Site Glossary

Terms and definitions as they appear on the site.

Glossary

The Hub employs terminology self-consistently throughout the site. However, some of these terms may be ambiguous or appear to overlap due to the common appears of these terms in the broader scientific community.

We define each term here, and how they relate to each other to reduce collisions of the terms as they apply elsewhere.

The terms here appear alphabetically and link to the primary page where the term applies (if applicable)

Biology

The virus itself operates through a specific set of proteins and interactions. However, it it is also helpful to understand and discuss overall biological functions, and whole virus mechanism overviews. Items which fall under the “Biology” category are the non-quantitative functional aspects and biological pathways which the virus employs, and can be employed against it. Any top-level or comprehensive discussions also fall into this category.

Links

Despite the best efforts of the Hub to gather all the sources we can. Not everything can or should fit here. There are amazing databases and external resources which are available to the community and these are classified as “links” to help.

Models

Derived and/or integrated structures from multiple data sources prepared for different tasks such as docking, FEP, virtual screening, etc. Effectively ready to go constructed molecular systems which can be used as inputs for myriad scientific research techniques.

Due to the significant overlap between SARS-CoV-2 (Common Name: COVID-19) and SARS-CoV (Common Name: SARS), many of the models could be applied for homology research. When a model, is of a SARS-CoV based nature, it will be explicitly denoted. If no notation appears, it is applicable to SARS-CoV-2.

Proteins

The biological proteins associated with the SARS-CoV-2 virus and host that impact the viral infection cycle.

Due to the significant overlap between SARS-CoV-2 (Common Name: COVID-19) and SARS-CoV (Common Name: SARS), many of the proteins applicable to both, but defer to SARS-CoV-2. When a structure, model, or simulation is of a SARS-CoV based nature, it will be explicitly denoted. If no notation appears, it is applicable to SARS-CoV-2.

Simulations

The datasets produced as a result of applying the models to different techniques. This would also include all the possible input files, scripts, etc. necessary to run the technique. For Molecular Dynamics, this would be things like the trajectory; for docking, this would be things like the poses and scores.

Due to the significant overlap between SARS-CoV-2 (Common Name: COVID-19) and SARS-CoV (Common Name: SARS), many of the simulations could be applied for homology research. When a simulation is of a SARS-CoV based nature, it will be explicitly denoted. If no notation appears, it is applicable to SARS-CoV-2.

Structures

Experimentally and calculated molecular structures of the proteins.

Sub-structures for each protein should be grouped under the primary structure.

Groupings of multiple protein structures are listed here if they were derived from experimental methods, however, for any sort of post-measurement modeling, they are in “Models.” For example, The Viral Spike S1 might be interacting with the Host ACE2 (for interfering with binding); this would be considered a “model.”

Due to the significant overlap between SARS-CoV-2 (Common Name: COVID-19) and SARS-CoV (Common Name: SARS), many of the structures could be applied for homology research. When a structure, is of a SARS-CoV based nature, it will be explicitly denoted. If no notation appears, it is applicable to SARS-CoV-2.

Targets

The biological mechanisms and functions which can be disrupted, inhibited, or amplified to actually reduce, prevent, or treat infection of the virus. This is can also be called “Target Modalities.”

Therapeutics

Molecules, drugs, antibodies, peptides, etc. which implement or act to disrupt Targets.

A “Therapeutic Modality” are the subcategories of these such as “small molecules” and “antibody”