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A Non-Redundant Benchmark for Symmetric Protein Docking

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Big Data Mining and Analytics 2019年第2期2卷 92-99页

作者： Yumeng Yan sheng-you huang Institute of Biophysics Huazhong University of Science and Technology

Symmetric proteins play important roles in many biological processes, such as signal transduction and molecular transportation. Therefore, determining the symmetric oligomeric structure of subunits is crucial to investigate the molecular mechanism of the related processes. Due to the high cost and technical difficulties associated with many experimental methods, computational approaches, such as molecular docking, have played an important complementary role in the determination of symmetric complex structures, in which a benchmark data set is pressingly needed. In the present work, we develop a comprehensive and non-redundant benchmark for symmetric protein docking based on the structures in the Protein Data Bank(PDB). The diverse dataset consists of 251 targets, including 212 cases with cyclic groups symmetry, 35 cases with dihedral groups symmetry, 3 cases with cubic groups symmetry, and 1 case with helical symmetry. According to the conformational changes in the interface between bound and unbound structures, the 251 targets were classified into three groups: 176 "easy",37 "medium", and 38 "difficult" cases. A preliminary docking test on the targets of cyclic groups symmetry with MZDOCK indicated that symmetric multimer docking remains challenging. The benchmark will be beneficial for the development of symmetric protein docking algorithms. The proposed benchmark data set is available for download at http://***/SDBenchmark/.

关键词： benchmark symmetric protein molecular docking scoring functions protein binding

How the “Folding Funnel” Depends on Size and Structure of Proteins?A View from the Scoring Function Perspective

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Tsinghua Science and Technology 2013年第5期18卷 462-468页

作者： sheng-you huang Gordon K. Springer the Research Support Computing University of Missouri Bioinformatics Consortium and Department of Computer Science University of Missouri

It has been well accepted that the folding energy landscape may resemble a funnel according to the theory of protein folding. This theory of ＂folding funnel＂ has been extensively studied and thought to play an important role in guiding the sampling process of the protein folding and refinement in protein structure prediction. Here, we have investigated the relationship between the ＂funnel likeness＂ of protein folding and the size/structure of the proteins based on a set of non-homologous proteins we have recently evaluated using a statistical mechanicsbased scoring function ITScorePro. It was found that larger proteins that consist of more helix/sheet structures tend to have a higher score-Root Mean Square Deviation（RMSD） correlation（or a more funnel like energy landscape）.Another measurement in protein folding, Z-score, has also shown some correlation with the size of the *** expected, proteins with a better ＂olding funnel likeness＂（or score-RMSD correlation） tend to have a betterpredicted conformation with a lower RMSD from their native structures. These findings can be extremely valuable for the development and improvement of sampling and scoring algorithms for protein structure prediction.

关键词： energy landscape folding funnel protein structure prediction scoring function protein folding

CHDOCK: a hierarchical docking approach for modeling C_n symmetric homo-oligomeric complexes

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Biophysics Reports 2019年第2期5卷 65-72页

作者： Yumeng Yan sheng-you huang Institute of Biophysics School of Physics Huazhong University of Science and Technology

Protein–protein interactions are crucial in many biological processes. Therefore, determining the complex structure between proteins is valuable for understanding the molecular mechanism and developing drugs. Many proteins like ion channels are formed by symmetric homo-oligomers. In this study, we have proposed a hierarchical docking algorithm to predict the structure of C_n symmetric protein complexes, which is referred to as CHDOCK. The symmetric binding modes were first constructed by an FFT-based docking algorithm and then optimized by our iterative scoring function for protein–protein interactions. When tested on a symmetric protein docking benchmark of 212 homooligomeric complexes with C_n symmetry, CHDOCK obtained a significantly better performance in binding mode predictions than three state-of-the-art symmetric docking methods, M-ZDOCK, SAM, and Symm Dock. When the top 10 predictions were considered, CHDOCK achieved a success rate of 44.81%and 72.17% for unbound docking and bound docking, respectively in comparison to those of 36.79%and 65.09% for M-ZDOCK, 31.60% and 54.25% for SAM, and 30.66% and 31.60% for Symm *** is computationally efficient and can normally complete a symmetric docking calculation within 30 min. The CHDOCK can be freely accessed by a web server at http://***/hsymdock/.

