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. Advances in relationship between pyroptosis and pulmonary arterial hypertension and therapeutic drugs
Qian YAN ; Yang SUN ; Jun-Peng LONG ; Jiao YAO ; Yu-Ting LIN ; Song-Wei YANG ; Yan-Tao YANG ; Gang PEI ; Qi-Di AI ; Nai-Hong CHEN ; Qian YAN ; Yang SUN ; Jun-Peng LONG ; Jiao YAO ; Yu-Ting LIN ; Song-Wei YANG ; Yan-Tao YANG ; Gang PEI ; Qi-Di AI ; Nai-Hong CHEN ; Sha-Sha LIU ; Nai-Hong CHEN
Chinese Pharmacological Bulletin 2024;40(1):25-30
Pyroptosis is the programmed death of cells accompanied by an inflammatory response and is widely involved in the development of a variety of diseases, such as infectious diseases, cardiovascular diseases, and neurodegeneration. It has been shown that cellular scorching is involved in the pathogenesis of pulmonary arterial hypertension ( PAH) in cardiovascular diseases. Patients with PAH have perivascular inflammatory infiltrates in lungs, pulmonary vasculopathy exists in an extremely inflam-matory microenvironment, and pro-inflammatory factors in cellular scorching drive pulmonary vascular remodelling in PAH patients. This article reviews the role of cellular scorch in the pathogenesis of PAH and the related research on drugs for the treatment of PAH, with the aim of providing new ideas for clinical treatment of PAH.
3.Prevalence and consultation behavior of childhood respiratory diseases in a hospital in Zhejiang Province in 2019-2021
Kaiyi YANG ; Guoqiang QI ; Zhiwen ZHU ; Jian HUANG ; Shasha HU ; Gang YU
Journal of Public Health and Preventive Medicine 2024;35(2):12-16
Objective To analyze the causes of changes in the prevalence of respiratory diseases and the reason for changes in medical visit behavior of children in Zhejiang Province during the winter and spring seasons of 2019-2021, and to provide important reference for the allocation of hospital resources, implementation of hierarchical diagnosis and treatment, and epidemic prevention and control. Methods A retrospective study was conducted on 256 937 outpatient medical records from January 23rd to April 23rd of each year from 2019 to 2021 at the Children's Hospital Affiliated to Zhejiang University School of Medicine. Statistical methods were used for data analysis. Results A total of 256 937 cases were selected in the present study, including 157 000 cases in 2019, 22 192 cases in 2020, and 77 745 cases in 2021. The number of patients to the Children's Hospital of Zhejiang University School of Medicine from outside Hangzhou accounted for 41.74%, 14.36% , and 18.53% in 2019-2021, respectively. For 0~2 years old , 3~6 years old , and 7~14 years old groups , the percentages of patients with upper respiratory tract infections were 49.54%, 45.95%, and 46.74%, respectively ; with lower respiratory tract infections were 42.90% , 31.76% , and 22.95% ; with influenza were 2.23% , 3.15% and 4.09%; and with asthma were 1.37%, 5.08%, and 8.15%, respectively. Conclusion From 2019 to 2021, there have been significant changes in the total number of respiratory diseases in children, the proportion of disease types, and the proportion of children's geographical composition. It is necessary to continue to monitor children's respiratory diseases, grasp the dynamic changes in their medical visits in real time, adjust the hospital admission model , implement the graded treatment policy, and promote the prevention and control of respiratory diseases in children.
4.Application of Mini-CEX evaluation Model Based on OBE concept in Clinical Practice Teaching of Neurology DePartment
Yanping LI ; Fei YANG ; Qian OUYANG ; Hongbin YU ; Gang WU ; Xiaolin DONG ; Huan WEI ; Qingyun LI ; Yi ZENG
Journal of Kunming Medical University 2024;45(3):192-197
Objective To explore the application effect of the Mini-CEX evaluation model based on the OBE concept in the clinical Practice teaching of neurology.Methods We Selected 100 students who will Practice in the Department of Neurology from 2022 to 2023 as the research objects,and divided them into the experimental group(n=50)and the control group(n=50).Under the guidance of the OBE concept,the experimental group was guided by learning outcomes,refined the teaching objectives,and applied the Mini-CEX evaluation mode for evaluation and feedback.In contrast,the control group adopted the traditional teaching mode.Combined with the observation data,we analyzed and compared the data of various indicators of the two groups of students at the beginning and end of the internship.Results At the end of the internship,the scores of clinical consultation,Physical examination,humanistic medicine,clinical diagnosis,health consultation,organizational effect,and overall evaluation of the experimental group were significantly improved and were higher than those of the control group.After the Practice,in terms of skill test scores,the experimental group scored higher than the control group,the difference was statistically significant(P<0.05),and the experimental group also scored higher in satisfaction evaluation than the control group.Conclusion The Mini-CEX evaluation teaching model based on the concept of OBE is applied to the clinical practice teaching of the neurology department,which can enhance the training effect of students'clinical practice skills.
