Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average ~70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.

Synthesis of (Ca,Nd)TiO3 powders by complex polymerization, Rietveld refinement and optical properties

Neodymium calcium titanate, (Ca(0.99)Nd(0.01))TiO(3) powders were synthesized by the complex polymerization method and heat treated at different temperatures for 2 h under air atmosphere. The structural evolution of these powders as a function of heat treatment temperature was analyzed by X-ray diffraction (XRD) and micro-Raman (MR) spectroscopy. The optical properties were investigated by Ultraviolet-visible (UV-vis) absorption spectroscopy and Photoluminescence (PL) measurements. XRD patterns, Rietveld refinement and MR spectra indicated that the powders heated treated at 750 degrees C for 2 h present an orthorhombic structure without secondary phases. UV-vis measurements suggested the presence of intermediary energy in disordered (Ca(0.99)Nd(0.01))TiO(3) powders. Broad and narrow bands were observed in the PL spectra of these powders when excited with 350 nm wavelength. The broad bands were associated to the structural defects and/or p-d electronic transitions while, the narrow bands were ascribed to f-f transitions arising from Nd(3+) ions.