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

Once the checks are passed, the data is collected, including the PDB file, the chains of the interacting subunits, the mutation, the wild-type and mutant affinities (K D , M ), the reference, the names of the proteins, the temperature at which the experiment is performed (T , K), the experimental method used (an extension of the category scheme of [22] ), notes on the entry and, when available, the association rate (k on , M −1 s −1 ), dissociation rate (k off , s −1 ), enthalpy (∆H, kcal.mol −1 ) and entropy (∆S, cal.mol −1 .K −1 ). For cases where multiple PDB entries are available, the higher resolution structure is chosen. Where affinities or kinetic or thermodynamic parameters are reported in different units, these are converted to the units specified above. In some cases, when not reported directly, K D , k on , k off , ∆H and ∆S were calculated using the relationships ∆G = ∆H − T ∆S = RT ln(K D ) and K D = 1/K A = k off /k on . To ensure consistency, the residue numbering in SKEMPI is the same as that reported in the PDB file. Thus the numbering is often shifted or altered compared to that in the cited paper such that, for instance, if a crystal structure of an antibody is reported in the Kabat numbering scheme but the mutation data is not, then the mutation data is converted before entry into SKEMPI. For all entries it is the case that the the affinity reported in the "wild-type" column corresponds to that of the PDB file, and the affinity in the "mutant" column is that after applying the specified mutation to the protein in the PDB file. Thus, where there are cases in which the PDB reports a mutant form and the entry corresponds to the reverse mutation back to the wild-type, the affinity of the former appears in the "wild-type" column and the latter in the "mutant" column. Such cases are noted in the database.