1.Reporting Status of Clinical Practice Guideline Protocols: A Systematic Analysis
Huayu ZHANG ; Xufei LUO ; Hui LIU ; Qi ZHOU ; Yishan QIN ; Ye WANG ; Yuanyuan YAO ; Haodong LI ; Xiaohui WANG ; Yaolong CHEN
Medical Journal of Peking Union Medical College Hospital 2026;17(1):255-262
To systematically analyzed the reporting status of core elements in publicly available clinical practice guideline(hereafter referred to as "guideline") protocols published domestically and internationally over the past decade, identified existing problems, and provided evidence to inform the standardized writing and publication of future guideline protocols. A systematic search was conducted in Chinese and English databases for clinical practice guideline protocols published during the past ten years. The basic characteristics and reporting of core elements—including registration information, conflict of interest management, evidence grading, development process and timeline planning, as well as dissemination and implementation—were extracted and analyzed. Chi-square tests were performed to explore associations between protocol characteristics and the reporting of core elements. A total of 94 guideline protocols were included, of which 67 were in Chinese(71.28%) and 27 were in English(28.72%). Overall, 82.98% of the guideline protocols were registered, 92.55% reported management of conflicts of interest, 97.87% reported evidence searching, 88.30% reported evidence grading, and 89.36% described dissemination and implementation strategies. However, only 55.32% reported the guideline development process, and merely 23.40% reported timeline planning. Further analysis indicated that the reporting of registration, evidence searching, development process, and timeline planning was associated with year of publication. Differences were observed between domestic and international guidelines in reporting registration, conflict of interest management, development process, time planning, and dissemination and implementation. Guidelines intended for development exhibited higher reporting rates for registration, development process, and dissemination and implementation compared to those planned for updating or adaptation. Although current guideline protocols demonstrate relatively adequate reporting of methodological elements, deficiencies remain in development process and timeline planning. Future efforts should focus on promoting the publication and standardized reporting of guideline protocols, enhancing the international recognition of registration platforms, and strengthening the development process and timeline planning to advance the scientific rigor and transparency of guideline development.
2.Analysis of diagnosis and treatment of Epstein-Barr virus-negative diffuse large B-cell lymphoma (GCB type) after kidney transplantation
Yan LI ; Xiaoyan ZHANG ; Xiang REN ; Tong XU ; Guohui WANG ; Ruochen QI ; Dongjuan WU ; Kepu LIU ; Weijun QIN ; Shuaijun MA
Organ Transplantation 2026;17(2):257-265
Objective To analyze the clinical and therapeutic characteristics of Epstein-Barr virus (EBV)-negative posttransplant lymphoproliferative disease (PTLD) with diffuse large B-cell lymphoma (DLBCL) in the context of specific cases and literature. Methods A case of EBV-negative DLBCL (GCB type) after kidney transplantation is reported. The patient was a 45-year-old male who underwent living-related kidney transplantation in 2016 and has been receiving triple immunosuppressive therapy with tacrolimus, mycophenolate mofetil and methylprednisolone since then. In 2024, the patient presented with intermittent fever, night sweats and gastrointestinal symptoms. The diagnosis was confirmed by endoscopic pathology, immunohistochemical staining and positron emission tomography/computed tomography. The R-CDOP regimen (rituximab + cyclophosphamide + liposomal doxorubicin + vincristine + dexamethasone) was used for treatment. Results The patient was diagnosed with EBV-negative DLBCL (GCB type, Ann Arbor stage Ⅳ B). After 4 cycles of R-CDOP chemotherapy, the efficacy assessment was partial remission, and the transplant kidney function remained stable. Conclusions For EBV-negative PTLD after kidney transplantation, it is necessary to break through the "virus-dependent" diagnostic thinking. In clinical practice, the focus should be on protecting the transplant kidney, and individualized treatment plans should be developed for patients.
