Guidelines for protein modelling
A simple checklist of items necessary to describe computer modelling studies is presented. Each of the items is provided with a brief description. Which items of the guidelines should be included in a certain article depends on the used modelling strategy. Before applying any computational analyses, one has to know the quality of used data as computational predictions can be useless if the starting point is wrong or severely biased.
Precalculated models for many proteins are available at ModBase (Pieper et al., 2014) and SwissModel Repository (Bienert et al., 2017), however, they do not provide full details as instructed in here. These models are predicted with automated pipelines, thus the modelling procedure is not optimized for each structure. Such models can still be useful for various applications when experimental structures have not been determined. When close enough structures are available, automatic models may be of higher quality than an inexperienced modeler can achieve. Users of any types of structural predictions must bear in mind and be aware of limitations of such models.