Status Codes and Target Roles for SSGCID and CSGID
Date: May 5, 2009
At the request of NIAID at the Annual Programmatic Meeting (November 19-20, 2008, Chicago, IL), the following reporting codes and code definitions have been developed and agreed upon. These codes will be used for NIAID reporting purposes by SSGCID and CSGID and made available to NIAID through each Center’s public web portal. When a target is reported at the codes below, this means the step has been successful.
All Targets Status Codes
- Target selected – Protein (or RNA) selected by Center & approved by NIAID
- Target cloned – All or part of ORF successfully cloned into at least one expression vector
- Protein expressed – Protein of the correct size expressed, may or may not be soluble
- Soluble protein expressed – An appropriate amount of soluble protein is observed in the lysate supernatant
- Protein purified – Milligram quantities of protein with >90% purity
- Protein crystallized – Crystals harvested for X-ray diffraction
- HSQC obtained – Usable (i.e. good enough to move forward with assignment) HSQC data obtained
- Diffraction data collected – Usable as defined by the metrics document
- NMR backbone assigned – Protein backbone assignments completed from NMR data
- Submitted to PDB – structure solved and submitted to PDB. Structure quality metrics as defined by the metrics document
- Work stopped – no further work planned on this target
Ligand Screening Status Codes
- Target selected for ligand screening – Protein (or RNA) selected by Center
- Experimental evidence of bound ligand(s) – By NMR, SPR, FTS and/or crystallization
- Ligand-bound structure submitted to PDB – X-Ray or NMR structure obtained and submitted to PDB
These roles define areas of biomedical interest for which we will categorize our targets.
- Known drug target – The gene product is the target of a drug which is currently on the market or in development. Minimally, inhibitors of the target will have been shown to block cell growth in the genus/species listed.
- Potential drug target – An ortholog of a known drug target, an essential gene or a homolog of an essential gene.
- Targets associated with virulence and/or pathogenesis- A gene product associated with pathogen adhesion, colonization, invasion, immune response inhibition or toxicity of the host cells.
- Vaccine candidate- A gene product identified as a vaccine candidate.
- Targets involved in drug resistance- The gene product is confirmed or suggested to be involved (directly or indirectly) in sdrug-target binding, drug degradation or drug removal all of which result in evolution over time of drug resistance.
- Targets showing phylogenetic evidence for essentiality, virulence or pathogenesis- Targets for which orthologues present in a pathogenic species/strain and absent in a non-pathogenic species/strain.
- Targets associated with innate immunity- Human proteins associated with non-adaptive immune mechanisms that recognize, and respond to, microorganisms, microbial products and antigens.
- Marker of infection- A biomarker, antigen or other protein used to detect pathogen infection.
- Targets of other biological interest- targets falling outside the categories described above.