3.Traditional Chinese Medicine Alleviates Dry Eye Disease by Regulating Tear Film Homeostasis: A Review
Sainan TIAN ; Bin'an WANG ; Yao CHEN ; Guicheng LIU ; Li TANG ; Pei LIU ; Genyan QIN ; Jun PENG ; Qinghua PENG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(7):172-181
Dry eye (DE) is a prevalent multifactorial disease of the ocular surface, clinically characterized by tear film homeostasis imbalance accompanied by related ocular surface symptoms. Specifically, the tear film is a thin liquid layer of tears covering the cornea and conjunctiva through blinking, while tear film homeostasis serves as the foundation for maintaining normal ocular surface structure and function. Insufficient tear secretion and excessive tear film evaporation lead to tear hyperosmolarity and the production of inflammatory mediators, disrupting tear film homeostasis and subsequently forming DE. Additionally, cascade reactions are triggered, resulting in a "vicious cycle of DE" that exacerbates the disease severity and prolongs its duration. Therefore, for DE treatment, it is crucial to restore tear film homeostasis and terminate this vicious cycle. Traditional Chinese medicine (TCM), which differentiates and treats DE based on systemic conditions, often achieves favorable therapeutic outcomes, offering additional treatment options for DE. Studies have demonstrated that TCM can alleviate DE by regulating tear film homeostasis and terminating the vicious cycle. This review systematically summarizes recent basic experimental research in China and abroad on TCM in alleviating DE by regulating tear film homeostasis, aiming to provide a theoretical basis for clinical treatment and an insight for research design.
4.Impact of birth weight on the trajectory of blood pressure among primary school students
CUI Chengpeng, YE Siyan, FANG Yanfei, LI Yan, PENG Zeqin, XIAO Yuqing, WU Meng, LIU Qin
Chinese Journal of School Health 2026;47(3):309-313
Objective:
To explore the early effects of birth weight at different gestational ages on blood pressure trajectory among primary school students, so as to provide evidence for incorporating gestational age birth weight into individualized early warning and intervention strategies for childhood hypertension.
Methods:
From May to November 2023, a purposeful sampling method was used to recruit 1 676 students in grade 1-3 from three primary schools in a certain urban district of Chongqing. Follow up assessments were conducted in May 2024(T1), November 2024(T2), and May 2025(T3). General demographic and birth related information were collected via self administered questionnaires, while height, weight and blood pressure were obtained through physical examinations. Linear mixed effects model was used to analyze the associations between birth weight at different gestational ages and blood pressure trajectories.
Results:
During the T1-T3 period, the systolic blood pressure of boys were 98.5 (93.0, 104.5 ),98.5 (93.5, 105.0), and 97.5 (92.5, 103.5)mmHg, respectively, while the diastolic blood pressure were 60.5 (56.5, 65.0), 61.5 ( 57.0 , 65.5), and 60.0 (56.0, 64.0)mmHg, respectively. For girls, the systolic blood pressure were 95.5 (90.0, 102.0),95.5 (90.5, 101.5), and 96.0 (90.5, 101.5)mmHg, respectively, and the diastolic blood pressure were 60.5 (56.0, 64.5 ),61.5 (57.5, 65.5), and 59.5 (56.0, 63.0)mmHg, respectively. Through Friedman test within both boys and girls, diostolic blood pressure were statistically significant across three measurements( χ 2=48.85,81.54,both P <0.01). The proportion of normal blood pressure increased , and the proportion of prehypertension and hypertension decreased with time( χ 2=39.72,25.62,both P < 0.01 ). Linear mixed effects model analysis revealed that after adjusting for age, sex, household income monthly, parental education, family history of hypertension and maternal pregnancy complications, large for gestational age had significantly higher trajectories of systolic ( β = 1.50) and diastolic( β =0.94) blood pressure compared to appropriate for gestational age(both P <0.01).
Conclusion
Large for gestational age is associated with elevated blood pressure trajectories during school age, and it may be considered as an early indicator for individualized screening and intervention for childhood hypertension.
