CRYSTALP2: sequence-based protein crystallization propensity prediction

A significant majority of the collocations used by CRYSTALP2 include residues with high conformational entropy, or low entropy and high potential to mediate crystal contacts; notably, such residues are utilized by surface entropy reduction methods. We show that the collocations provide complementary information to the hydrophobicity and isoelectric point. Tests on four datasets show that CRYSTALP2 outperforms several existing sequence-based predictors (CRYSTALP, OB-score, and SECRET). CRYSTALP2's accuracy, MCC, and AROC range between 69.3 and 77.5%, 0.39 and 0.55, and 0.72 and 0.79, respectively. Our predictions are similar in quality and are complementary to the predictions of the most recent ParCrys and XtalPred methods. Our results also suggest that, as work in protein crystallization continues (thereby enlarging the population of proteins with known crystallization propensities), the prediction quality of the CRYSTALP2 method should increase. The prediction model and the datasets used in this contribution can be downloaded from http://biomine.ece.ualberta.ca/CRYSTALP2/CRYSTALP2.html webcite.CRYSTALP2 provides relatively accurate crystallization propensity predictions for a given protein chain that either outperform or complement the existing approaches. The proposed method can be used to support current efforts towards improving the success rate in obtaining diffraction-quality crystals.Structural genomics is a word-wide initiative aimed at producing a comprehensive mapping of the protein structure space [1]. The resulting knowledge of the tertiary structure of proteins will be vitally important for understanding and manipulating the biochemical and cellular functions of a given protein. This is an important step in rational drug design [2] and provides valuable insights into important diseases [3]. There are several different ways to obtain the structure including X-ray diffraction, electron microscopy, and NMR. Although a majority of protein structures are obt