2. Use systematic names and descriptions
Systematic descriptions should be used in relation to models (and elsewhere), when systematics exists. Relevant areas in relation to molecular models include names of organisms (taxonomy), gene and protein names (Gray et al., 2015), variations in proteins (HGVS nomenclature) (den Dunnen and Antonarakis, 2001), names of files (sequence and PDB ids), variation effects and consequences (Variation Ontology annotations (Vihinen, 2014)), etc. In the case of sequence ids, version numbers must be included unless LRGs (Dalgleish et al., 2010) are used.
Example: Variations in human BTK gene and translated protein (LRG_128) lead to XLA, a X-chromosomal primary immunodeficiency (OMIM # 300755). Variant p.R28C has been identified in XLA patients.