5.Research Progress of Traditional Chinese Medicine in Improving Diabetic Retinopathy Based on Nrf2 Signaling Pathway
Xueqing LIU ; Xinyu ZHONG ; Tingting WANG ; Ning WANG ; Man LIU ; Li WU ; Lili WU ; Lingling QIN ; Tonghua LIU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(9):69-78
Diabetic retinopathy (DR) is a microvascular complication of diabetes and one of its most common complications. Prolonged hyperglycemia induces oxidative stress, inflammatory responses, apoptosis, and pathological angiogenesis, ultimately disrupting the blood-retinal barrier(BRB) and leading to visual impairment or even blindness. Recent studies show that the nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathway plays an important role in the development of DR's pathological changes. Meanwhile, Chinese herbal monomers have been shown to modulate the Nrf2 signaling pathway, thereby intervening in the development of DR. In terms of inhibiting oxidative stress, saponin compounds such as platycodin-D and ginsenoside Rb1 downregulate the expression of malondialdehyde (MDA), thereby ameliorating retinal oxidative stress. Flavonoids such as total flavonoids from Pueraria lobata flower and puerarin upregulate the expression of superoxide dismutase (SOD) and glutathione peroxidase (GPx), effectively clearing lipid peroxides. Regarding the suppression of inflammation, phenolic compounds like resveratrol and chlorogenic acid inhibit the nuclear factor kappa B (NF-κB) pathway, reducing the release of tumor necrosis factor-alpha (TNF-α) and mitigating inflammatory responses. In the context of inhibiting apoptosis, polysaccharides such as Polygonatum sibiricum polysaccharide and Angelica sinensis polysaccharide downregulate the expression of the pro-apoptotic protein Bcl-2-associated X protein (Bax) and suppress the activity of the executioner Caspase-3, thereby reducing the apoptosis rate. As for the inhibition of neovascularization, compounds including bilobalide and physcion significantly decrease the protein expression of vascular endothelial growth factor (VEGF), leading to a reduction in retinal pathological angiogenesis. Furthermore, Chinese herbal compound prescriptions such as Tongluo Zhujing pills, Yiqi Huoxue Yangyin decoction, Qiming granules, and Danlou tablets can also intervene in the onset and progression of DR through the mechanisms described above. In summary, both Chinese herbal monomers and Chinese herbal compound prescriptions can modulate the Nrf2 signaling pathway to inhibit oxidative stress, alleviate inflammation, and participate in maintaining BRB integrity, suppressing retinal neovascularization, and preventing neurodegeneration, thereby delaying the progression of DR. Therefore, this paper reviews and summarizes recent studies at home and abroad on how traditional Chinese medicine (TCM) works to treat DR, and the relationship between the Nrf2 pathway and DR. It aims to provide research ideas for preventing and treating DR.
6.Preparation,characterization and quantitative analysis of β-cyclodextrin inclusion complex with volatile oil from Qianghuo qushi qingwen granules
Yicheng SUN ; Lingrui QIN ; Kaiping ZOU ; Chenguang ZHAO ; Li DOU ; Shun LIU ; Lingang ZHAO
China Pharmacy 2026;37(6):746-751
OBJECTIVE To prepare the β -cyclodextrin ( β -CD) inclusion complex with volatile oil from Qianghuo qushi qingwen granules, and to characterize and quantitatively analyze the inclusion complex. METHODS The comprehensive scores calculated by inclusion rate and inclusion compound yield were used as indicators for screening the inclusion method. The single-factor experiments and Box-Behnken response surface experiments were used to op timize the inclusion conditions, with the above comprehensive score as response value, and taking the ratio of β -CD to volatile oil, inclusion temperature and inclusion time as indexes. The volatile oil inclusion complex of Qianghuo qushi qingwen granules was prepared according to the determined optimal process, followed by validation. Ultraviolet (UV)-visible spectroscopy, thin-layer chromatography (TLC), and microscopic imaging were also performed. Ultra-high performance liquid chromatography was used to determine the contents of perillaldehyde, pogostone and atractylodin. RESULTS The saturation aqueous solution method was adopted. The optimal inclusion process conditions were as follows: the ratio of β -CD to volatile oil was 7.5∶1, the inclusion temperature was 40 ℃, and the inclusion time was 2.2 h. In three verification experiments, the average inclusion rate was 72.32%, the average yield of inclusion compound was 74.45%, the average comprehensive score was 72.96 points, and the relative error with the predicted value (74.15 points) of the model was 1.61%. UV-visible spectroscopy, TLC and microscopic imaging showed that β -CD and volatile oil successfully formed a new inclusion complex. The average contents of perillaldehyde, pogostone and atractylodin were 4.498 2, 0.814 9, 0.905 7 mg/g, respectively, with RSDs of 0.31%, 0.56% and 0.63% ( n =3). CONCLUSIONS A stable and feasible preparation process of the volatile oil inclusion complex of Qianghuo qushi qingwen granules is successfully established.