关键词： Molecular docking Symmetric docking C n symmetry Shape complementarity Protein–protein interactions

Temporal Change in Treatment Patterns of Metastatic Colorectal Cancer and Its Association with Patient Survival:A Retrospective Cohort Study Based on an Intelligent Big-Data Platform

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Engineering 2021年第4期7卷 526-533页

作者： Zi-Xian Wang Yi-Chen Yao Zong-Jiong Mai Wu-Hao Lin you-sheng huang Ying Jin Hui-Yan Luo Dong-sheng Zhang Feng-Hua Wang Feng Wang Gong Chen Pei-Rong Ding Yun-Fei Yuan Yu-Hong Li Jin-Hua huang Zhi-Zhong Pan Rui-Hua Xu Department of Medical Oncology State Key Laboratory of Oncology in South China&Collaborative Innovation Center for Cancer MedicineSun Yat-sen University Cancer CenterGuangzhou 510060China Artificial Intelligence Laboratory Sun Yat-sen University Cancer CenterGuangzhou 510060China Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer Chinese Academy of Medical SciencesGuangzhou 510060China Department of Colorectal Surgery Sun Yat-sen University Cancer CenterGuangzhou 510060China Department of Hepatobiliary Surgery Sun Yat-sen University Cancer CenterGuangzhou 510060China Department of Minimally Invasive Therapy Sun Yat-sen University Cancer CenterGuangzhou 510060China

There is a lack of high-quality,large-scale,real-world evidence from patients with metastatic colorectal cancer(mCRC),especially in *** remains unclear whether efforts to improve the quality of care for mCRC would improve patient survival outcomes in real-world *** the basis of an intelligent bigdata platform,we established a large-scale retrospective cohort of mCRC *** investigated the temporal changes in the systemic and local treatment(resection,ablation,or radiation to liver,lung,or extrahepatic and/or extrapulmonary metastases)patterns of mCRC,and whether these changes were associated with improved overall survival(OS)over *** July 2012 and December 2018,3403 eligible patients were included in this *** median OS was 42.8 months(95%confidence interval(CI),40.7–46.6)for the entire cohort,25.6 months(95%CI,24.7–26.9)for those treated with systemic therapy only,and not reached(95%CI,78.6 months–not reached)for those receiving local *** utility rate of local therapy increased continuously from 37.9%in 2012–2014 to 46.9%in 2017–2018.A dramatic increase in the utility rate of either cetuximab or bevacizumab was observed since 2017(39.9%,43.2%,and 60.3%in 2012–2014,2015–2016,and 2017–2018,respectively).Compared with 2012–2014,the OS of the entire population significantly improved in 2015–2016(hazard ratio(HR)=0.87(95%CI,0.78–0.99);P=0.034),but not for patients receiving systemic therapy only(HR=0.99(95%CI,0.86–1.14);P=0.889),whereas an improved OS was found in 2015–2018 for both the entire population(HR=0.75(95%CI,0.70–0.81);P<0.001)and for patients receiving systemic therapy only(HR=0.83(95%CI,0.77–0.91);P<0.001).In summary,the quality of care for mCRC,as indicated by the utility rate of targeted and local therapies,has been continuously improving over time in this study cohort,which is associated with continuously improving survival outcomes for these patients.

关键词： Metastatic colorectal cancer Real-world evidence Treatment pattern Survival Big-data platform

Residual circulating tumor DNA after adjuvant chemotherapy effectively predicts recurrence of stage II-III gastric cancer

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Cancer Communications 2023年第12期43卷 1312-1325页

作者： Shu-Qiang Yuan Run-Cong Nie you-sheng huang Ying-Bo Chen Si-Yu Wang Xiao-Wei Sun Yuan-Fang Li Ze-Kun Liu Yan-Xing Chen Yi-Chen Yao Yu Xu Hai-Bo Qiu Yao Liang Wei Wang Ze-Xian Liu Qi Zhao Rui-Hua Xu Zhi-Wei Zhou Feng Wang Department of Gastric Surgery Sun Yat-sen University Cancer Center State Key Laboratory of Oncology in South China Collaborative Innovation Center for Cancer Medicine Guangzhou Guangdong P. R. China Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer Chinese Academy of Medical Sciences Guangzhou Guangdong P. R. China Department of Medical Oncology Sun Yat-sen University Cancer Center State Key Laboratory of Oncology in South China Collaborative Innovation Center for Cancer Medicine Sun Yat-sen University Guangzhou Guangdong P. R. China Bioinformatics Platform Sun Yat-sen University Cancer Center Guangzhou Guangdong P. R. China

