1.Prediction of Protein Thermodynamic Stability Based on Artificial Intelligence
Lin-Jie TAO ; Fan-Ding XU ; Yu GUO ; Jian-Gang LONG ; Zhuo-Yang LU
Progress in Biochemistry and Biophysics 2025;52(8):1972-1985
In recent years, the application of artificial intelligence (AI) in the field of biology has witnessed remarkable advancements. Among these, the most notable achievements have emerged in the domain of protein structure prediction and design, with AlphaFold and related innovations earning the 2024 Nobel Prize in Chemistry. These breakthroughs have transformed our ability to understand protein folding and molecular interactions, marking a pivotal milestone in computational biology. Looking ahead, it is foreseeable that the accurate prediction of various physicochemical properties of proteins—beyond static structure—will become the next critical frontier in this rapidly evolving field. One of the most important protein properties is thermodynamic stability, which refers to a protein’s ability to maintain its native conformation under physiological or stress conditions. Accurate prediction of protein stability, especially upon single-point mutations, plays a vital role in numerous scientific and industrial domains. These include understanding the molecular basis of disease, rational drug design, development of therapeutic proteins, design of more robust industrial enzymes, and engineering of biosensors. Consequently, the ability to reliably forecast the stability changes caused by mutations has broad and transformative implications across biomedical and biotechnological applications. Historically, protein stability was assessed via experimental methods such as differential scanning calorimetry (DSC) and circular dichroism (CD), which, while precise, are time-consuming and resource-intensive. This prompted the development of computational approaches, including empirical energy functions and physics-based simulations. However, these traditional models often fall short in capturing the complex, high-dimensional nature of protein conformational landscapes and mutational effects. Recent advances in machine learning (ML) have significantly improved predictive performance in this area. Early ML models used handcrafted features derived from sequence and structure, whereas modern deep learning models leverage massive datasets and learn representations directly from data. Deep neural networks (DNNs), graph neural networks (GNNs), and attention-based architectures such as transformers have shown particular promise. GNNs, in particular, excel at modeling spatial and topological relationships in molecular structures, making them well-suited for protein modeling tasks. Furthermore, attention mechanisms enable models to dynamically weigh the contribution of specific residues or regions, capturing long-range interactions and allosteric effects. Nevertheless, several key challenges remain. These include the imbalance and scarcity of high-quality experimental datasets, particularly for rare or functionally significant mutations, which can lead to biased or overfitted models. Additionally, the inherently dynamic nature of proteins—their conformational flexibility and context-dependent behavior—is difficult to encode in static structural representations. Current models often rely on a single structure or average conformation, which may overlook important aspects of stability modulation. Efforts are ongoing to incorporate multi-conformational ensembles, molecular dynamics simulations, and physics-informed learning frameworks into predictive models. This paper presents a comprehensive review of the evolution of protein thermodynamic stability prediction techniques, with emphasis on the recent progress enabled by machine learning. It highlights representative datasets, modeling strategies, evaluation benchmarks, and the integration of structural and biochemical features. The aim is to provide researchers with a structured and up-to-date reference, guiding the development of more robust, generalizable, and interpretable models for predicting protein stability changes upon mutation. As the field moves forward, the synergy between data-driven AI methods and domain-specific biological knowledge will be key to unlocking deeper understanding and broader applications of protein engineering.
