We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy.
The Regional Ocean Modeling System (ROMS) 4-dimensional variational (4D-Var) data 1 assimilation tool has been used to compute two sequences of circulation analyses for the 2 U.S. west coast. One sequence of analyses spans the period 1980-2010 and is subject to 3 surface forcing derived from relatively low resolution atmospheric products from the Cross-4 Calibrated Multi-Platform wind product (CCMP) and the European Centre for Medium 5 Range Weather Forecasts (ECMWF) reanalysis project. The second sequence spans the 6 shorter period 1999-2012 and is subject to forcing derived from a high resolution product from 7 the Naval Research Laboratory Coupled Ocean Atmosphere Mesoscale Prediction System 8 (COAMPS). The two analyses periods are divided into eight day windows, and all available 9 satellite observations of sea surface temperature and sea surface height, as well as in situ 10 hydrographic profiles are assimilated into ROMS using 4D-Var. The performance of the 11 system is monitored in terms of the cost function and the statistics of the innovations, and 12 the impact of data assimilated on the circulation is assessed by comparing the posterior 13 circulation estimates with the prior circulation and the circulation from a run of the model 14 without data assimilation, with particular emphasis on eddy kinetic energy. This is part I 15 of a two part series, and the circulation variability of the 4D-Var analyses is documented in 16 part II.17
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