Background Circulating tumor DNA(ctDNA)is a promising biomarker for predicting relapse in multiple solid ***,the predictive value of ctDNA for disease recurrence remains indefinite in locoregional gastric cancer(GC).Here,we aimed to evaluate the predictive value of ctDNA in this *** From 2016 to 2019,100 patients with stage II/III resectable GC were recruited in this prospective cohort study(NCT02887612).Primary tumors were collected during surgical resection,and plasma samples were collected perioperatively and within 3 months after adjuvant chemotherapy(ACT).Somatic variants were captured via a targeted sequencing panel of 425 cancer-related *** plasma was defined as ctDNA-positive only if one or more variants detected in the plasma were presented in at least 2%of the primary *** Compared with ctDNA-negative patients,patients with positive postoperative ctDNA had moderately higher risk of recurrence[hazard ratio(HR)=2.74,95%confidence interval(CI)=1.37–5.48;P=0.003],while patients with positive post-ACT ctDNA showed remarkably higher risk(HR=14.99,95%CI=3.08-72.96;P<0.001).Multivariate analyses indicated that both postoperative and post-ACT ctDNA positivity were independent predictors of recurrence-free survival(RFS).Moreover,post-ACT ctDNA achieved better predictive performance(sensitivity,77.8%;specificity,90.6%)than both postoperative ctDNA and serial cancer antigen.A comprehensive model incorporating ctDNA for recurrence risk prediction showed a higher C-index(0.78;95%CI=0.71–0.84)than the model without ctDNA(0.71;95%CI=0.64–0.79;P=0.009).Conclusions Residual ctDNA after ACT effectively predicts high recurrence risk in stage II/III GC,and the combination of tissue-based and circulating tumor features could achieve better risk prediction.

关键词： gastric cancer ctDNA chemotherapy postoperative recurrence

Deciphering the role of ultra-low-loaded rhodium in NiFe-MIL-53 for superior oxygen evolution reaction

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Journal of Energy Chemistry 2025年第1期100卷 77-86页

作者： Jinzhi Jia Jinhua Zhang Kailu Guo Lanyue Zhang Gening Du Hao you Junfeng huang Mudong Tu Hua Li Yong Peng Wei Dou Cailing Xu State Key Laboratory of Applied Organic Chemistry College of Chemistry and Chemical Engineering School of Materials and Energy Lanzhou University College of Chemistry and Chemical Engineering Luoyang Normal University

Designing highly active and stable electrocatalysts of oxygen evolution reaction （OER） is one of the crucial *** this study,a novel OER electrocatalyst,NiFe-MIL-53 modified with ultra-low rhodium（Rh@NiFe-MIL-53）,is successfully prepared via the hydrothermal ***-situ Raman spectroscopy and electrochemical impedance spectroscopy reveal that the doped Rh accelerates the phase transformation of NiFe-MIL-53 and the in-situ formed Rh@NiFeOOH is the actual active *** importantly,the enhanced reversibility of electrochemical reconstruction between NiFeOOH and NiFe（OH）2after doping Rh is beneficial for improving the electrochemical stability of the catalyst.X-ray photoelectron spectroscopy spectra show the strong electronic interaction between single-atom Rh and Ni/Fe in Rh@***,theoretical calculations confirm that the integration of single-atom Rh into the NiFeOOH successfully reduces the band gap,regulates the d-band center （εd）,accelerates the charge transfer,and optimizes the adsorption behavior of oxygen-containing intermediates,thereby lowering the energy barrier of rate-determining ***,the optimized Rh@NiFe-MIL-53 exhibits excellent OER activity （240 mV） with a small Tafel slope of 48.2 mV dec-1and long-term durability (over1270 h at 10 m A cm-2and 110 h at 200 mA cm-2).This work presents a new perspective on designing highly efficient OER electrocatalysts.

关键词： NiFe-MIL-53 Rh Electrochemical reconstruction Catalytic mechanism Oxygen evolution reaction

Inhibiting SHP2 reduces glycolysis, promotes microglial M1 polarization, and alleviates secondary inflammation following spinal cord injury in a mouse model

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Neural Regeneration Research 2025年第3期20卷 858-872页

作者： Xintian Ding Chun Chen Heng Zhao Bin Dai Lei Ye Tao Song Shuai huang Jia Wang Tao you Department of Orthopedics The First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui ProvinceChina Department of Orthopedics Provincial Hospital Affiliated to Anhui Medical UniversityHefeiAnhui ProvinceChina

Reducing the secondary inflammatory response, which is partly mediated by microglia, is a key focus in the treatment of spinal cord injury. Src homology 2-containing protein tyrosine phosphatase 2(SHP2), encoded by PTPN11, is widely expressed in the human body and plays a role in inflammation through various mechanisms. Therefore, SHP2 is considered a potential target for the treatment of inflammation-related diseases. However, its role in secondary inflammation after spinal cord injury remains unclear. In this study, SHP2 was found to be abundantly expressed in microglia at the site of spinal cord injury. Inhibition of SHP2 expression using siRNA and SHP2 inhibitors attenuated the microglial inflammatory response in an in vitro lipopolysaccharide-induced model of inflammation. Notably, after treatment with SHP2 inhibitors, mice with spinal cord injury exhibited significantly improved hind limb locomotor function and reduced residual urine volume in the bladder. Subsequent in vitro experiments showed that, in microglia stimulated with lipopolysaccharide, inhibiting SHP2 expression promoted M2 polarization and inhibited M1 polarization. Finally, a co-culture experiment was conducted to assess the effect of microglia treated with SHP2 inhibitors on neuronal cells. The results demonstrated that inflammatory factors produced by microglia promoted neuronal apoptosis, while inhibiting SHP2 expression mitigated these effects. Collectively, our findings suggest that SHP2 enhances secondary inflammation and neuronal damage subsequent to spinal cord injury by modulating microglial phenotype. Therefore, inhibiting SHP2 alleviates the inflammatory response in mice with spinal cord injury and promotes functional recovery postinjury.

