Structural screening of the Protein Data Bank for metal sites compatible with hydrogen-evolving catalysts: criteria, code and results

Frozen criteria, programs, input identifier lists, thresholds and complete results of a structural screen of the non-redundant Protein Data Bank for metal sites whose first coordination sphere matches that of a catalyst with experimentally measured hydrogen evolution. The screen covers 26,811 representative X-ray structures at 2.5 Å or better, of which 1,350 contain a site with Fe, Ni, Co, Mo or W, giving 4,119 sites in 277 sphere formulas. Sites are compared by least-squares superposition of the first coordination sphere within exact-composition groups, against positive and negative reference catalysts, using thresholds derived from the references themselves and fixed before execution. The deposit contains the three executions: the first, whose thresholds fell below the chain-to-chain variation of the reference structures; the second, in which a measured floor was applied; and the third, which adds an explicit rule for alternative conformations and partial occupancy. The criteria documents are dated, the manifest gives the SHA-256 of every file, and the programs are byte-identical to those that produced the reported numbers. Version 2 adds the third execution and two controls that were not part of the frozen protocol: a cross-metal comparison of the iron-heme sites against the cobalt-myoglobin geometry, and a hand-curated negative reference for iron myoglobin applied to the screen. It also adds the dated criteria document for the new rule, the programs that produced both controls, and their per-site outputs. The results of version 1 are unchanged and remain in the deposit. Licence: CC BY 4.0 for data and documents, MIT for the code.