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Tools 2020: A compilation of tools for protein science

Given the extraordinary impact and ongoing value of the Protein Data Bank (PDB) it has to have pride of place in this issue (Goodsell et al. https://doi.org/10.1002/pro.3730). We should not forget that following the introduction of the PDB there were a number of well-known labs which strongly resisted the proposition that the coordinates and supporting data for all published structures be publicly released. Ever-increasing peer pressure from those who did deposit their data led to the expectation that “everyone needs to release their data.” Regrettably this is not the case in some other areas of science. Of the 155,000 or so atom-level 3D structures of biomolecules in the PDB, about 90% were determined by Xray crystallography. It is often stated that X-ray crystallography gives “static” information, although this must be qualified. Even before the structure of any protein was determined it was known that exposure of oxygen-free crystals of hemoglobin to air caused the crystals to crack. Thus, the binding of oxygen to hemoglobin was associated with some conformational change which was of sufficient strength and magnitude to overcome the protein– protein contacts which stabilized the crystal. Once the first protein crystal structures were determined it was apparent from the electron density that side-chains on the surface of the protein were often much more mobile than those in the core, and so on. The wealth of structural information in the PDB has made it possible to better define the stereochemistry of biomolecules. This, in turn, has provided guidelines against which newly determined structures can be evaluated. Here, Jane and David Richardson and coworkers (Prisant et al. https://doi.org/10.1002/pro.3786) describe the latest developments in the MolProbity web service for model validation. Their report is directed especially toward needs in cryo-electronmicroscopy. Also, Gert Vriend and colleagues (Lange et al. https:// doi.org/10.1002/pro.3788) describe a wide variety of facilities which support and exploit the use of PDB-derived structural data in bioinformatics studies. The DALI web server was introduced by Liisa Holm and Chris Sander 25 years ago and has been an invaluable resource ever since. Here Dr. Holm (https://doi.org/ 10.1002/pro.3749) updates DALI and gives insights into the extraordinary insights which it can provide. With the benefit of experience she also contrasts what DALI can and cannot do. ConSurf is a bioinformatics tool for accurately estimating the evolutionary rate of each protein in a protein family. Ben-Tal and coworkers (https://doi.org/10.1002/pro.3779) show that these evolutionary relationships can reveal structural and functional importance of specific positions.