We present a short overview of the system governing data processing and automatic evaluation of predictions in CASP6, implemented at the Livermore Protein Structure Prediction Center. The system incorporates interrelated facilities for registering participants, collecting prediction targets from crystallographers and NMR spectroscopists and making them available to the CASP6 participants, accepting predictions and providing their preliminary evaluation, and finally, storing and visualizing results. We have automatically evaluated predictions submitted to CASP6 using criteria and methods developed over the successive CASP experiments. Also, we have tested a new evaluation technique based on non-rigid-body type superpositions. Approximately the same number of predictions has been submitted to CASP6 as to all previous CASPs combined, making navigation through and understanding of the data particularly challenging. To facilitate this, we have substantially modernized all data handling procedures, including implementation of a dedicated relational database. An overview of our redesigned website is also presented (http://predictioncenter.org/casp6/). Proteins 2005;Suppl 7:19–23. © 2005 Wiley-Liss, Inc.