2.HAN Mingxiang's Experience in Staged and Syndrome-Based Treatment of Chronic Obstructive Pulmonary Disease
Jian DING ; Hui TAO ; Gang CHENG ; Weizhen GUO ; Zegeng LI ; Ya MAO ;
Journal of Traditional Chinese Medicine 2025;66(8):780-785
This paper summarizes Professor HAN Mingxiang's clinical experience in treating chronic obstructive pulmonary disease (COPD). He believes that the key pathomechanism of COPD in the acute exacerbation stage is the invasion of external pathogens triggering latent illness, while lung qi deficiency is the primary mechanism in the stable stage. The core pathological factors throughout disease progression are deficiency, phlegm, and blood stasis. Treatment emphasizes a staged and syndrome-based approach. During the acute exacerbation stage, for wind-cold invading the lung syndrome, the self-formulated Sanzi Wenfei Decoction (三子温肺汤) is used to relieve the exterior, dispel cold, warm the lung, and resolve phlegm. For phlegm-dampness obstructing the lung syndrome, Huatan Jiangqi Fomulation (化痰降气方) is prescribed to warm the lung, transform phlegm, descend qi, and calm wheezing. For phlegm-heat obstructing the lung syndrome, Qingfei Huatan Fomulation (清肺化痰方) is applied to clear heat, resolve phlegm, moisten the lung, and stop coughing. For phlegm and blood stasis interlocking syndrome, Qibai Pingfei Fomulation (芪白平肺方) is used to tonify qi, resolve phlegm, and activate blood circulation to remove stasis. During the stable stage, for lung qi deficiency syndrome, Shenqi Wenfei Decoction (参芪温肺汤) is employed to warm the lung, tonify qi, resolve phlegm, and eliminate turbidity. For lung-spleen qi deficiency syndrome, Shenqi Buzhong Decoction (参芪补中汤) is utilized to strengthen the spleen, tonify qi, and reinforce metal (lung) from earth (spleen). For lung-kidney deficiency syndrome, Shenqi Tiaoshen Fomulation (参芪调肾方) is prescribed to tonify the lung, warm yang, and regulate kidney function to calm wheezing. These strategies provide insights into the traditional Chinese medicine treatment of COPD.
3.Evidence-based guideline for diagnosis and early fixation of severe open tibiofibular fractures (version 2025)
Yongjun RUI ; Yongqing XU ; Qingtang ZHU ; Xin WANG ; Zhao XIE ; Shanlin CHEN ; Jingyi MI ; Xianyou ZHENG ; Juyu TANG ; Xiaoheng DING ; Aixi YU ; Tao SONG ; Jianxi HOU ; Jian QI ; Xinyu FAN ; Jun FEI ; Lin GUO ; Xingwen HAN ; Weixu LI ; Aiguo WANG ; Yun XIE ; Tao XING ; Meng LI ; Baoqing YU ; Yan ZHUANG ; Xiaoqing HE ; Tao SUN ; Pengcheng LI ; Jihui JU ; Hongxiang ZHOU ; Haidong REN ; Guangyue ZHAO ; Gang ZHAO ; Yongwei WU ; Jun LIU ; Yunhong MA ; Yapeng WANG
Chinese Journal of Trauma 2025;41(11):1021-1034
Severe open tibiofibular fractures account for approximately 28.1% of all open fractures. Among them, Gustilo-Anderson type IIIB/C fractures present significant clinical challenges due to associated bone and soft tissue defects, high infection rates, and risk of amputation. Inadequate preoperative assessment may lead to suboptimal emergency surgical planning or intraoperative complications. Historically, external fixation was often preferred, but this approach has been associated with limitations such as restricted joint mobility, delayed bone union, joint stiffness, and disuse osteoporosis, resulting in poor functional recovery. With advancements of debridement techniques, standardization of antibiotic use, and popularization of early soft tissue coverage, early internal fixation has gained broader acceptance. Nevertheless, controversies persist regarding the choice of fixation method, timing of definitive fixation, use of reamed versus unreamed intramedullary nailing, and necessity of fibular fixation. To standardize the diagnosis and early management of severe open tibiofibular fractures, reduce complication rates, and improve functional recovery, the Society of Microsurgery of the Chinese Medical Association organized a panel of domestic experts to develop the Evidence-based guideline for the diagnosis and early fixation of severe open tibiofibular fractures ( version 2025), using evidence-based methodology. The guidelines provided 12 recommendations covering diagnostic and early fixation strategies of severe open tibiofibular fractures, aiming to provide clinicians with scientifically grounded and standardized guidance.
