Publication
This article deals with computational tools for the analysis of protein structures, and how they bring information about dynamic and functional aspects of proteins. A focus on online tools is intentional given their ease of use, but important tools available only as programs are also listed. After a briefing on how to find experimental structures and how to model unknown structures, the article discusses tools and methods to analyze sequences and sequence alignments in a structural context, and then to the analysis of protein structures itself. The latter point, deep focus of this article, discusses tools to analyze and visualize proteins, their geometrical and chemical structural quality, their cores and surfaces, their interactions with other proteins, small molecules and other biomacromolecules, their dynamics over different timescales at varied levels of resolution, and their functional and regulatory sites. The article ends with a glance at how molecular simulations can further help investigate biomolecular structure and function, potentially covering all of the above at higher level of detail but often at prohibitive cost.