Accurate structure prediction of biomolecular interactions with AlphaFold 3.

The introduction of AlphaFold 21 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design2-6. Here we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture that is capable of predicting the joint structure of complexes including proteins, nucleic acids, small molecules, ions and modified residues. The new AlphaFold model demonstrates substantially improved accuracy over many previous specialized tools: far greater accuracy for protein-ligand interactions compared with state-of-the-art docking tools, much higher accuracy for protein-nucleic acid interactions compared with nucleic-acid-specific predictors and substantially higher antibody-antigen prediction accuracy compared with AlphaFold-Multimer v.2.37,8. Together, these results show that high-accuracy modelling across biomolecular space is possible within a single unified deep-learning framework.

Investigations into the nature of spontelectrics: nitrous oxide diluted in xenon.

The recent discovery of a new class of solids displaying bulk spontaneous electric fields as high as 10(8) V m(-1), so-called 'spontelectrics', poses fundamental and unresolved problems in solid state physics. The purpose of the present work is to delve more deeply into the nature of the interactions which give rise to the spontelectric effect in films of nitrous oxide (N2O), by observing the variation of the spontaneous field as the N2O molecules are physically removed from one another by dilution in Xe. Data, obtained using the ASTRID storage ring, are presented for films diluted by factors ξ = Xe/N2O of 0.9 to 67, at deposition temperatures of 38 K, 44 K and 48 K, where films are laid down by deposition from a gas mixture. Results show that the spontelectric field decreases as ξ increases and that at ξ = 67 for 44 K deposition, the spontelectric effect is absent. Reflection-absorption infrared spectroscopy (RAIRS) data are also reported, providing insight into the structure of Xe/N2O films and specifically showing that N2O remains dispersed in the Xe/N2O films prepared here. A simplified theoretical model is developed which illustrates that electric fields can be understood in terms of dilution-dependent dipole orientation. This model is used to reproduce experimental data up to an average molecular separation, s, of ≥1.25 nm apart, ∼4 times that associated with pure solid N2O. The disappearance of the spontelectric effect at larger average distances of separation, between s = 1.25 nm and s = 1.75 nm, is a phenomenon which cannot be described by any existing model but which shows that dipole-dipole interactions are an essential ingredient for the creation of the spontelectric state.

Electric field structures in thin films: formation and properties.

A newly discovered class of molecular materials, so-called "spontelectrics", display spontaneous electric fields. Here we show that the novel properties of spontelectrics can be used to create composite spontelectrics, illustrating how electric fields in solid films may be structured on the nanoscale by combining layers of different spontelectric materials. This is demonstrated using the spontelectric materials nitrous oxide, toluene, isoprene, isopentane, and CF2Cl2. These yield a variety of tailored electric field structures, with individual layers harboring fields between 10(7) and 10(8) V/m. Fields may be of the same sign or of opposite sign, the latter enabling the creation of nanoscale potential wells. The formation of fields is followed using an established electron beam technique, employing the ASTRID synchrotron storage ring. The influence of temperature on heterolayer structures, displaying new Curie effects, and the nature of the interfacial region between different spontelectrics are also discussed.