7.Mechanisms of Bushen Tongluo Jiangzhuo Prescription in Improving Renal Fibrosis in Rats with Chronic Kidney Disease Based on PI3K/Akt/mTOR Signaling Pathway
Xincui BAO ; Baosheng ZHAO ; Lingling QIN ; Haiyan WANG ; Jing YANG ; You WANG ; Lijia WU ; Yujin LI ; Ming GAO ; Cuiyan LYU ; Tonghua LIU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(6):100-108
ObjectiveTo investigate the mechanisms by which Bushen Tongluo Jiangzhuo prescription improves renal fibrosis in rats with chronic kidney disease (CKD) through the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt)/mammalian target of rapamycin (mTOR) signaling pathway. MethodsSeventy specific pathogen-free (SPF) Sprague-Dawley (SD) rats were randomly divided into a control group (n=15) and a modeling group (n=55). Rats in the modeling group were administered a 2.5% adenine suspension at a dose of 200 mg·kg-1·d-1 by gavage for 4 weeks to establish a CKD model. Successfully modeled rats were randomly divided into a model group, an irbesartan group (20.25 mg·kg-1·d-1), and Bushen Tongluo Jiangzhuo prescription low-, medium-, and high-dose groups (5.82, 11.64, and 23.28 g·kg-1·d-1, respectively), with 10 rats in each group. Each group was administered an equal volume of physiological saline, the corresponding concentration of irbesartan, or Bushen Tongluo Jiangzhuo prescription by gavage for 12 weeks. Body weight and renal function indices were dynamically monitored. Serum creatinine (SCr), blood urea nitrogen (BUN), urine albumin-to-creatinine ratio (ACR), 24-hour urinary total protein (24 hUTP), aspartate aminotransferase (AST), alanine aminotransferase (ALT), interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) levels were measured using an automatic biochemical analyzer. Renal histopathological changes were observed by hematoxylin-eosin (HE) and Masson staining. Immunohistochemistry (IHC) was used to detect the expression of PI3K, Akt, phosphorylated Akt (p-Akt), and mTOR in renal tissues. Western blot was performed to assess the protein expression of PI3K, p-Akt, Akt, phosphorylated mTOR (p-mTOR), and mTOR in renal tissues. Real-time quantitative polymerase chain reaction (Real-time PCR) was used to determine the mRNA expression levels of PI3K, Akt, and mTOR in renal tissues. ResultsCompared with the model group, rats in the irbesartan group and the low-, medium-, and high-dose Bushen Tongluo Jiangzhuo prescription groups showed significantly decreased levels of SCr, BUN, ACR, 24 hUTP, IL-1β, IL-6, and TNF-α (P<0.01). AST levels were significantly increased (P<0.01), while no significant difference was observed in ALT levels. Histopathological examination revealed that, compared with the model group, renal tubular epithelial cell edema and necrosis and Bowman's capsule dilation were alleviated, inflammatory cell infiltration was reduced, and interstitial and glomerular fibrosis was markedly improved in all treatment groups, with the most pronounced effect observed in the high-dose Bushen Tongluo Jiangzhuo prescription group. Real-time PCR results showed that mRNA expression levels of PI3K, Akt, and mTOR were significantly downregulated in the high-dose group (P<0.01). IHC results demonstrated that PI3K and p-Akt expression levels in renal tissues were significantly decreased in the high-dose group (P<0.01). Western blot analysis further confirmed that the expression levels of PI3K, p-Akt/Akt, and p-mTOR/mTOR were significantly reduced in the high-dose group (P<0.01). ConclusionBushen Tongluo Jiangzhuo prescription improves renal function indices in CKD rats, reduces collagen deposition in renal tissues, and decreases serum inflammatory factor levels. Its protective effect on renal function may be achieved by activating autophagy through downregulation of the PI3K/Akt/mTOR signaling pathway, thereby alleviating renal fibrosis.
8.Advances in reno-protective effects of traditional Chinese medicine in the treatment of hyperuricemia
Xiaoting ZHOU ; Yu DUAN ; Xingyuan LI ; Qin LIU ; Aijun LIU
Journal of Pharmaceutical Practice and Service 2026;44(4):167-172
Hyperuricemia (HUA) is a common metabolic disorder characterized by persistently elevated serum uric acid levels, leading to uric acid-related renal injury through complex mechanisms involving inflammation, oxidative stress, and fibrosis. Key traditional Chinese medicine (TCM) formulas (e.g., Simiao Powder, Tongfengning) and individual herbal compounds (alkaloids, flavonoids, polysaccharides) with urate-lowering and renal protective properties were systematically summarized, including their mechanisms of regulating uric acid transporters (organic anion transporter 3, urate anion transporter 1, glucose transporter type 9), inhibiting inflammatory responses (via NF-κB signaling), reducing oxidative stress (via mitochondrial pathways and antioxidant enzyme enhancement), and attenuating renal fibrosis (via PI3K/AKT signaling). The challenges of current studies mainly focus on unclear mechanisms of action and insufficient clinical research. Future research may further explore TCM resources, clarify dual-action mechanisms of urate reduction and renal protection, and identify new therapeutic strategies for hyperuricemia-related renal injury.
