Advertisement
Research Article

Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments

  • Roberto Mosca,

    Affiliations: Institute for Research in Biomedicine, Barcelona, Spain, Barcelona Supercomputing Center, Barcelona, Spain

    X
  • Carles Pons,

    Affiliations: Barcelona Supercomputing Center, Barcelona, Spain, National Institute of Bioinformatics (INB), Barcelona, Spain

    X
  • Juan Fernández-Recio,

    Affiliation: Barcelona Supercomputing Center, Barcelona, Spain

    X
  • Patrick Aloy mail

    patrick.aloy@irbbarcelona.org

    Affiliations: Institute for Research in Biomedicine, Barcelona, Spain, Barcelona Supercomputing Center, Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

    X
  • Published: August 28, 2009
  • DOI: 10.1371/journal.pcbi.1000490

Reader Comments (2)

Post a new comment on this article

ambitious but...

Posted by raik on 19 Sep 2010 at 15:40 GMT

This is a very ambitious work but it quite obviously was rushed out. My two main concerns are:
(1) about 10% of the supposed homology models are, in fact, genuine yeast structures with 100% sequence identity between template and target.
(2) presumably, many of the docking runs are "re-docking" two structures that have been taken from the same co-crystallized complex -- a situation that is very different from the real docking of "unbound" structures. The authors admit that this "may" be the reason for the surprisingly high success rate. It is really frustrating that they don't give us the actual number -- it's a simple matter of counting. Without knowing this fraction of re-docking, it is difficult to evaluate the reliability of the method or the reported success rates.

My overall impression is that of an important job, left unfinished. This is all the more unfortunate, as there evidently has been a tremendous amount of work invested.

No competing interests declared.