Comparative Model of 2019-nCoV Protease Mpro for Computational Analysis

A 306-amino-acid comparative model of the main protease (Mpro) from the novel coronavirus 2019-nCoV, built by Christian Gruber. The model was constructed using sequence data from the Wuhan seafood market pneumonia virus genome (NCBI MN908947.3) and aligned with known SARS proteases, showing 96.1% sequence identity to the SARS crystal structure 2H2Z. Scientists worldwide use this model for computational studies to develop vaccines against 2019-nCoV.

Use Cases

• Perform molecular docking simulations based on the 3D protein model.
• Conduct molecular dynamics (MD) studies to analyze protein stability and interactions.
• Run cavity analysis on the protease structure to identify potential drug binding sites.
• Apply AI-based methods for virtual screening of compound libraries against the model.

Strengths

• The model is based on a specific, published viral genome sequence (NCBI MN908947.3).
• It shows high sequence identity (96.1%) and similarity (98.7%) to a known SARS crystal structure (2H2Z).
• The author reports receiving positive feedback from the China CDC regarding its contribution.

Limitations

• The model is a computational prediction; its accuracy is not confirmed by an experimental crystal structure.
• Column-level documentation is absent; field semantics must be inferred after download.
• Row count and data format are unknown, which may limit suitability assessment.

Provenance

Source

Christian Gruber, based on data from Wu et al. and sequence alignments with SARS proteases.

Collection Method

Comparative modeling via multiple sequence alignment with known SARS protease structures (PDB 5N5O, 2H2Z).

Time Range

Based on virus first reported in 2019 and genome published in January 2020.

Geography

Virus outbreak originated in Wuhan, China; data is genomic and not geographically specific.