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"Huang, Sheng"
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The HDOCK server for integrated protein–protein docking
The HDOCK server (
http://hdock.phys.hust.edu.cn/
) is a highly integrated suite of homology search, template-based modeling, structure prediction, macromolecular docking, biological information incorporation and job management for robust and fast protein–protein docking. With input information for receptor and ligand molecules (either amino acid sequences or Protein Data Bank structures), the server automatically predicts their interaction through a hybrid algorithm of template-based and template-free docking. The HDOCK server distinguishes itself from similar docking servers in its ability to support amino acid sequences as input and a hybrid docking strategy in which experimental information about the protein–protein binding site and small-angle X-ray scattering can be incorporated during the docking and post-docking processes. Moreover, HDOCK also supports protein–RNA/DNA docking with an intrinsic scoring function. The server delivers both template- and docking-based binding models of two molecules and allows for download and interactive visualization. The HDOCK server is user friendly and has processed >30,000 docking jobs since its official release in 2017. The server can normally complete a docking job within 30 min.
The HDOCK server is developed for template-based and template-free protein–protein docking, using amino acid sequences or PDB structures as inputs. HDOCK can incorporate SAXS data and can be applied to protein–RNA/DNA docking.
Journal Article
Improvement of cryo-EM maps by simultaneous local and non-local deep learning
Cryo-EM has emerged as the most important technique for structure determination of macromolecular complexes. However, raw cryo-EM maps often exhibit loss of contrast at high resolution and heterogeneity over the entire map. As such, various post-processing methods have been proposed to improve cryo-EM maps. Nevertheless, it is still challenging to improve both the quality and interpretability of EM maps. Addressing the challenge, we present a three-dimensional Swin-Conv-UNet-based deep learning framework to improve cryo-EM maps, named EMReady, by not only implementing both local and non-local modeling modules in a multiscale UNet architecture but also simultaneously minimizing the local smooth L1 distance and maximizing the non-local structural similarity between processed experimental and simulated target maps in the loss function. EMReady was extensively evaluated on diverse test sets of 110 primary cryo-EM maps and 25 pairs of half-maps at 3.0–6.0 Å resolutions, and compared with five state-of-the-art map post-processing methods. It is shown that EMReady can not only robustly enhance the quality of cryo-EM maps in terms of map-model correlations, but also improve the interpretability of the maps in automatic de novo model building.
Map post-processing is crucial for cryo-EM modeling building. Here, the authors present a deep learning approach to improve both the quality and interpretability of cryo-EM maps by simultaneously considering local and non-local effects.
Journal Article
Post-acute care for frail older people decreases 90-day emergency room visits, readmissions and mortality: An interventional study
To evaluate the effects of post-acute care (PAC) on frail older adults after acute hospitalization in Taiwan.
This was a multicenter interventional study. Frail patients aged ≥ 75 were recruited and divided into PAC or control group. The PAC group received comprehensive geriatric assessment (CGA) and multifactorial intervention including exercise, nutrition education, and medicinal adjustments for two to four weeks, while the control group received only CGA. Outcome measures included emergency room (ER) visits, readmissions, and mortality within 90 days after PAC.
Among 254 participants, 205 (87.6±6.0 years) were in the PAC and 49 (85.2±6.0 years) in the control group. PAC for more than two weeks significantly decreased 90-day ER visits (odds ratio [OR] 0.21, 95% confidence interval [CI] 0.10-0.43; p = 0.024), readmissions (OR 0.30, 95% CI 0.16-0.56; p < 0.001), and mortality (OR 0.20, 95% CI 0.04-0.87; p = 0.032). Having problems in self-care was an independent risk factor for 90-day ER visits (OR 2.11, 95% CI 1.17-3.78; p = 0.012), and having problems in usual activities was an independent risk factor for 90-day readmissions (OR 2.69, 95% CI 1.53-4.72; p = 0.001) and mortality (OR 3.16, 95% CI 1.16-8.63; p = 0.024).
PAC program for more than two weeks could have beneficial effects on decreasing ER visits, readmissions, and mortality after an acute illness in frail older patients. Those who perceived severe problems in self-care and usual activities had a higher risk of subsequent adverse outcomes.
ClinicalTrials.gov NCT Identifier: NCT05452395.
Journal Article
Topological Phases Protected by Point Group Symmetry
We consider symmetry-protected topological (SPT) phases with crystalline point group symmetry, dubbed point group SPT (pgSPT) phases. We show that such phases can be understood in terms of lower-dimensional topological phases with on-site symmetry and that they can be constructed as stacks and arrays of these lower-dimensional states. This provides the basis for a general framework to classify and characterize bosonic and fermionic pgSPT phases, which can be applied for arbitrary crystalline point group symmetry and in arbitrary spatial dimensions. We develop and illustrate this framework by means of a few examples, focusing on three-dimensional states. We classify bosonic pgSPT phases and fermionic topological crystalline superconductors with Z2P (reflection) symmetry, electronic topological crystalline insulators (TCIs) with U(1)×Z2P symmetry, and bosonic pgSPT phases with C2v symmetry, which is generated by two perpendicular mirror reflections. We also study surface properties, with a focus on gapped, topologically ordered surface states. For electronic TCIs, we find a Z8×Z2 classification, where the Z8 corresponds to known states obtained from noninteracting electrons, and the Z2 corresponds to a “strongly correlated” TCI that requires strong interactions in the bulk. Our approach may also point the way toward a general theory of symmetry-enriched topological phases with crystalline point group symmetry.
