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1. Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes

   https://doi.org/10.1093/nar/gkae1085  

   Balu, Sucharitha; Huget, Susie; Medina Reyes, Juan_Jose; Ragueneau, Eliot; Panneerselvam, Kalpana; Fischer, Samantha_N; Claussen, Erin_R; Kourtis, Savvas; Combe, Colin W.; Meldal, Birgit_H_M; et al (November 2024, Nucleic Acids Research)

   Abstract The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated reference database for molecular complexes. It is a unifying web resource linking aggregated data on composition, topology and the function of macromolecular complexes from 28 species. In addition to significantly extending the number of manually curated complexes, we have massively extended the coverage of the human complexome through the incorporation of high confidence assemblies predicted by machine-learning algorithms trained on large-scale experimental data. The current content of the portal comprising 2150 human complexes has been augmented by 14 964 machine-learning (ML) predicted complexes from hu.MAP3.0. We have refactored the website to enable easy search and filtering of these different classes of protein complexes and have implemented the Complex Navigator, a visualisation tool to facilitate comparison of related complexes in the context of orthology or paralogy. We have embedded the Rhea reaction visualisation tool into the website to enable users to view the catalytic activity of enzyme complexes. 

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2. Polytopal Complex Construction and Use in Persistent Homology

   https://doi.org/10.1109/ICDMW58026.2022.00087  

   Singh, Rohit P.; Wilsey, Philip A. (November 2022, ICDM Workshop on High Dimensional Data Mining)

   Topological Data Analysis (TDA) is a data mining technique to characterize the topological features of data. Persistent Homology (PH) is an important tool of TDA that has been applied to a wide range of applications. However its time and space complexities motivates a need for new methods to compute the PH of high-dimensional data. An important, and memory intensive, element in the computation of PH is the complex constructed from the input data. In general, PH tools use and focus on optimizing simplicial complexes; less frequently cubical complexes are also studied. This paper develops a method to construct polytopal complexes (or complexes constructed of any mix of convex polytopes) in any dimension Rn . In general, polytopal complexes are significantly smaller than simplicial or cubical complexes. This paper includes an experimental assessment of the impact that polytopal complexes have on memory complexity and output results of a PH computation. 

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3. Luminescent Bimetallic Two-Coordinate Gold(I) Complexes Utilizing Janus Carbenes

   https://doi.org/10.1021/jacs.3c07743  

   Ma, Jie; Schaab, Jonas; Paul, Sritoma; Forrest, Stephen R.; Djurovich, Peter I.; Thompson, Mark E. (September 2023, Journal of the American Chemical Society)

   A series of bimetallic carbene-metal-amide (cMa) complexes have been prepared with bridging biscarbene ligands to serve as a model for the design of luminescent materials with large oscillator strengths and small energy differences between the singlet and triplet states (dE ST). The complexes have a general structure (R2N)Au(:carbene—carbene:)Au(NR2). The bimetallic complexes show solvation-dependent absorption and emission that is analyzed in detail. It is found that the molar absorptivity of the bimetallic complexes is correlated with the energy barrier to rotation of the metal-ligand bond. The bimetallic cMa complexes also exhibit short emission lifetimes (t = 200-300 ns) with high photoluminescence efficiencies (PL >95%). The radiative rates of bimetallic cMa complexes are 3 to 4 times faster than that of the corresponding monometallic complexes. Analysis of temperature-dependent luminescence data indicates that the lifetime for the singlet state (τ_(S_1 )) of bimetallic cMa complexes are near 12 ns with a dE ST of 40 50 meV. The presented compounds provide a general design for cMa complexes to achieve small values for dE ST while retaining high radiative rates. Solution processed OLEDs made using two of the complexes as luminescent dopants show high efficiency and low roll-off at high luminance. 

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4. Comparing Morse Complexes Using Optimal Transport: An Experimental Study

   https://doi.org/10.1109/VIS54172.2023.00017  

   Li, Mingzhe; Storm, Carson; Li, Austin Yang; Needham, Tom; Wang, Bei (October 2023, 2023 IEEE Visualization and Visual Analytics (VIS))

   Morse complexes and Morse-Smale complexes are topological descriptors popular in topology-based visualization. Comparing these complexes plays an important role in their applications in feature correspondences, feature tracking, symmetry detection, and uncertainty visualization. Leveraging recent advances in optimal transport, we apply a class of optimal transport distances to the comparative analysis of Morse complexes. Contrasting with existing comparative measures, such distances are easy and efficient to compute, and naturally provide structural matching between Morse complexes. We perform an experimental study involving scientific simulation datasets and discuss the effectiveness of these distances as comparative measures for Morse complexes. We also provide an initial guideline for choosing the optimal transport distances under various data assumptions. 

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5. hu.MAP3.0: Atlas of human protein complexes by integration of > 25,000 proteomic experiments

   https://doi.org/10.1101/2024.10.11.617930  

   Fischer, Samantha N; Claussen, Erin R; Kourtis, Savvas; Sdelci, Sara; Orchard, Sandra; Hermjakob, Henning; Kustatscher, Georg; Drew, Kevin (October 2024, bioRxiv)

   Abstract Macromolecular protein complexes carry out most functions in the cell including essential functions required for cell survival. Unfortunately, we lack the subunit composition for all human protein complexes. To address this gap we integrated >25,000 mass spectrometry experiments using a machine learning approach to identify > 15,000 human protein complexes. We show our map of protein complexes is highly accurate and more comprehensive than previous maps, placing ∼75% of human proteins into their physical contexts. We globally characterize our complexes using protein co-variation data (ProteomeHD.2) and identify co-varying complexes suggesting common functional associations. Our map also generates testable functional hypotheses for 472 uncharacterized proteins which we support using AlphaFold modeling. Additionally, we use AlphaFold modeling to identify 511 mutually exclusive protein pairs in hu.MAP3.0 complexes suggesting complexes serve different functional roles depending on their subunit composition. We identify expression as the primary way cells and organisms relieve the conflict of mutually exclusive subunits. Finally, we import our complexes to EMBL-EBI’s Complex Portal (https://www.ebi.ac.uk/complexportal/home) as well as provide complexes through our hu.MAP3.0 web interface (https://humap3.proteincomplexes.org/). We expect our resource to be highly impactful to the broader research community. 

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