SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation

Justina Jankauskaite; Brian Jiménez-García; Justas Dapkunas; Juan Fernández-Recio; Iain H. Moal

Just over two fifths of the data come from the previous version of SKEMPI [47] , comprised mostly of data found in literature sources which came to the authors' attention, in some cases during the data collection for the structural affinity benchmark [33] and following references therein. Some entries in SKEMPI 1.1 were found by checking the references in the ASEdb [71] and PINT [36] databases, although not all the data passed the checks required for inclusion (see section II-B). Similarly, most of the new data in SKEMPI 2.0 was found by searching the literature, partly in tandem with the literature search for the more recent structural affinity benchmark [73] . During data collection three other relevant databases were published: ABbind [67] , PROXiMATE [31] and dbMPIKT [41] . Their references were checked if they were not already included. Data from these sources comprise 4%, 3% and 6% of SKEMPI 2.0 respectively. As with ASEdb and PINT, none of the data were directly copied into SKEMPI. Moreover, the cited papers were read and data entered using the same checks and procedures as other entries.