5.A study of drugs related to contraindications in children in the 2020 edition of the Chinese Pharmacopoeia
Yu YANG ; Rui-Ling ZHAO ; Xin-Wen XU ; Zhi-Gang ZHAO
The Chinese Journal of Clinical Pharmacology 2024;40(9):1355-1359
Objective The varieties of chemical drugs prohibited for children in the 2020 edition of Chinese Pharmacopoeia were analyzed.Provide a technical basis for the development of a list of drugs prohibited by children.This is requirement of China's Children's Development Program(2021-2030).Methods Drug inserts are collected through websites such as"PharmaIntelligence",from which information on children's prohibitions is extracted,and drugs with consistent information on children's prohibitions are analyzed in the instructions of different manufacturers.Results Among the 1 741 kinds of chemicals,there are a total of 240 drugs with consistent information on the prohibition of children in the instructions of different manufacturers,of which 113 are labeled"prohibited"for children of different ages,53 are"not suitable"for children of different ages,38 are"not recommended""for children of different ages,and 36 are labeled with other children's prohibition related information.According to the classification of the clinical drug instructions involving 21 categories.Including anti-infective drugs(77),nonsteroidal anti-inflammatory drugs and anti-gout drugs(28),nervous system drugs(20),psychotropic drugs(16),digestive system drugs(16),endocrine system drugs(16),etc.Conclusion Children are at a special stage of growth and development,and the pharmacological and toxicological characteristics of drugs in children are different from those in adults.The risk-benefit ratio of drugs used in children needs continuous research to provide more detailed evidence for drug use and ensure the safety of drug use in children.
6.Comparison of short-term safety of two anastomotic techniques when resecting Siewert type II adenocarcinoma of the esophagogastric junction: a multicenter retrospective cohort study
Haikun ZHOU ; Xiaopeng GAO ; Feiyu SHI ; Jingyu WANG ; Qinchuan YANG ; Shisen LI ; Jinqiang LIU ; Panpan JI ; Weidong WANG ; Pengfei YU ; Ruiqi GAO ; Xin GUO ; Gang JI ; Jiangpeng WEI
Chinese Journal of Gastrointestinal Surgery 2024;27(1):47-53
Objective:In this study, we aimed to compare the short-term safety of two digestive tract reconstruction techniques, laparoscopic total abdominal overlap anastomosis and laparoscopic-assisted end-to-side anastomosis, following radical resection of Siewert Type II adenocarcinoma of the esophagogastric junction.Methods:In this retrospective cohort study, we analyzed relevant clinical data of 139 patients who had undergone radical surgery for Siewert Type II esophagogastric junction adenocarcinoma. These included 89 patients treated at the First Affiliated Hospital of Air Force Medical University from November 2021 to July 2023, 36 patients treated at the First Affiliated Hospital of Xi'an Jiaotong University from December 2020 to June 2021, and 14 patients treated at the Yuncheng Central Hospital in Shanxi Province from September 2021 to November 2022. The group consisted of 107 men (77.0%) and 32 women (23.0%) of mean age 62.5±9.3 years. Forty-eight patients underwent laparoscopic total abdominal overlap anastomosis (overlap group), and 91 laparoscopic-assisted end-to-side anastomosis (end-to-side group). Clinical data, surgical information, pathological findings, postoperative recovery, and related complications were compared between the two groups.Results:There were no significant differences in general clinical data between the overlap and end-to-side anastomosis groups (all P>0.05), indicating comparability. There was no significant difference in operation time (267.2±60.1 minutes vs. 262.8±70.6 minutes, t=0.370, P=0.712). However, the intraoperative blood loss in the overlap group (100 [50, 100] mL) was significantly lower compared to the end-to-side group (100[50, 