- CPORT: a Consensus Interface Predictor and its Performance in Prediction-driven Docking with HADDOCK
- Sjoerd J de Vries, Alexandre MJJ Bonvin PloSOne, DOI: 10.1371/journal.pone.0017695 (2011).
Supplementary material for:
- We have combined six interface prediction web servers into a consensus method called CPORT (Consensus Prediction Of interface Residues in Transient complexes) and show that CPORT gives more stable and reliable predictions than each of the individual predictors on its own. A protocol was developed to integrate CPORT predictions into our data-driven docking program HADDOCK. This prediction-driven docking protocol presents an alternative to ab initio docking, the docking of complexes without the use of any information.
Prediction-driven docking was performed on a large and diverse set of protein-protein complexes in a blind manner. Our results indicate that the performance of the HADDOCK-CPORT combination is competitive with ZDOCK-ZRANK, a state-of-the-art ab initio docking/scoring combination. Finally, the original interface predictions could be further improved by interface post-prediction (contact analysis of the docking solutions).
- This pages provides access to supplementary material related to this work.
- The following information is provided on this page:
- The list of all complexes considered with the chain information. The first chain corresponds to the largest component (chain A in the docking, receptor in the RMSD calculation), the other corresponds to the the smallest component (chain B in the docking, ligand in the RMSD calculation).
- The classification of all complexes as rigid/medium/hard and enzyme/other. See the docking benchmark paper for a detailed definition.
- Gzipped tar archive of tools to analyse the results. A description of its content can be found here.
- Gzipped tar archive of cport-specific information. A description of its content can be found here.
- Analysis (CPORT prediction and docking results) of the various complexes (see below).
- The following links gives access to the CPORT predictions and HADDOCK results for the various complexes used for testing. A description of the content of each directory can be found here.
- The corresponding gzipped tar archives for the above complexes can be downloaded by clicking on the links below (variable size between ~20 and 450 MB per complex).