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Since the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14), AlphaFold2 has become the standard method for protein tertiary structure prediction. One remaining challenge is to further improve its prediction. We developed a new version of the MULTICOM system to sample diverse multiple sequence alignments (MSAs) and structural templates to improve the input for AlphaFold2 to generate structural models. The models are then ranked by both the pairwise model similarity and AlphaFold2 self-reported model quality score. The top ranked models are refined by a novel structure alignment-based refinement method powered by Foldseek. Moreover, for a monomer target that is a subunit of a protein assembly (complex), MULTICOM integrates tertiary and quaternary structure predictions to account for tertiary structural changes induced by protein-protein interaction. The system participated in the tertiary structure prediction in 2022 CASP15 experiment. Our server predictor MULTICOM_refine ranked 3rd among 47 CASP15 server predictors and our human predictor MULTICOM ranked 7th among all 132 human and server predictors. The average GDT-TS score and TM-score of the first structural models that MULTICOM_refine predicted for 94 CASP15 domains are ~0.80 and ~0.92, 9.6% and 8.2% higher than ~0.73 and 0.85 of the standard AlphaFold2 predictor respectively. 

We develop a machine learning-based model to predict the Raman tilt induced in a multiwavelength signal propagating through a 50km optical fiber deployed in the COSMOS testbed. The neural network model achieves a mean prediction error of 0.02–0.13 dB for randomly loaded channels. 

Abstract Deep learning methods that achieved great success in predicting intrachain residue-residue contacts have been applied to predict interchain contacts between proteins. However, these methods require multiple sequence alignments (MSAs) of a pair of interacting proteins (dimers) as input, which are often difficult to obtain because there are not many known protein complexes available to generate MSAs of sufficient depth for a pair of proteins. In recognizing that multiple sequence alignments of a monomer that forms homomultimers contain the co-evolutionary signals of both intrachain and interchain residue pairs in contact, we applied DNCON2 (a deep learning-based protein intrachain residue-residue contact predictor) to predict both intrachain and interchain contacts for homomultimers using multiple sequence alignment (MSA) and other co-evolutionary features of a single monomer followed by discrimination of interchain and intrachain contacts according to the tertiary structure of the monomer. We name this tool DNCON2_Inter. Allowing true-positive predictions within two residue shifts, the best average precision was obtained for the Top-L/10 predictions of 22.9% for homodimers and 17.0% for higher-order homomultimers. In some instances, especially where interchain contact densities are high, DNCON2_Inter predicted interchain contacts with 100% precision. We also developed Con_Complex, a complex structure reconstruction tool that uses predicted contacts to produce the structure of the complex. Using Con_Complex, we show that the predicted contacts can be used to accurately construct the structure of some complexes. Our experiment demonstrates that monomeric multiple sequence alignments can be used with deep learning to predict interchain contacts of homomeric proteins. 

Abstract MotivationDeep learning has revolutionized protein tertiary structure prediction recently. The cutting-edge deep learning methods such as AlphaFold can predict high-accuracy tertiary structures for most individual protein chains. However, the accuracy of predicting quaternary structures of protein complexes consisting of multiple chains is still relatively low due to lack of advanced deep learning methods in the field. Because interchain residue–residue contacts can be used as distance restraints to guide quaternary structure modeling, here we develop a deep dilated convolutional residual network method (DRCon) to predict interchain residue–residue contacts in homodimers from residue–residue co-evolutionary signals derived from multiple sequence alignments of monomers, intrachain residue–residue contacts of monomers extracted from true/predicted tertiary structures or predicted by deep learning, and other sequence and structural features. ResultsTested on three homodimer test datasets (Homo_std dataset, DeepHomo dataset and CASP-CAPRI dataset), the precision of DRCon for top L/5 interchain contact predictions (L: length of monomer in a homodimer) is 43.46%, 47.10% and 33.50% respectively at 6 Å contact threshold, which is substantially better than DeepHomo and DNCON2_inter and similar to Glinter. Moreover, our experiments demonstrate that using predicted tertiary structure or intrachain contacts of monomers in the unbound state as input, DRCon still performs well, even though its accuracy is lower than using true tertiary structures in the bound state are used as input. Finally, our case study shows that good interchain contact predictions can be used to build high-accuracy quaternary structure models of homodimers. Availability and implementationThe source code of DRCon is available at https://github.com/jianlin-cheng/DRCon. The datasets are available at https://zenodo.org/record/5998532#.YgF70vXMKsB. Supplementary informationSupplementary data are available at Bioinformatics online. 

Proteins interact to form complexes. Predicting the quaternary structure of protein complexes is useful for protein function analysis, protein engineering, and drug design. However, few user-friendly tools leveraging the latest deep learning technology for inter-chain contact prediction and the distance-based modelling to predict protein quaternary structures are available. To address this gap, we develop DeepComplex, a web server for predicting structures of dimeric protein complexes. It uses deep learning to predict inter-chain contacts in a homodimer or heterodimer. The predicted contacts are then used to construct a quaternary structure of the dimer by the distance-based modelling, which can be interactively viewed and analysed. The web server is freely accessible and requires no registration. It can be easily used by providing a job name and an email address along with the tertiary structure for one chain of a homodimer or two chains of a heterodimer. The output webpage provides the multiple sequence alignment, predicted inter-chain residue-residue contact map, and predicted quaternary structure of the dimer. DeepComplex web server is freely available at http://tulip.rnet.missouri.edu/deepcomplex/web_index.html 

A<sc>bstract</sc> Inclusive and differential cross sections for Higgs boson production in proton-proton collisions at a centre-of-mass energy of 13.6 TeV are measured using data collected with the CMS detector at the LHC in 2022, corresponding to an integrated luminosity of 34.7 fb⁻¹. Events with the diphoton final state are selected, and the measured inclusive fiducial cross section is$${\sigma }_{\text{fid}}={74}\pm {11}{\left({\text{stat}}\right)}_{-4}^{+5}\left({\text{syst}}\right)$$fb, in agreement with the standard model prediction of 67.8 ± 3.8 fb. Differential cross sections are measured as functions of several observables: the Higgs boson transverse momentum and rapidity, the number of associated jets, and the transverse momentum of the leading jet in the event. Within the uncertainties, the differential cross sections agree with the standard model predictions. 

A measurement is presented of the cross section in proton-proton collisions for the production of two $W$bosons and one $Z$boson. It is based on data recorded by the CMS experiment at the CERN LHC at center-of-mass energies $\sqrt{s}=13$and 13.6 TeV, corresponding to an integrated luminosity of $200{\mathrm{fb}}^{-1}$. Events with four charged leptons (electrons or muons) in the final state are selected. Both nonresonant $WWZ$production and $ZH$production, with the Higgs boson decaying into two $W$bosons, are reported. For the first time, the two processes are measured separately in a simultaneous fit. Combining the two modes, signal strengths relative to the standard model (SM) predictions of ${0.75}_{-0.29}^{+0.34}$and ${1.74}_{-0.60}^{+0.71}$are measured for $\sqrt{s}=13$and 13.6 TeV, respectively. The observed (expected) significance for the triboson signal is 3.8 (2.5) standard deviations for $\sqrt{s}=13.6\mathrm{TeV}$, thus providing the first evidence for triboson production at this center-of-mass energy. Combining the two modes and the two center-of-mass energies, the inclusive signal strength relative to the SM prediction is measured to be ${1.03}_{-0.28}^{+0.31}$, with an observed (expected) significance of 4.5 (5.0) standard deviations.