Input files and files with coordinates and topologies of the ligand-protein complexes which were used to obtain the models using single structures or an ensemble of structures to represent each ligand-protein complex in the paper: "Prediction of Drug-Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis", by Ariane Nunes Alves, Fabian Ormersbach and Rebecca Wade. The dataset contains 33 inhibitors of p38 MAP kinase. COMBINE analysis was performed to predict dissociation rate constants. The code for ensemble COMBINE analysis can be obtained at: https://github.com/HITS-MCM/ensembleCOMBINE.