ResearchPub Date : 2024-08-26eCollection Date: 2024-01-01DOI: 10.34133/research.0458
Yilun Zhou, Yinghui Xie, Xiaolu Liu, Mengjie Hao, Zhongshan Chen, Hui Yang, Geoffrey I N Waterhouse, Shengqian Ma, Xiangke Wang
{"title":"Single-Molecule Traps in Covalent Organic Frameworks for Selective Capture of C<sub>2</sub>H<sub>2</sub> from C<sub>2</sub>H<sub>4</sub>-Rich Gas Mixtures.","authors":"Yilun Zhou, Yinghui Xie, Xiaolu Liu, Mengjie Hao, Zhongshan Chen, Hui Yang, Geoffrey I N Waterhouse, Shengqian Ma, Xiangke Wang","doi":"10.34133/research.0458","DOIUrl":"10.34133/research.0458","url":null,"abstract":"<p><p>Removing trace amounts of acetylene (C<sub>2</sub>H<sub>2</sub>) from ethylene (C<sub>2</sub>H<sub>4</sub>)-rich gas mixtures is vital for the supply of high-purity C<sub>2</sub>H<sub>4</sub> to the chemical industry and plastics sector. However, selective removal of C<sub>2</sub>H<sub>2</sub> is challenging due to the similar physical and chemical properties of C<sub>2</sub>H<sub>2</sub> and C<sub>2</sub>H<sub>4</sub>. Here, we report a \"single-molecule trap\" strategy that utilizes electrostatic interactions between the one-dimensional (1D) channel of a covalent organic framework (denoted as COF-1) and C<sub>2</sub>H<sub>2</sub> molecules to massively enhance the adsorption selectivity toward C<sub>2</sub>H<sub>2</sub> over C<sub>2</sub>H<sub>4</sub>. C<sub>2</sub>H<sub>2</sub> molecules are immobilized via interactions with the O atom of C=O groups, the N atom of C≡N groups, and the H atom of phenyl groups in 1D channels of COF-1. Due to its exceptionally high affinity for C<sub>2</sub>H<sub>2</sub>, COF-1 delivered a remarkable C<sub>2</sub>H<sub>2</sub> uptake of 7.97 cm<sup>3</sup>/g at 298 K and 0.01 bar, surpassing all reported COFs and many other state-of-the-art adsorbents under similar conditions. Further, COF-1 demonstrated outstanding performance for the separation of C<sub>2</sub>H<sub>2</sub> and C<sub>2</sub>H<sub>4</sub> in breakthrough experiments under dynamic conditions. COF-1 adsorbed C<sub>2</sub>H<sub>2</sub> at a capacity of 0.17 cm<sup>3</sup>/g at 2,000 s/g when exposed to 0.5 ml/min C<sub>2</sub>H<sub>4</sub>-rich gas mixture (99% C<sub>2</sub>H<sub>4</sub>) at 298 K, directly producing high-purity C<sub>2</sub>H<sub>4</sub> gas at a rate of 3.95 cm<sup>3</sup>/g. Computational simulations showed that the strong affinity between C<sub>2</sub>H<sub>2</sub> and the single-molecule traps of COF-1 were responsible for the excellent separation performance. COF-1 is also robust, providing a promising new strategy for the efficient removal of trace amounts of C<sub>2</sub>H<sub>2</sub> in practical C<sub>2</sub>H<sub>4</sub> purification.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"7 ","pages":"0458"},"PeriodicalIF":11.0,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11345538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142073796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ResearchPub Date : 2024-08-20eCollection Date: 2024-01-01DOI: 10.34133/research.0460
Linghang Wang, Huitao Yu, Wei Feng
{"title":"Photothermal Phase Change Energy Storage Materials: A Groundbreaking New Energy Solution.","authors":"Linghang Wang, Huitao Yu, Wei Feng","doi":"10.34133/research.0460","DOIUrl":"10.34133/research.0460","url":null,"abstract":"<p><p>To meet the demands of the global energy transition, photothermal phase change energy storage materials have emerged as an innovative solution. These materials, utilizing various photothermal conversion carriers, can passively store energy and respond to changes in light exposure, thereby enhancing the efficiency of energy systems. Photothermal phase change energy storage materials show immense potential in the fields of solar energy and thermal management, particularly in addressing the intermittency issues of solar power. Their multifunctionality and efficiency offer broad application prospects in new energy technologies, construction, aviation, personal thermal management, and electronics.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"7 ","pages":"0460"},"PeriodicalIF":11.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334572/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142009333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ResearchPub Date : 2024-08-19eCollection Date: 2024-01-01DOI: 10.34133/research.0457
