MimoDB 2.0: a mimotope database and beyond

Abstract

Mimotopes are peptides with affinities to given targets. They are readily obtained through biopanning against combinatorial peptide libraries constructed by phage display and other display technologies such as mRNA display, ribosome display, bacterial display and yeast display. Mimotopes have been used to infer the protein interaction sites and networks; they are also ideal candidates for developing new diagnostics, therapeutics and vaccines. However, such valuable peptides are not collected in the central data resources such as UniProt and NCBI GenPept due to their 'unnatural' short sequences. The MimoDB database is an information portal to biopanning results of random libraries. In version 2.0, it has 15,633 peptides collected from 849 papers and grouped into 1818 sets. Besides the core data on panning experiments and their results, broad background information on target, template, library and structure is included. An accompanied benchmark has also been compiled for bioinformaticians to develop and evaluate their new models, algorithms and programs. In addition, the MimoDB database provides tools for simple and advanced searches, structure visualization, BLAST and alignment view on the fly. The experimental biologists can easily use the database as a virtual control to exclude possible target-unrelated peptides. The MimoDB database is freely available at http://immunet.cn/mimodb.

Figure 1.

Benchmark Mapitope, Episearch and MimoPro with MimoBench. The string under the X-axis is the case tested. Each case has the format: PDB ID_Mimotope Set ID, where the left part is the PDB code of corresponding target–template structure, the right part is entry ID of the mimotope set. (A) Antibody–antigen group, (B) receptor–ligand group and (C) other protein–protein interaction group.

Figure 2.

Success cases of Mapitope, Episearch and MimoPro with AUC above 0.8. The cases are written in the same format described in Figure 1.