ABSTRACT We introduce an updated non-redundant protein-RNA docking benchmark version 3.0 (PRDBv3.0) containing 197 test cases curated from 288 unique protein–RNA complexes available in the Protein Data Bank until July 2024. Among these, 27 are unbound–unbound (UU) type where both the binding partners are available in their unbound states, 160 are unbound–bound (UB) type where only the protein is available in unbound state and remaining 10 are bound–unbound (BU) type where only the RNA is available in unbound state. The benchmark is categorized into three classes based on the conformational flexibility of the protein interface: 117 rigid-body (R) complexes with minimal structural changes, 41 semi-flexible (S) complexes showing moderate conformational changes and 29 full-flexible (F) complexes with significant conformational changes. The current benchmark represents a 62\% increase in the number of test cases compared to its previous version. Binding affinity (Kd) values for a subset of 105 protein–RNA complexes from PRDBv3.0 are catalogued along with additional experimental details to develop a comprehensive protein–RNA affinity benchmark. Moreover, a total of 255 unique RNA-binding domains, present in RNA-binding proteins, are also catalogued in this updated benchmark. PRDBv3.0 will facilitate the evaluation of both rigid-body and flexible docking methods as well as the methods that aim to predict binding affinity. The updated benchmark is freely available at http://www.csb.iitkgp.ac.in/applications/PRDBv3/PRDBv3.php.
