical predictions for SARS-CoV-2 proteins.
Kagami, Luciano; Roca-Martínez, Joel; Gavaldá-García, Jose; Ramasamy, Pathmanaban; Feenstra, K Anton; Vranken, Wim F.
  • Kagami L; Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, 1050, Brussels, Belgium.
  • Roca-Martínez J; Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, 1050, Brussels, Belgium.
  • Gavaldá-García J; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
  • Ramasamy P; VIB Structural Biology Research Centre, Pleinlaan 2, 1050, Brussels, Belgium.
  • Feenstra KA; Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, 1050, Brussels, Belgium.
  • Vranken WF; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
BMC Mol Cell Biol ; 22(1): 23, 2021 Apr 23.
Article in English | MEDLINE | ID: covidwho-1201947
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ABSTRACT

BACKGROUND:

The SARS-CoV-2 virus, the causative agent of COVID-19, consists of an assembly of proteins that determine its infectious and immunological behavior, as well as its response to therapeutics. Major structural biology efforts on these proteins have already provided essential insights into the mode of action of the virus, as well as avenues for structure-based drug design. However, not all of the SARS-CoV-2 proteins, or regions thereof, have a well-defined three-dimensional structure, and as such might exhibit ambiguous, dynamic behaviour that is not evident from static structure representations, nor from molecular dynamics simulations using these structures. MAIN We present a website ( https//bio2byte.be/sars2/ ) that provides protein sequence-based predictions of the backbone and side-chain dynamics and conformational propensities of these proteins, as well as derived early folding, disorder, ß-sheet aggregation, protein-protein interaction and epitope propensities. These predictions attempt to capture the inherent biophysical propensities encoded in the sequence, rather than context-dependent behaviour such as the final folded state. In addition, we provide the biophysical variation that is observed in homologous proteins, which gives an indication of the limits of their functionally relevant biophysical behaviour.

CONCLUSION:

The https//bio2byte.be/sars2/ website provides a range of protein sequence-based predictions for 27 SARS-CoV-2 proteins, enabling researchers to form hypotheses about their possible functional modes of action.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Viral Proteins / SARS-CoV-2 Type of study: Prognostic study Limits: Humans Language: English Journal: BMC Mol Cell Biol Year: 2021 Document Type: Article Affiliation country: S12860-021-00362-w

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Viral Proteins / SARS-CoV-2 Type of study: Prognostic study Limits: Humans Language: English Journal: BMC Mol Cell Biol Year: 2021 Document Type: Article Affiliation country: S12860-021-00362-w