关键词： apoptosis glycolysis inflammatory response microglia neurons polarization spinal cord injury Src homology 2-containing protein tyrosine phosphatase 2

中重度原发性高血压3种治疗方案的药物经济学评价

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广东药学院学报 2010年第4期26卷 409-411页

作者：罗畅然黄有胜东莞市虎门医院药剂科广东东莞523902 东莞市虎门医院心内科广东东莞523902

目的对3种临床常用治疗中重度原发性高血压方案[硝苯地平缓释片、缬沙坦片;缬沙坦氢氯噻嗪（复方制剂）]进行药物经济学评价。方法选择94例中重度原发性高血压病患者,随机分成3组。硝苯地平缓释片组：单用硝苯地平缓释片30mg,每天1次;... 详细信息

目的对3种临床常用治疗中重度原发性高血压方案[硝苯地平缓释片、缬沙坦片;缬沙坦氢氯噻嗪（复方制剂）]进行药物经济学评价。方法选择94例中重度原发性高血压病患者,随机分成3组。硝苯地平缓释片组：单用硝苯地平缓释片30mg,每天1次;缬沙坦片组：缬沙坦片80mg,每天1次;缬沙坦氢氯噻嗪（复方制剂）合用组：1粒,每天1次;3组疗程均为12周,观察3组的疗效并进行成本效果分析法和敏感度分析。结果 3组治疗方案对中重度原发性高血压的治疗效果差异无显著性,成本差异有显著性。结论缬沙坦片治疗中重度原发性高血压成本效果比最佳,值得临床推广。

关键词：原发性高血压药物经济学成本效果分析法敏感度分析

Hypoxia-preconditioned bone marrow-derived mesenchymal stem cells protect neurons from cardiac arrest-induced pyroptosis

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Neural Regeneration Research 2025年第4期20卷 1103-1123页

作者： Xiahong Tang Nan Zheng Qingming Lin Yan you Zheng Gong Yangping Zhuang Jiali Wu Yu Wang Hanlin huang Jun Ke Feng Chen shengli Clinical Medical College of Fujian Medical University Fujian Medical UniversityFuzhouFujian ProvinceChina Department of Emergency Fujian Provincial HospitalFuzhouFujian ProvinceChina Fujian Provincial Key Laboratory of Emergency Medicine FuzhouFujian ProvinceChina The Second Department of Intensive Care Unit Fujian Provincial Hospital South BranchFuzhouFujian ProvinceChina

Cardiac arrest can lead to severe neurological impairment as a result of inflammation,mitochondrial dysfunction,and post-cardiopulmonary resuscitation neurological *** preconditioning has been shown to improve migration and survival of bone marrow–derived mesenchymal stem cells and reduce pyroptosis after cardiac arrest,but the specific mechanisms by which hypoxia-preconditioned bone marrow–derived mesenchymal stem cells protect against brain injury after cardiac arrest are *** this end,we established an in vitro co-culture model of bone marrow–derived mesenchymal stem cells and oxygen–glucose deprived primary neurons and found that hypoxic preconditioning enhanced the protective effect of bone marrow stromal stem cells against neuronal pyroptosis,possibly through inhibition of the MAPK and nuclear factor κB ***,we transplanted hypoxia-preconditioned bone marrow–derived mesenchymal stem cells into the lateral ventricle after the return of spontaneous circulation in an 8-minute cardiac arrest rat model induced by *** results showed that hypoxia-preconditioned bone marrow–derived mesenchymal stem cells significantly reduced cardiac arrest–induced neuronal pyroptosis,oxidative stress,and mitochondrial damage,whereas knockdown of the liver isoform of phosphofructokinase in bone marrow–derived mesenchymal stem cells inhibited these *** conclude,hypoxia-preconditioned bone marrow–derived mesenchymal stem cells offer a promising therapeutic approach for neuronal injury following cardiac arrest,and their beneficial effects are potentially associated with increased expression of the liver isoform of phosphofructokinase following hypoxic preconditioning.

关键词： bone marrow–derived mesenchymal stem cells cardiac arrest cardiac resuscitation hypoxic preconditioning liver isoform of phosphofructokinase mitochondria neuroinflammation oxidative stress pyroptosis reactive oxygen species