Jian Dong, Binjia Ruan, Lijun Zhang, Ai Wei, Chuling Li, Neng Tang, Linxi Zhu, Qing Jiang, Wangsen Cao
{"title":"DNA Methylation-Mediated GPX4 Transcriptional Repression and Osteoblast Ferroptosis Promote Titanium Particle-Induced Osteolysis.","authors":"Jian Dong, Binjia Ruan, Lijun Zhang, Ai Wei, Chuling Li, Neng Tang, Linxi Zhu, Qing Jiang, Wangsen Cao","doi":"10.34133/research.0457","DOIUrl":"10.34133/research.0457","url":null,"abstract":"<p><p>Metal wear particles generated by the movement of joint prostheses inevitably lead to aseptic osteolytic damage and ultimately prosthesis loosening, which are aggravated by various types of regulated cell death of bone. Nevertheless, the exact cellular nature and regulatory network underlying osteoferroptosis are poorly understood. Here, we report that titanium particles (TP) induced severe peri-implant osteolysis and ferroptotic changes with concomitant transcriptional repression of a key anti-ferroptosis factor, GPX4, in a mouse model of calvarial osteolysis. GPX4 repression was accompanied by an increase in DNA methyltransferases (DNMTs) 1/3a/3b and hypermethylation of the <i>Gpx4</i> promoter, which were partly mediated by the transcriptional regulator/co-repressor KLF5 and NCoR. Conversely, treatment with SGI-1027, a DNMT-specific inhibitor, resulted in marked reversal of <i>Gpx4</i> promoter hypermethylation and GPX4 repression, as well as improvement in ferroptotic osteolysis to a similar extent as with a ferroptosis inhibitor, liproxstatin-1. This suggests that epigenetic GPX4 repression and ferroptosis caused by the increase of DNMT1/3a/3b have a causal influence on TP-induced osteolysis. In cultured primary osteoblasts and osteoclasts, GPX4 repression and ferroptotic changes were observed primarily in osteoblasts that were alleviated by SGI-1027 in a GPX4 inactivation-sensitive manner. Furthermore, we developed a mouse strain with <i>Gpx4</i> haplodeficiency in osteoblasts (<i>Gpx4</i> <sup>Ob+/-</sup>) that exhibited worsened ferroptotic osteolysis in control and TP-treated calvaria and largely abolished the anti-ferroptosis and osteoprotective effects of SGI-1027. Taken together, our results demonstrate that DNMT1/3a/3b elevation, resulting GPX4 repression, and osteoblastic ferroptosis form a critical epigenetic pathway that significantly contributes to TP-induced osteolysis, and that targeting DNMT aberration and the associated osteoferroptosis could be a potential strategy to prevent or slow down prosthesis-related osteolytic complications.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"7 ","pages":"0457"},"PeriodicalIF":11.0,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11331012/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142005130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ResearchPub Date : 2024-08-15eCollection Date: 2024-01-01DOI: 10.34133/research.0455
Yanling Hu, Guisheng Zeng, Yue Wang, Dongliang Yang
{"title":"Nanorobots to Treat <i>Candida albicans</i> Infection.","authors":"Yanling Hu, Guisheng Zeng, Yue Wang, Dongliang Yang","doi":"10.34133/research.0455","DOIUrl":"10.34133/research.0455","url":null,"abstract":"<p><p><i>Candida albicans</i> is an opportunistic fungal pathogen of humans. It causes a variety of infections ranging from superficial mucocutaneous conditions to severe systemic diseases that result in substantial morbidity and mortality. This pathogen frequently forms biofilms resistant to antifungal drugs and the host immune system, leading to treatment failures. Recent research has demonstrated the potential of nanorobots to penetrate biological barriers and disrupt fungal biofilms. In this perspective paper, we provide a brief overview of recent breakthroughs in nanorobots for candidiasis treatment and discuss current challenges and prospects.