A loop closure-based sequential algorithm, PRODA_MATCH, was developed to match catalytic residues onto a scaffold for enzyme design in silico. The computational complexity of this algorithm is polynomial with respect to the number of active sites, the number of catalytic residues, and the maximal iteration number of cyclic coordinate descent steps. This matching algorithm is independent of a rotamer library that enables the catalytic residue to take any required conformation during the reaction coordinate. The catalytic geometric parameters defined between functional groups of transition state (TS) and the catalytic residues are continuously optimized to identify the accurate position of the TS. Pseudo-spheres are introduced for surrounding residues, which make the algorithm take binding into account as early as during the matching process. Recapitulation of native catalytic residue sites was used as a benchmark to evaluate the novel algorithm. The calculation results for the test set show that the native catalytic residue sites were successfully identified and ranked within the top 10 designs for 7 of the 10 chemical reactions. This indicates that the matching algorithm has the potential to be used for designing industrial enzymes for desired reactions.
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