The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.

We present the seventh report on the performance of methods for predicting the atomic resolution structures of protein complexes offered as targets to the community-wide initiative on the Critical Assessment of Predicted Interactions (CAPRI). Performance was evaluated on the basis of 36114 models of protein complexes submitted by 57 groups-including 13 automatic servers-in prediction Rounds held during the years 2016-2019 for 8 proteinprotein, 3 protein-peptide, and 5 protein-oligosaccharide targets with different length ligands. Six of the protein-protein targets represented challenging hetero-complexes, due to factors such as availability of distantly related templates for the individual subunits, or for the full complex, inter-domain flexibility, conformational adjustments at the binding region, or the multi-component nature of the complex. The main challenge for the protein-peptide and protein-oligosaccharide complexes was to accurately model the ligand conformation and its interactions at the interface. Encouragingly, models of acceptable quality, or better, were obtained for a total of 6 protein-protein complexes, which included 4 of the challenging hetero-complexes and a homo-decamer. But fewer of these targets were predicted with medium or higher accuracy. High accuracy models were obtained for 2 of the 3 proteinpeptide targets, and for one of the protein-oligosaccharide targets. The remaining proteinsugar targets were predicted with medium accuracy. Our analysis indicates that progress in predicting increasingly challenging and diverse types of targets is due to closer integration of This article is protected by copyright. All rights reserved. template-based modeling techniques with docking, scoring and model refinement procedures, and to significant incremental improvements in the underlying methodologies.

We present the results for CAPRI Round 46, the third joint CASP‐CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo‐oligomers and 6 heterocomplexes. Eight of the homo‐oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher‐order assemblies. These were more difficult to model, as their prediction mainly involved “ab‐initio” docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance “gap” was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template‐based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.