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"10 ","pages":"0455"},"PeriodicalIF":11.0,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11324951/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141988722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Designs and Applications for the Multimodal Flexible Hybrid Epidermal Electronic Systems.","authors":"Ding Li, Tianrui Cui, Zigan Xu, Shuoyan Xu, Zirui Dong, Luqi Tao, Houfang Liu, Yi Yang, Tian-Ling Ren","doi":"10.34133/research.0424","DOIUrl":"10.34133/research.0424","url":null,"abstract":"<p><p>Research on the flexible hybrid epidermal electronic system (FHEES) has attracted considerable attention due to its potential applications in human-machine interaction and healthcare. Through material and structural innovations, FHEES combines the advantages of traditional stiff electronic devices and flexible electronic technology, enabling it to be worn conformally on the skin while retaining complex system functionality. FHEESs use multimodal sensing to enhance the identification accuracy of the wearer's motion modes, intentions, or health status, thus realizing more comprehensive physiological signal acquisition. However, the heterogeneous integration of soft and stiff components makes balancing comfort and performance in designing and implementing multimodal FHEESs challenging. Herein, multimodal FHEESs are first introduced in 2 types based on their different system structure: all-in-one and assembled, reflecting totally different heterogeneous integration strategies. Characteristics and the key design issues (such as interconnect design, interface strategy, substrate selection, etc.) of the 2 multimodal FHEESs are emphasized. Besides, the applications and advantages of the 2 multimodal FHEESs in recent research have been presented, with a focus on the control and medical fields. Finally, the prospects and challenges of the multimodal FHEES are discussed.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"7 ","pages":"0424"},"PeriodicalIF":11.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11310101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141917399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ResearchPub Date : 2024-08-06eCollection Date: 2024-01-01DOI: 10.34133/research.0426
Zeye Liu, Jing Xu, Chengliang Yin, Guojing Han, Yue Che, Ge Fan, Xiaofei Li, Lixin Xie, Lei Bao, Zimin Peng, Jinduo Wang, Yan Chen, Fengwen Zhang, Wenbin Ouyang, Shouzheng Wang, Junwei Guo, Yanqiu Ma, Xiangzhi Meng, Taibing Fan, Aihua Zhi, Dawaciren, Kang Yi, Tao You, Yuejin Yang, Jue Liu, Yi Shi, Yuan Huang, Xiangbin Pan
{"title":"Development and External Validation of an Artificial Intelligence-Based Method for Scalable Chest Radiograph Diagnosis: A Multi-Country Cross-Sectional Study.","authors":"Zeye Liu, Jing Xu, Chengliang Yin, Guojing Han, Yue Che, Ge Fan, Xiaofei Li, Lixin Xie, Lei Bao, Zimin Peng, Jinduo Wang, Yan Chen, Fengwen Zhang, Wenbin Ouyang, Shouzheng Wang, Junwei Guo, Yanqiu Ma, Xiangzhi Meng, Taibing Fan, Aihua Zhi, Dawaciren, Kang Yi, Tao You, Yuejin Yang, Jue Liu, Yi Shi, Yuan Huang, Xiangbin Pan","doi":"10.34133/research.0426","DOIUrl":"10.34133/research.0426","url":null,"abstract":"<p><p><b>Problem:</b> Chest radiography is a crucial tool for diagnosing thoracic disorders, but interpretation errors and a lack of qualified practitioners can cause delays in treatment. <b>Aim:</b> This study aimed to develop a reliable multi-classification artificial intelligence (AI) tool to improve the accuracy and efficiency of chest radiograph diagnosis. <b>Methods:</b> We developed a convolutional neural network (CNN) capable of distinguishing among 26 thoracic diagnoses. The model was trained and externally validated using 795,055 chest radiographs from 13 datasets across 4 countries. <b>Results:</b> The CNN model achieved an average area under the curve (AUC) of 0.961 across all 26 diagnoses in the testing set. COVID-19 detection achieved perfect accuracy (AUC 1.000, [95% confidence interval {CI}, 1.000 to 1.000]), while effusion or pleural effusion detection showed the lowest accuracy (AUC 0.8453, [95% CI, 0.8417 to 0.8489]). In external validation, the model demonstrated strong reproducibility and generalizability within the local dataset, achieving an AUC of 0.9634 for lung opacity detection (95% CI, 0.9423 to 0.9702). The CNN outperformed both radiologists and nonradiological physicians, particularly in trans-device image recognition. Even for diseases not specifically trained on, such as aortic dissection, the AI model showed considerable scalability and enhanced diagnostic accuracy for physicians of varying experience levels (all <i>P</i> < 0.05). Additionally, our model exhibited no gender bias (<i>P</i> > 0.05). <b>Conclusion:</b> The developed AI algorithm, now available as professional web-based software, substantively improves chest radiograph interpretation. This research advances medical imaging and offers substantial diagnostic support in clinical settings.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"7 ","pages":"0426"},"PeriodicalIF":11.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11301699/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141898078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ResearchPub Date : 2024-08-05eCollection Date: 2024-01-01DOI: 10.34133/research.0396