4.The therapeutic effects of newly formulated Tadalafil tablets on rats with pathological cardiac hypertrophy through regulation of NF-κB signaling pathway
Xue-di ZHANG ; Ye-ding SONG ; Li-mei LI ; Hao-yan CHEN ; Hua-sui CUI ; Zheng-gang ZHAO ; Zi-jian ZHAO ; Yun-ping MU ; Fang-hong LI
Chinese Pharmacological Bulletin 2025;41(8):1485-1492
Aim To investigate the therapeutic effects of a newly developed Tadalafil tablets on pathological myocardial hypertrophy induced by abdominal aortic constriction(AAC)in rats,as well as its influence on the activation of the NF-κB signaling pathway in myo-cardial cells.Methods SD rats were randomly divid-ed into 4 groups:the sham operation group(Sham),the model group(AAC),the tadalafil new tablet treat-ment group(N-Tad,5 mg·kg-1),and the positive control drug treatment group(Cialis,10 mg·kg-1g).The AAC model group and treatment group rats under-went blunt dissection and constrictive ligation of the abdominal aorta at the left renal artery branch point during surgery,while the Sham group rats only had their arteries separated without any constrictive liga-tion.Rats in the treatment groups received either N-Tad or Cialis via gavage three days after modeling,while rats in the sham group and the model group re-ceived physiological saline daily for 8 weeks.Small an-imal ultra-high-resolution echocardiography and hemo-dynamic assessment were applied to evaluate left ven-tricular function in each group of rats,and the calcula-tion of the left ventricular mass index was conducted.By employing Western blot and RT-PCR.we assessed the impact of this treatment on the expression of the hy-pertrophy factor atrial natriuretic peptide(ANP),phosphorylated NF-κB p65 protein(p-NF-κB p65),and phosphorylated IκB-α in the left heart tissue of rats and in H9c2 cardiomyocytes.Results Compared to the Sham group,the AAC rats exhibited a significant decrease in left heart function,an increase in left ven-tricular mass index,and a notable increase in ANP and p-p65 expression in the left heart tissue(P<0.05).Both N-Tad and Cialis treatments could significantly enhance left ventricular function,decrease left ventric-ular mass index,and inhibit the expression of ANP and phosphorylated NF-κB p65 in rats with myocardial hy-pertrophy(P<0.05).Notably,the therapeutic effect of low-dose N-Tad was comparable to that of high-dose Cialis.At the cellular level,Tadalafil significantly in-hibited the activation of the NF-κB signaling pathway and reduced the expression of associated proteins in H9c2 cardiomyocytes.Conclusions N-Tad can sig-nificantly inhibit p65 and IκB-α phosphorylation,and the activation of the NF-κB signaling pathway,reduce ANP expression,and improve pathological myocardial hypertrophy,as well as mitigate left heart function damage caused by abdominal aortic constriction.