Journal Article
Three-fold rotational defects in two-dimensional transition metal dichalcogenides
As defects frequently govern the properties of crystalline solids, the precise microscopic knowledge of defect atomic structure is of fundamental importance. We report a new class of point defects in single-layer transition metal dichalcogenides that can be created through 60° rotations of metal–chalcogen bonds in the trigonal prismatic lattice, with the simplest among them being a three-fold symmetric trefoil-like defect. The defects, which are inherently related to the crystal symmetry of transition metal dichalcogenides, can expand through sequential bond rotations, as evident from
in situ
scanning transmission electron microscopy experiments, and eventually form larger linear defects consisting of aligned 8–5–5–8 membered rings. First-principles calculations provide insights into the evolution of rotational defects and show that they give rise to p-type doping and local magnetic moments, but weakly affect mechanical characteristics of transition metal dichalcogenides. Thus, controllable introduction of rotational defects can be used to engineer the properties of these materials.
Defects in a crystalline solid can have a dramatic effect on the material’s properties. Here, the authors demonstrate a class of defects in two-dimensional transition metal dichalcogenides mediated by chalcogen vacancies and inherently related to the crystal symmetry
Journal Article
First Batch of z ≈ 11–20 Candidate Objects Revealed by the James Webb Space Telescope Early Release Observations on SMACS 0723-73
On 2022 July 13, NASA released to the whole world the data obtained by the James Webb Space Telescope (JWST) Early Release Observations (ERO). These are the first set of science-grade data from this long-awaited facility, marking the beginning of a new era in astronomy. In the study of the early universe, JWST will allow us to push far beyond z ≈ 11, the redshift boundary previously imposed by the 1.7 μm red cutoff of the Hubble Space Telescope (HST). In contrast, JWST’s NIRCam reaches ∼5 μm. Among the JWST ERO targets there is a nearby galaxy cluster SMACS 0723-73, which is a massive cluster and has been long recognized as a potential “cosmic telescope” in amplifying background galaxies. The ERO six-band NIRCam observations on this target have covered an additional flanking field not boosted by gravitational lensing, which also sees far beyond HST. Here we report the result from our search of candidate objects at z > 11 using these ERO data. In total, there are 87 such objects identified by using the standard “dropout” technique. These objects are all detected in multiple bands and therefore cannot be spurious. For most of them, their multiband colors are inconsistent with known types of contaminants. If the detected dropout signature is interpreted as the expected Lyman break, it implies that these objects are at z ≈ 11–20. The large number of such candidate objects at such high redshifts is not expected from the previously favored predictions and demands further investigations. JWST spectroscopy on such objects will be critical.
Journal Article
Pushing the accuracy limit of shape complementarity for protein-protein docking
Background
Protein-protein docking is a valuable computational approach for investigating protein-protein interactions. Shape complementarity is the most basic component of a scoring function and plays an important role in protein-protein docking. Despite significant progresses, shape representation remains an open question in the development of protein-protein docking algorithms, especially for grid-based docking approaches.
Results
We have proposed a new pairwise shape-based scoring function (LSC) for protein-protein docking which adopts an exponential form to take into account long-range interactions between protein atoms. The LSC scoring function was incorporated into our FFT-based docking program and evaluated for both bound and unbound docking on the protein docking benchmark 4.0. It was shown that our LSC achieved a significantly better performance than four other similar docking methods, ZDOCK 2.1, MolFit/G, GRAMM, and FTDock/G, in both success rate and number of hits. When considering the top 10 predictions, LSC obtained a success rate of 51.71% and 6.82% for bound and unbound docking, respectively, compared to 42.61% and 4.55% for the second-best program ZDOCK 2.1. LSC also yielded an average of 8.38 and 3.94 hits per complex in the top 1000 predictions for bound and unbound docking, respectively, followed by 6.38 and 2.96 hits for the second-best ZDOCK 2.1.
Conclusions
The present LSC method will not only provide an initial-stage docking approach for post-docking processes but also have a general implementation for accurate representation of other energy terms on grids in protein-protein docking. The software has been implemented in our HDOCK web server at
http://hdock.phys.hust.edu.cn/
.
Journal Article
Probing the edge-related properties of atomically thin MoS2 at nanoscale
Defects can induce drastic changes of the electronic properties of two-dimensional transition metal dichalcogenides and influence their applications. It is still a great challenge to characterize small defects and correlate their structures with properties. Here, we show that tip-enhanced Raman spectroscopy (TERS) can obtain distinctly different Raman features of edge defects in atomically thin MoS
2
, which allows us to probe their unique electronic properties and identify defect types (e.g., armchair and zigzag edges) in ambient. We observed an edge-induced Raman peak (396 cm
−1
) activated by the double resonance Raman scattering (DRRS) process and revealed electron–phonon interaction in edges. We further visualize the edge-induced band bending region by using this DRRS peak and electronic transition region using the electron density-sensitive Raman peak at 406 cm
−1
. The power of TERS demonstrated in MoS
2
can also be extended to other 2D materials, which may guide the defect engineering for desired properties.
Probing inevitable defects in two- dimensional materials is challenging. Here, the authors tackle this issue by using tip-enhanced Raman spectroscopy (TERS) to obtain distinctly different Raman features of edge defects in atomically thin MoS
2
, and further probe their unique electronic properties as well as identify the armchair and zigzag edges.
Journal Article