Shuang Liu, Fei Li, Shiyu Zhou, Jianfei Hua, Warren B Mori, Chan Joshi, Wei Lu
{"title":"A Scalable, High-Efficiency, Low-Energy-Spread Laser Wakefield Accelerator Using a Tri-Plateau Plasma Channel.","authors":"Shuang Liu, Fei Li, Shiyu Zhou, Jianfei Hua, Warren B Mori, Chan Joshi, Wei Lu","doi":"10.34133/research.0396","DOIUrl":"10.34133/research.0396","url":null,"abstract":"<p><p>The emergence of multi-petawatt laser facilities is expected to push forward the maximum energy gain that can be achieved in a single stage of a laser wakefield acceleration (LWFA) to tens of giga-electron volts, which begs the question-is it likely to impact particle physics by providing a truly compact particle collider? Colliders have very stringent requirements on beam energy, acceleration efficiency, and beam quality. In this article, we propose an LWFA scheme that can for the first time simultaneously achieve hitherto unrealized acceleration efficiency from the laser to the electron beam of >20% and a sub-1% energy spread using a stepwise plasma structure and a nonlinearly chirped laser pulse. Three-dimensional high-fidelity simulations show that the nonlinear chirp can effectively mitigate the laser waveform distortion and lengthen the acceleration distance. This, combined with an interstage rephasing process in the stepwise plasma, can triple the beam energy gain compared to that in a uniform plasma for a fixed laser energy, thereby dramatically increasing the efficiency. A dynamic beam loading effect can almost perfectly cancel the energy chirp that arises during the acceleration, leading to the sub-percent energy spread. This scheme is highly scalable and can be applied to petawatt LWFA scenarios. Scaling laws are obtained, which suggest that electron beams with parameters relevant for a Higgs factory could be reached with the proposed high-efficiency, low-energy-spread scheme.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"7 ","pages":"0396"},"PeriodicalIF":11.0,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11298259/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141890016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ResearchPub Date : 2024-08-05eCollection Date: 2024-01-01DOI: 10.34133/research.0416
Yuehan Xu, Tao Wang, Peng Huang, Guihua Zeng
{"title":"Integrated Distributed Sensing and Quantum Communication Networks.","authors":"Yuehan Xu, Tao Wang, Peng Huang, Guihua Zeng","doi":"10.34133/research.0416","DOIUrl":"10.34133/research.0416","url":null,"abstract":"<p><p>The integration of sensing and communication can achieve ubiquitous sensing while enabling ubiquitous communication. Within the gradually improving global communication, the integrated sensing and communication system based on optical fibers can accomplish various functionalities, such as urban structure imaging, seismic wave detection, and pipeline safety monitoring. With the development of quantum communication, quantum networks based on optical fiber are gradually being established. In this paper, we propose an integrated sensing and quantum network (ISAQN) scheme, which can achieve secure key distribution among multiple nodes and distributed sensing under the standard quantum limit. The continuous variables quantum key distribution protocol and the round-trip multiband structure are adopted to achieve the multinode secure key distribution. Meanwhile, the spectrum phase monitoring protocol is proposed to realize distributed sensing. It determines which node is vibrating by monitoring the frequency spectrum and restores the vibration waveform by monitoring the phase change. The scheme is experimentally demonstrated by simulating the vibration in a star structure network. Experimental results indicate that this multiuser quantum network can achieve a secret key rate of approximately 0.7 Mbits/s for each user under 10-km standard fiber transmission, and its network capacity is 8. In terms of distributed sensing, it can achieve a vibration response bandwidth ranging from 1 Hz to 2 kHz, a strain resolution of 0.50 <math><mi>n</mi> <mi>ε</mi> <mo>/</mo> <msqrt><mi>Hz</mi></msqrt> </math> , and a spatial resolution of 0.20 m under shot-noise-limited detection. The proposed ISAQN scheme enables simultaneous quantum communication and distributed sensing in a multipoint network, laying a foundation for future large-scale quantum networks and high-precision sensing networks.