9.Electroacupuncture Ameliorates NLRP3-mediated Pyroptosis in Spinal Cord Injury Rats by Reshaping The Gut Microbiota
Yin-Jie CUI ; Hong-Ru LI ; Jing-Yi LIU ; Hai-Lin DU ; Shu-Wen LIU ; Yuan YANG ; Chen-Guang ZHENG ; Jian-Qin XIANG ; Xiao-Juan SONG
Progress in Biochemistry and Biophysics 2026;53(5):1132-1153
ObjectiveSpinal cord injury (SCI) directly impairs the regulatory function of the autonomic nervous system, induces intestinal dysfunction, and significantly reduces patients’ quality of life. Preclinical studies have shown that electroacupuncture (EA) therapy can regulate the brain-gut axis and is used to treat central nervous system diseases such as major depressive disorder, Alzheimer’s disease and Parkinson’s disease. Recent research has established that fecal microbiota transplantation (FMT) from EA-treated SCI rats restored intestinal motility and colonic morphology. However, it remains unclear whether the regulation of gut microbiota by EA therapy directly contributes to neural repair after SCI. This study aims to explore whether gut microbiota mediates the neuroprotective effect of EA in the treatment of SCI and its possible mechanism. MethodsThe study employed RNA transcriptome analysis of spinal cord tissue to characterize gene expression profiles and to identify key signaling pathways following EA treatment for SCI. Hematoxylin-Eosin (HE) staining and Nissl staining were used to observe the morphological changes in spinal cord tissue. Western blot (WB) and enzyme-linked immunosorbent assay (ELISA) were applied to detect the effects of EA on the expression of proteins related to nucleotide-binding domain leucine-rich repeat and pyrin domain-containing receptor 3 (NLRP3) -dependent pyroptosis. Using 16S rDNA sequencing, the study observed alterations in gut microbiota diversity and community composition in SCI rats. Prior to establishing SCI models, rats were pretreated with an antibiotic cocktail to induce gut dysbiosis, and the effects on intestinal function and spinal cord neural repair were evaluated. FMT was performed to investigate the regulatory effects of post-EA FMT on motor function, general status, liver and spleen indices, and NLRP3-mediated pyroptosis in SCI rats. ResultsEA improved motor function and reduced regulated neuronal cell death in SCI rats. Transcriptomic analysis demonstrated the activation of immune- and inflammation-related pathways post-SCI, including NOD-like receptors, nuclear factor-kappa B(NF-κB), and Toll-like receptor (TLR) pathways. EA primarily influenced intestinal inflammation and autoimmune functions. 16S rDNA sequencing illustrated that EA did not alter the diversity of gut microbiota. However, EA altered the gut microbiota composition in SCI rats, increasing Lactobacillus and Akkermansia genera while rebalancing the Firmicutes/Bacteroidetes ratio. Furthermore, depletion of gut microbiota by antibiotics disrupted the intestinal barrier, reduced the expression of intestinal barrier proteins Zonula Occludens-1 (ZO-1) and Occludin, elevated serum lipopolysaccharide-binding protein (LBP) levels, exacerbated spinal cord tissue damage, and hindered motor function recovery in SCI rats. FMT from donors treated with EA reduced LBP levels in the intestine, blood, and spinal cord of rats, inhibited the TLR4 myeloid differentiation primary response protein 88 (MyD88)-NF‑κB pathway and NLRP3-dependent pyroptosis, and improved motor function. On the other hand, FMT treatment resulted in decreased body weight and food intake, whereas FMT using EA-treated donors effectively alleviated these alterations. ConclusionEA effectively alleviated neuroinflammatory responses in rats with SCI, primarily through regulating the gut microbiota and suppressing the NLRP3-dependent pyroptosis signaling pathway.