175] mL, Z=2.776, P=0.005). Compared to the end-to-side group, longer distances between the tumor and distal resection margin proximal(1.7±1.0 cm vs. 1.3±0.9 cm, t=2.487, P=0.014) and the tumor and distal resection margin (9.5±2.9 cm vs. 7.9±3.5 cm, t=2.667, P=0.009) were achieved in the overlap group. Compared with the end-to-side group, the overlap group achieved significantly earlier postoperative ambulation (1.0 [1.0, 2.0] days vs. 2.0 [1.0, 3.0] days, Z=3.117, P=0.002), earlier time to first drink (4.7±2.6 days vs. 6.2±3.0 days, t=2.851, P=0.005), and earlier time to first meal (6.0±2.7 days vs. 7.1±3.0 days, t=2.170, P=0.032). However, the hospitalization costs were higher in the overlap group (113, 105.5±37, 766.3) yuan vs. (97, 250.2±27, 746.9) yuan; this difference is significant ( t=2.818, P=0.006). There were no significant differences between the two groups in postoperative hospital stay, total number of lymph nodes cleared, or time to first postoperative flatus (all P>0.05). The incidence of surgery-related complications was 22.9%(11/48) in the overlap group and 19.8% (18/91) in the end-to-side group; this difference is not significant (χ2=0.187, P=0.831). Further comparison of complications using the Clavien-Dindo classification also showed no significant differences ( Z=0.406, P=0.685). Conclusions:Both laparoscopic total abdominal overlap anastomosis and laparoscopic-assisted end-to-side anastomosis are feasible for radical surgery for Siewert Type II esophagogastric junction adenocarcinoma. Laparoscopic total abdominal overlap anastomosis achieves longer proximal and distal resection margins and better postoperative recovery; however, end-to-side anastomosis is more cost-effective.
7.Application of droplet digital PCR in etiological diagnosis of severe acute pancreatitis patients with suspected bloodstream infection
Xin-Yu WANG ; Gang LI ; Wen-Jian MAO ; Jie YANG ; Jing-Zhu ZHANG ; Lu KE ; Wei-Qin LI ; Zhi-Hui TONG
Chinese Journal of Infection Control 2024;23(1):9-15
Objective To explore the value of droplet digital polymerase chain reaction(ddPCR)in the etiological diagnosis of severe acute pancreatitis(SAP)patients with suspected bloodstream infection(BSI).Methods SAP patients admitted to the department of critical care medicine in a hospital July to September 2022 were enrolled.When BSI was suspected,venous blood was collected for both ddPCR detection and blood culture(BC)with antimi-crobial susceptibility testing(AST)simultaneously.The time required for two detection methods was recorded,and the detection results of ddPCR and BC were compared.The etiological diagnostic efficacy of ddPCR was calculated,and the correlation between the value of pathogen load detected by ddPCR and the level of infection parameters was explored.Results A total of 22 patients were included in the analysis,and 52 venous blood specimens were collec-ted for detection.BC revealed 17 positive specimens(32.7%)and 29 pathogenic strains,while ddPCR showed 41 positive specimens(78.8%)and 73 pathogenic strains.Detection time required for ddPCR was significantly lower than that of BC([0.16±0.03]days vs[5.92±1.20]days,P<0.001).Within the detection range of ddPCR and taking BC results as the gold standard,the sensitivity and specificity of ddPCR were 80.0%and 28.6%,respective-ly.With the combined assessment of BSI based on non-blood specimen microbial evidence within a week,the sensi-tivity and specificity of ddPCR detection increased to 91.9%and 76.9%,respectively.ddPCR detected resistance genes of blaKPC,blaNDM/IMP,VanA/VanM,and mecA from 19,9,6,and 5 specimens,respectively.Correlation analysis showed a positive correlation between pathogen load and levels of C-reactive protein as well as procalcitonin(r=0.347,0.414,P<0.05).Conclusion As a supplementary detection method for BC in BSI diagnosis,ddPCR has the advantages of higher sensitivity and shorter detection time,and is worthy of further exploration in clinical application.
