virusMED

Metal binding sites, antigen epitopes, and drug binding sites are viral protein hotspots that control how viruses interact with their hosts. Like Google maps organizes and annotates points of interest on the planet, virus-M-E-D (Metal binding sites, antigenic Epitopes, and Drug binding sites) recognizes the relative locations of individual hotspots of viral proteins, and depicts a collection of maps upon which newly-characterized functional sites can be marked as they are being discovered. While we define drug as small molecule compounds collected by the DrugBank database, other small molecules binders observed in complex viral protein structures were also cataloged.

VirusMED's rich set of annotation tags about virus species, strains, hosts, proteins, metal ions, specific antibodies, and FDA approved drugs permits fast screening of viral protein hotspots tailored to a particular research problem. VirusMED connects a reliable structural resource and a custom-built virus search engine, laying a foundation for the rational design of preventative and therapeutic agents targeting viral infections.

Cite us: Zhang H, Chen P, Ma H, Woińska M, Liu D, Cooper DR, Peng G, Peng Y, Deng L, Minor W, Zheng H (2021) VirusMED: an atlas of hotspots of viral proteins. IUCr J. 8(6):931-942.

Since September 27, 2021, the cover story has been downloaded 6402 times. virusMED has served 1799 requests by 191 users from 26 countries. Date updated: 2024-12-08



Gallery of commonly-encountered virus families that infect ...
... human and other vertebrates
Retroviridae
e.g. HIV-1
Coronaviridae
e.g. SARS-CoV-2
Orthomyxoviridae
e.g. Influenza A virus
Picornaviridae
e.g. Enterovirus A
Caliciviridae
e.g. Norwalk virus
Herpesviridae
e.g. Human γ-herpesvirus 4
Adenoviridae
e.g. Human adenovirus 2
Filoviridae
e.g. Ebola virus
Poxviridae
e.g. Vaccinia virus
Paramyxoviridae
e.g. Human respirovirus 3
Papillomaviridae
e.g. HPV-18
Polyomaviridae
e.g. Human polyomavirus 2
... human, other vertebrates, and invertebrates
Flaviviridae
e.g. Hepacivirus C
Reoviridae
e.g. Rotavirus A
Togaviridae
e.g. Chikungunya virus
... plants or protozoa
Virgaviridae
e.g. Tobacco mosaic virus
Tombusviridae
e.g. Carnation mottle virus
Mimiviridae
e.g. Mimivirus
... bacteria
Myoviridae
e.g. phage T4
Podoviridae
e.g. Salmonella virus P22
Siphoviridae
e.g. phage λ

Hotspot statistics of the virusMED database
Hotspot feature Number of virus families Number of virus species Number of virus strains Number of PDB structures Number of hotspots Number of unique proteins Number of unique hotspots
Metal binding sites 80 332 636 3,804 12,315 1,016 2,631
Epitopes 34 107 316 2,802 26,913 530 2,176
Drug binding sites 74 295 627 7,829 24,114 1,083 3,158
All hotspots 94 428 1,015 11,827 63,342 1,993 7,965