10.A Computational Perspective on Differences Between MHC-I and MHC-II in TCR-pMHC Structure Prediction Resources: Review and Benchmarking
Xiao-Qin WU ; Da-Wei LIU ; Bin-Yu LI ; Yang LIU ; Yang CAO ; Wen-Tao DAI
Progress in Biochemistry and Biophysics 2026;53(5):1376-1399
The initiation of adaptive immune responses relies on the precise recognition and interpretation of antigenic information. In this process, the specific binding of T cell receptors (TCRs) to peptide-major histocompatibility complex (pMHC) molecules represents one of the key molecular events in the initiation of adaptive immune responses. Accordingly, the structural features of TCR-pMHC complexes provide a fundamental basis for dissecting antigen recognition mechanisms and support rational vaccine design, therapeutic target discovery in TCR-based immunotherapy, and TCR identification and optimization. However, experimental determination of TCR-pMHC structures remains costly, time-consuming, and limited in coverage, making computational approaches essential for rapidly obtaining reliable structural information. Computational methods for predicting the structures of TCR-pMHC complexes have advanced rapidly in recent years, driven by progress in deep learning-based modeling frameworks and the increasing availability of structural and sequence resources. Despite these developments, most existing tools do not adequately distinguish the key structural and biophysical differences between MHC class I (MHC-I) and MHC class II (MHC-II) complexes during model construction. As a consequence, their predictive performance differs substantially between class I and class II complexes. In general, structural predictions for class I complexes outperform those for class II complexes. This discrepancy may be related to several fundamental differences between the two systems, including the architecture of the peptide-binding groove, the distribution of peptide lengths, and the properties of peptide flanking residues (PFRs). Compared with MHC-I molecules, MHC-II molecules usually bind longer antigenic peptides, which typically range from 13 to 25 amino acids in length. PFRs at both termini of these peptides participate in regulating the overall conformation of TCR-pMHC class II complexes and exert a pronounced effect on the geometric and physicochemical characteristics of the TCR-pMHC binding interface. Furthermore, within the TCR recognition interface, the complementarity-determining regions (CDRs) consist of segments that differ markedly in conformational behavior. They commonly include regions that are relatively rigid and structurally stable, together with highly flexible segments exhibiting substantial conformational plasticity. These rigidity-flexibility features constitute an essential structural basis enabling TCRs to recognize diverse peptide-MHC ligands and to accommodate conformational heterogeneity at the interface. However, many current modeling tools, in an effort to enforce global conformational stability or reduce structural noise, tend to over-constrain intrinsically flexible regions. Such oversimplification may lead to inappropriate rigidification of flexible CDR loops, resulting in local structural distortions, compromised interface geometry, or even complete modeling failure for specific complexes. Against this background, the review approaches the field from the perspective of computational differences between MHC-I and MHC-II complexes. We first systematically organize and summarize available resources related to TCRs and pMHCs, including structural datasets, sequence databases, prediction tools, and benchmarking studies. We then focus on five representative tools capable of predicting both class I and class II complexes—AlphaFold2, AlphaFold3, TCRmodel2, tFold-TCR, and TCR-pHLA_ModellerS. After excluding structures present in the training sets of these tools, we constructed a benchmark dataset comprising 25 class I and 10 class II TCR-pMHC complexes in the bound state and conducted a systematic evaluation using this dataset. We first employ widely used general evaluation metrics, including All-Atom Root Mean Square Deviation (All-Atom RMSD), Backbone RMSD, Template Modeling score (TM-score), and DockQ, to assess the global conformational accuracy and interface modeling quality of class I and class II complexes. For class II complexes, we propose for the first time a peptide flanking residue deviation index, including the PFRs-Deviation Index (PFRs-DI), N-PFR-Deviation Index (N-PFR-DI), and C-PFR-Deviation Index (C-PFR-DI), to quantitatively characterize conformational deviations in PFRs. In addition, we propose the CDR conformational consistency index (CCC) designed to qualitatively evaluate the ability of prediction tools to capture TCR CDR conformational flexibility. These metrics collectively assess a tool’s ability to model both overall conformation and critical functional regions, thereby addressing the limitations of existing evaluation criteria that overemphasize global structure while inadequately capturing modeling quality in key functional areas. This establishes a unified analytical framework for MHC-I and MHC-II complexes to guide data resource selection, modeling strategy formulation, and evaluation system development. The framework further advances computational modeling and provides crucial support for multi-scale analysis of TCR-pMHC recognition mechanisms and their biological functions.


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