8.Analysis of inorganic elements in different batches of earthworm polypeptides by ICP-MS combined with chemometrics technology
Hong-liu YANG ; Wei-ting ZHONG ; Yu-shi GUO ; Shu-qi LI ; Jin-chai QI ; Yong-gang LIU ; Tao MA
Acta Pharmaceutica Sinica 2024;59(4):1040-1047
To establish a method for determining 26 inorganic elements in earthworm polypeptide and determine the elemental content in different batches of earthworm polypeptide, microwave digestion method was used to pre-treat the samples, and ICP-MS method was used to determine the content of 26 elements in different batches of earthworm polypeptide. The linear relationships of 26 elements were good in the range of 0-1 000 μg·L-1, with
9.Phylogenetic analysis and pathogenesis study of a new deletion mutation causing inherited FⅩ deficiency
Dongyan FU ; Xiaomei LU ; Yalin YU ; Lidong ZHAO ; Lei WANG ; Jia YANG ; Jiawei ZHENG ; Duanyang WANG ; Linhua YANG ; Gang WANG
Chinese Journal of Hematology 2024;45(10):902-908
Objective:To analyze the F10 gene mutations in a Chinese pedigree affected with the deficiency of the hereditary coagulation factor X (FX), resulting from a new deletion mutation, and to study the associated molecular pathogenesis.Methods:Next generation sequencing (NGS) was performed to screen the genetic mutations in the proband which were then verified by Sanger sequencing. The FX activity (FX∶C) of probands and their family members was detected using the blood clotting method, and the mutation sites of the family members were analyzed using Sanger sequencing. The pathogenicity of the mutation site was predicted by using the online bioinformatics software, Mutation Taster. The SWISS-MODEL software was used for stimulating the three-dimensional models of the wild-type and mutant proteins for analyzing the influence of the mutation site on the structure and function of the proteins, and for analyzing the difference between the catalytic residues of the wild-type and the mutant proteins. The level of the F10 gene mRNA was quantitatively analyzed by qRT-PCR (quantitative reverse transcription polymerase chain reaction) method by constructing plasmids, transfecting human embryonic kidney 293T cells (HEK 293T), and analyzing the splicing of the mutated site by RT-PCR method. The levels of FⅩ∶Ag in cell lysates and cell culture media (both inside and outside the cells) were detected by the ELISA (enzyme linked immunosorbent assay) method.Results:A medium-grade factor X deficiency with a 36.42% FⅩ∶C ratio was detected in the proband by the coagulation method. NGS analysis demonstrated a heterozygous deletion mutation in exon 8:c.902_919del (p.Ala301_Glu306del) in the proband. Sanger sequencing analysis indicated that some members of the family (mother and grandfather) were also carriers of the corresponding deletion mutation. Online bioinformatics software predicted the pathogenic nature of the c.902_919del mutation, with a pathogenic score of 0.999. The 3D protein structure model analysis indicated that the c.902_919del mutation resulted in the disappearance of a segment of β-fold in the protein structure, thereby shortening the preceding segment of the β-fold and a subsequent loss of hydrogen bonds between adjacent amino acids with no significant difference in the side chain conformation of the key catalytic residues compared to the wild-type. mRNA splicing analysis indicated the absence of alternative splicing changes in the mutation, and qRT-PCR results indicated the absence of a statistically significant difference between the mRNA levels of F10 gene and wild-type mRNA in cells expressing c.902_919del mutant. The ELISA results indicated that there was no statistically significant difference in the FX∶Ag levels of the mutant cell culture medium and the lysate.Conclusions:In this pedigree, the heterozygous mutation in exon 8 of F10 gene (c.902_919del, p.Ala301_Glu306del) caused the hereditary factor Ⅹ deficiency.
10.Development status and countermeasures of medical device industry in Jilin Province
Yu-Heng YANG ; Wen-Yuan JIA ; Yun LIU ; Yong-Zheng YAN ; Yun-Gang LUO ; Guo-Min LIU
Chinese Medical Equipment Journal 2024;45(7):67-71
The development status of medical device industry in Jilin Province was described,and the main problems during the development of medical device industry in Jilin Province was analyzed.Some countermeasures were put forward including enlarging the industrial scale,constructing business incubators in the field of medical device,guaranteeing the market access of the products,accelerating the registration and approval,strengthening the cross-discipline construction and forming medical-industrial institutes.References were provided for the development of medical device industry in Jilin Province.[Chinese Medical Equipment Journal,2024,45(7):67-71]


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