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"7 ","pages":"0416"},"PeriodicalIF":11.0,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11298414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141894151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ResearchPub Date : 2024-08-01eCollection Date: 2024-01-01DOI: 10.34133/research.0423
Qing Ma, Wentai Zhang, Xiaohui Mou, Nan Huang, Haimang Wang, Hongyu Zhang, Zhilu Yang
{"title":"Bioinspired Zwitterionic Block Polymer-Armored Nitric Oxide-Generating Coating Combats Thrombosis and Biofouling.","authors":"Qing Ma, Wentai Zhang, Xiaohui Mou, Nan Huang, Haimang Wang, Hongyu Zhang, Zhilu Yang","doi":"10.34133/research.0423","DOIUrl":"10.34133/research.0423","url":null,"abstract":"<p><p>Thrombosis and infection are 2 major complications associated with central venous catheters (CVCs), resulting in substantial mortality and morbidity. The concurrent long-term administration of antibiotics and anticoagulants to address these complications have been demonstrated to cause severe side effects such as antibiotic resistance and bleeding. To mitigate these complications with minimal or no drug utilization, we developed a bioinspired zwitterionic block polymer-armored nitric oxide (NO)-generating functional coating for surface modification of CVCs. This armor was fabricated by precoating with a Cu-dopamine (DA)/selenocysteamine (SeCA) (Cu-DA/SeCA) network film capable of catalytically generating NO on the CVCs surface, followed by grafting of a zwitterionic p(DMA-<i>b</i>-MPC-<i>b</i>-DMA) polymer brush. The synergistic effects of active attack by NO and copper ions provided by Cu-DA/SeCA network and passive defense by zwitterionic polymer brush imparted the CVCs surface with durable antimicrobial properties and marked inhibition of platelets and fibrinogen. The in vivo studies confirmed that the surface-armored CVCs could effectively reduce inflammation and inhibit thrombosis, indicating a promising potential for clinical applications.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"7 ","pages":"0423"},"PeriodicalIF":11.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11290871/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141875845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Highly Accurate and Efficient Deep Learning Paradigm for Full-Atom Protein Loop Modeling with KarmaLoop.","authors":"Tianyue Wang, Xujun Zhang, Odin Zhang, Guangyong Chen, Peichen Pan, Ercheng Wang, Jike Wang, Jialu Wu, Donghao Zhou, Langcheng Wang, Ruofan Jin, Shicheng Chen, Chao Shen, Yu Kang, Chang-Yu Hsieh, Tingjun Hou","doi":"10.34133/research.0408","DOIUrl":"10.34133/research.0408","url":null,"abstract":"<p><p>Protein loop modeling is a challenging yet highly nontrivial task in protein structure prediction. Despite recent progress, existing methods including knowledge-based, ab initio, hybrid, and deep learning (DL) methods fall substantially short of either atomic accuracy or computational efficiency. To overcome these limitations, we present KarmaLoop, a novel paradigm that distinguishes itself as the first DL method centered on full-atom (encompassing both backbone and side-chain heavy atoms) protein loop modeling. Our results demonstrate that KarmaLoop considerably outperforms conventional and DL-based methods of loop modeling in terms of both accuracy and efficiency, with the average RMSDs of 1.77 and 1.95 Å for the CASP13+14 and CASP15 benchmark datasets, respectively, and manifests at least 2 orders of magnitude speedup in general compared with other methods. Consequently, our comprehensive evaluations indicate that KarmaLoop provides a state-of-the-art DL solution for protein loop modeling, with the potential to hasten the advancement of protein engineering, antibody-antigen recognition, and drug design.</p>","PeriodicalId":21120,"journal":{"name":"Research","volume":"7 ","pages":"0408"},"PeriodicalIF":11.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11268956/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141760670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}