PROCOS: Computational analysis of protein–protein complexes

Abstract One of the main challenges in protein–protein docking is a meaningful evaluation of the many putative solutions. Here we present a program (PROCOS) that calculates a probability‐like measure to be native for a given complex. In contrast to scores often used for analyzing complex structures, the calculated probabilities offer the advantage of providing a fixed range of expected values. This will allow, in principle, the comparison of models corresponding to different targets that were solved with the same algorithm. Judgments are based on distributions of properties derived from a large database of native and false complexes. For complex analysis PROCOS uses these property distributions of native and false complexes together with a support vector machine (SVM). PROCOS was compared to the established scoring schemes of ZRANK and DFIRE. Employing a set of experimentally solved native complexes, high probability values above 50% were obtained for 90% of these structures. Next, the performance of PROCOS was tested on the 40 binary targets of the Dockground decoy set, on 14 targets of the RosettaDock decoy set and on 9 targets that participated in the CAPRI scoring evaluation. Again the advantage of using a probability‐based scoring system becomes apparent and a reasonable number of near native complexes was found within the top ranked complexes. In conclusion, a novel fully automated method is presented that allows the reliable evaluation of protein–protein complexes. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011