ProPairs: A Data Set for Protein-Protein Docking
ProPairs provides a set of protein-protein docking complexes with their unbound structures.
The set can be used to benchmark or to test docking algorithms.
- Protein-protein complexes with unbound binding partners
- interface-aligned and superposed PDB files of bound and unbound structures
- mapping of cofactors between protein-protein complexes and their unbound structures
- Non-redundant set of protein-protein complexes
- clustering of all detected interfaces
- only representative protein-protein complexes with their most representative unbound structures
- Novel, fully automatic algorithm
- deterministic selection of structures
- assigns suitable unbound structures to at least one of the two binding partners
- uses only protein structures and biological assembly information from the PDB
- frequent updates that include latest structures of PDB
- Open source
- transparent procedure
- easy to generate own sets
For a multi-chain protein complex different partitions into two binding partners are possible. Here, we use the existence of corresponding unbound structures in the PDB as the criterion for legitimate partitions of the considered protein complexes.
|Apr/17 2018||Updated data set (PDB snapshot: Jan/2018) with additional 308 novel, non-redundant interfaces (105 with two unbound structures)|
|Jun/16 2017||Updated data set (PDB snapshot: Jan/2017) with additional 331 novel, non-redundant interfaces (110 with two unbound structures) + updated webpage (Commit)|
|Apr/26 2016||Updated data set (PDB snapshot: Jan/2016) + support interactive filtering by number of S2 bonds (Commit)|
|Feb/18 2016||ProPairs supports using time-stamped yearly snapshots of the PDB archive. (Commit)|
|Jul/06 2015||The ProPairs webpage provides the data sets as single ZIP archives containing all PDB files. See "Raw data" for download links. (Commit)|
Please send comments and questions to firstname.lastname@example.org