5.The therapeutic effects of newly formulated Tadalafil tablets on rats with pathological cardiac hypertrophy through regulation of NF-κB signaling pathway
Xue-di ZHANG ; Ye-ding SONG ; Li-mei LI ; Hao-yan CHEN ; Hua-sui CUI ; Zheng-gang ZHAO ; Zi-jian ZHAO ; Yun-ping MU ; Fang-hong LI
Chinese Pharmacological Bulletin 2025;41(8):1485-1492
Aim To investigate the therapeutic effects of a newly developed Tadalafil tablets on pathological myocardial hypertrophy induced by abdominal aortic constriction(AAC)in rats,as well as its influence on the activation of the NF-κB signaling pathway in myo-cardial cells.Methods SD rats were randomly divid-ed into 4 groups:the sham operation group(Sham),the model group(AAC),the tadalafil new tablet treat-ment group(N-Tad,5 mg·kg-1),and the positive control drug treatment group(Cialis,10 mg·kg-1g).The AAC model group and treatment group rats under-went blunt dissection and constrictive ligation of the abdominal aorta at the left renal artery branch point during surgery,while the Sham group rats only had their arteries separated without any constrictive liga-tion.Rats in the treatment groups received either N-Tad or Cialis via gavage three days after modeling,while rats in the sham group and the model group re-ceived physiological saline daily for 8 weeks.Small an-imal ultra-high-resolution echocardiography and hemo-dynamic assessment were applied to evaluate left ven-tricular function in each group of rats,and the calcula-tion of the left ventricular mass index was conducted.By employing Western blot and RT-PCR.we assessed the impact of this treatment on the expression of the hy-pertrophy factor atrial natriuretic peptide(ANP),phosphorylated NF-κB p65 protein(p-NF-κB p65),and phosphorylated IκB-α in the left heart tissue of rats and in H9c2 cardiomyocytes.Results Compared to the Sham group,the AAC rats exhibited a significant decrease in left heart function,an increase in left ven-tricular mass index,and a notable increase in ANP and p-p65 expression in the left heart tissue(P<0.05).Both N-Tad and Cialis treatments could significantly enhance left ventricular function,decrease left ventric-ular mass index,and inhibit the expression of ANP and phosphorylated NF-κB p65 in rats with myocardial hy-pertrophy(P<0.05).Notably,the therapeutic effect of low-dose N-Tad was comparable to that of high-dose Cialis.At the cellular level,Tadalafil significantly in-hibited the activation of the NF-κB signaling pathway and reduced the expression of associated proteins in H9c2 cardiomyocytes.Conclusions N-Tad can sig-nificantly inhibit p65 and IκB-α phosphorylation,and the activation of the NF-κB signaling pathway,reduce ANP expression,and improve pathological myocardial hypertrophy,as well as mitigate left heart function damage caused by abdominal aortic constriction.
6.Evidence-based guideline for diagnosis and early fixation of severe open tibiofibular fractures (version 2025)
Yongjun RUI ; Yongqing XU ; Qingtang ZHU ; Xin WANG ; Zhao XIE ; Shanlin CHEN ; Jingyi MI ; Xianyou ZHENG ; Juyu TANG ; Xiaoheng DING ; Aixi YU ; Tao SONG ; Jianxi HOU ; Jian QI ; Xinyu FAN ; Jun FEI ; Lin GUO ; Xingwen HAN ; Weixu LI ; Aiguo WANG ; Yun XIE ; Tao XING ; Meng LI ; Baoqing YU ; Yan ZHUANG ; Xiaoqing HE ; Tao SUN ; Pengcheng LI ; Jihui JU ; Hongxiang ZHOU ; Haidong REN ; Guangyue ZHAO ; Gang ZHAO ; Yongwei WU ; Jun LIU ; Yunhong MA ; Yapeng WANG
Chinese Journal of Trauma 2025;41(11):1021-1034
Severe open tibiofibular fractures account for approximately 28.1% of all open fractures. Among them, Gustilo-Anderson type IIIB/C fractures present significant clinical challenges due to associated bone and soft tissue defects, high infection rates, and risk of amputation. Inadequate preoperative assessment may lead to suboptimal emergency surgical planning or intraoperative complications. Historically, external fixation was often preferred, but this approach has been associated with limitations such as restricted joint mobility, delayed bone union, joint stiffness, and disuse osteoporosis, resulting in poor functional recovery. With advancements of debridement techniques, standardization of antibiotic use, and popularization of early soft tissue coverage, early internal fixation has gained broader acceptance. Nevertheless, controversies persist regarding the choice of fixation method, timing of definitive fixation, use of reamed versus unreamed intramedullary nailing, and necessity of fibular fixation. To standardize the diagnosis and early management of severe open tibiofibular fractures, reduce complication rates, and improve functional recovery, the Society of Microsurgery of the Chinese Medical Association organized a panel of domestic experts to develop the Evidence-based guideline for the diagnosis and early fixation of severe open tibiofibular fractures ( version 2025), using evidence-based methodology. The guidelines provided 12 recommendations covering diagnostic and early fixation strategies of severe open tibiofibular fractures, aiming to provide clinicians with scientifically grounded and standardized guidance.
