Citing SARS-CoV-2 Proteome-3D
Abstract
The severe acute respiratory syndrome coronavirus 2 is rapidly growing infectious disease, widely spread with high mortality rates. Since the release of the SARS-CoV-2 genome sequence in March 2020, there has been an international focus on developing target-based drug discovery that requires knowledge of the 3D structure of the proteome. Where there are no experimentally solved structures, our group has created 3D models with coverage closer to 100% and characterised them using state-of-the-art computational approaches. Models of protomers and oligomers, together with predictions of a substrate and allosteric binding sites, protein-ligand docking, SARS-CoV-2 protein to human protein interactions, as well as impacts of mutations, are freely available for download. These provide essential information for computational drug discovery, both to evaluate targets and design new potential therapeutics. These are implemented in SARS CoV2 3D, a comprehensive and user-friendly database available at http://sars3d.com/.
Querying the Database:
The database can be queried in two ways; table on the right that contains gene_id and gene name, and sunburst viewer on the left that contains gene_id.
APIs
The currently implemented API includes queries by gene_id represented on the home page in the queries section. A query takes a single identifier such as nsp1, N, and ORF6, etc and returns the information about the gene in JSON files.
Interactive 3D Viewer:
The MolStar presents the three-dimensional (3D) structure of proteins, it has multiple features such as presenting the target structure sequence calculating the interactions such as hydrogen bonding, Pi stacking, etc between selected resides or ligand. All these features will give the end-user a better understanding of the protein structure. Extensive user guide of how to use the MOL* can be fount at: https://www.rcsb.org/3d-view/molstar/help/getting-started
Sequence Viewer:
The UniProt viewer that is very powerful visualizations that integrate data curated by UniProt teams including domain and site prediction, topology in one viewer. This viewer has the advantage of automatically picking up any information updates to UniProt in the near future. Extensive user guide of how to use the UniProt Viewer can be fount at: https://www.rcsb.org/3d-view/molstar/help/getting-started
Model/PDB tables:
All the structures inside Model and PDB table can be loaded into the MOL* viewer, PDB table appears only for targets with experimentally solved structures such as nsp5, and disappears for gene without structures present in the RCSB such as E.
Mutations Table:
Multiple tools has been used to predict the impact of mutations. Table appear and disappear in the present of data. for example no mutations table in nsp1., wherease there are mutations table in nsp5.
SAR CoV-2 & Human Proteins interaction Table:
Download All protein-protein Docking ResultsAll the structures inside SAR CoV-2 & Human Proteins interaction Table table can be loaded into the MOL* viewer, Table appear and disappear in the present of data. for example no protein-protein docking table in nsp1., wherease there are mutations table in nsp9.
Binding Site Predictions Table:
The fpocket calculation in the Binding Site Predictions table ONLY for structure represented in the Model/PDB table. Structures in the Other tables such as PDB Hits table are not calculated.