7.Risk factors for bronchopulmonary dysplasia in twin preterm infants:a multicenter study
Yu-Wei FAN ; Yi-Jia ZHANG ; He-Mei WEN ; Hong YAN ; Wei SHEN ; Yue-Qin DING ; Yun-Feng LONG ; Zhi-Gang ZHANG ; Gui-Fang LI ; Hong JIANG ; Hong-Ping RAO ; Jian-Wu QIU ; Xian WEI ; Ya-Yu ZHANG ; Ji-Bin ZENG ; Chang-Liang ZHAO ; Wei-Peng XU ; Fan WANG ; Li YUAN ; Xiu-Fang YANG ; Wei LI ; Ni-Yang LIN ; Qian CHEN ; Chang-Shun XIA ; Xin-Qi ZHONG ; Qi-Liang CUI
Chinese Journal of Contemporary Pediatrics 2024;26(6):611-618
Objective To investigate the risk factors for bronchopulmonary dysplasia(BPD)in twin preterm infants with a gestational age of<34 weeks,and to provide a basis for early identification of BPD in twin preterm infants in clinical practice.Methods A retrospective analysis was performed for the twin preterm infants with a gestational age of<34 weeks who were admitted to 22 hospitals nationwide from January 2018 to December 2020.According to their conditions,they were divided into group A(both twins had BPD),group B(only one twin had BPD),and group C(neither twin had BPD).The risk factors for BPD in twin preterm infants were analyzed.Further analysis was conducted on group B to investigate the postnatal risk factors for BPD within twins.Results A total of 904 pairs of twins with a gestational age of<34 weeks were included in this study.The multivariate logistic regression analysis showed that compared with group C,birth weight discordance of>25%between the twins was an independent risk factor for BPD in one of the twins(OR=3.370,95%CI:1.500-7.568,P<0.05),and high gestational age at birth was a protective factor against BPD(P<0.05).The conditional logistic regression analysis of group B showed that small-for-gestational-age(SGA)birth was an independent risk factor for BPD in individual twins(OR=5.017,95%CI:1.040-24.190,P<0.05).Conclusions The development of BPD in twin preterm infants is associated with gestational age,birth weight discordance between the twins,and SGA birth.
8.Real-time traking and virtual reality technology-assisted trauma orthopaedic surgery robot for femoral neck fractures
Wei-Gang LOU ; Jian-Ming CHEN ; Shuai-Yi WANG ; Hai-Yang LI ; Ding XU
China Journal of Orthopaedics and Traumatology 2024;37(2):124-128
Objective To investigate the effectiveness of real-time tracking and virtual reality technology(RTVI)used to assist the intraoperative alignment of the trauma orthopaedic surgery robot for the treatment of femoral neck fractures and its impact on the treatment outcome.Methods A retrospective analysis was conducted on 60 patients with femoral neck fractures treated with trauma orthopedic robotic surgery from September 2020 to September 2022.Patients were divided into two groups according to whether RTVI technology was used during surgery to assist robotic surgery.There were 28 patients in the RTVI group(12 males and 16 females),with an average age of(46.2±9.3)years old ranging from 28 to 60 years old.There were 32 patients in the simple Tianji surgical robot group,including 15 males and 17 females,aged(48.2±7.8)years old ranging from 32 to 58.The number of registered fluoroscopy,operation time,total number of intraoperative fluoroscopy,intraoperative blood loss,and hospitalization time of the two groups of patients were observed and recorded.All patients received regular follow-up after surgery,and hip X-rays were routinely reviewed to record Garden alignment index,fracture healing time,postoperative complications,and Harris score.Results All 60 patients were followed up.The RTVI group was followed up for 9 to 16 months with an average of(13.0±l.2)months,and the Tianji surgical robot group alone was followed up for 10 to 14 months with an average of(12.0±1.3)months.During the follow-up period,the femoral neck fractures of both groups of patients healed well,and no complications such as internal fixation loosening and incision infection occurred.The number of registered fluoroscopy,operation time,and number of intraoperative fluoroscopy of patients in the RTVI group were significantly better than those in the simple Tianji surgical robot group(P<0.01).There was no statistically significant difference in intraoperative blood loss,hospital stay,Garden alignment index,fracture healing time,and hip Harris score between two groups(P>0.05).Conclusion Although RTVI technology assisted by the surgical robot for femoral neck fracture surgery has little impact on its postoperative outcome,it can effectively reduce the operating time,the number of intraoperative X-ray projections,and the risk of intraopera-tive radiation exposure to patients.It also shortened the learning curve of the operator and better reflected the precision and ef-ficiency of the trauma orthopaedic surgery robot.
9.Pharmacokinetic study of Noiiglutide injection,INS068 injection and the compound preparation in Chinese healthy subjects
Xiao-Dong XING ; Ji-Gang ZHANG ; Kai SHEN ; Ming-Jian ZHANG ; Yi-Xin ZHA ; Shu-Jing JIN ; Mei XU ; Wen-Yuan XUE ; Xue-Ying DING
The Chinese Journal of Clinical Pharmacology 2023;39(23):3449-3454
Objective To compare the pharmaceutics and drug interactions of noiiglutide injection,INS068 injection,HR17031 Injection,and noiiglutide+INS068 injection in healthy subjects Methods This was a single center,randomized,open-label,4-cycle,4-cohort trial.Healthy subjects were allocated to 4 groups randomly.HR17031(17 U/0.04 mg),INS068(17 U),noliglycopeptide(0.04 mg),and INS068(17 U)combined with noiiglutide(0.04 mg)were injected subcutaneously into the abdomenon on day 1,8,15 and 22 respectively.Venous blood was collected at different timing before and after administration,and the concentrations of noiiglutide in plasma and INS068 in serum were measured by HPLC-MS/MS method.Relevant pharmacokinetic parameters were calculated using the WinNonlin non compartment model.Results In HR17031,INS068,and INS068 combined with noiiglutide groups,the main pharmacokinetic parameters of INS068 in serum were calculated and listed as follows:Cmax were(19.50±4.06),(18.10±4.56)and(18.40±5.81)ng·mL-1,tmax was 12,10 and 8 h,t1/2 was(9.27±1.70),(11.00±2.81)and(11.0±3.18)h,AUC0-twere(505.00±62.20),(498.00±70.50)and(491.00±74.20)ng·mL-1·h.In HR17031,noiiglutide,and INS068 combined with noiiglutide groups,the main pharmacokinetic parameters of noiiglutide in plasma were calculated and listed as follows:Cmax were(3.61±0.82),(4.63±0.87)and(4.54±0.86)ng·mL-1,tmax was all 8.00 h,t1/2 was(10.50±1.61),(9.49±1.40)and(9.55±1.61)h,AUC0-twere(94.30±20.10),(106.00±20.20)and(105.00±19.00)ng·mL-1·h.Conclusion There was no significant difference in bioavailability of INS068 and noiiglutide in HR17031 compared with INS068 and noiiglutide whether combined or used alone.
10.Trends of Oral Cancer Mortality in China from 1990 to 2019 and a 15-Year Predictive Analysis Based on a Bayesian Age-Period-Cohort Model.
Jian Chang GU ; Ji Wu SONG ; Yun LIU ; Xiao Lan WANG ; Shuang Shuang XU ; Liang Liang ZHANG ; Yun Xia LIU ; Gang DING
Biomedical and Environmental Sciences 2023;36(6):553-556

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