1.A review of transformer models in drug discovery and beyond.
Jian JIANG ; Long CHEN ; Lu KE ; Bozheng DOU ; Chunhuan ZHANG ; Hongsong FENG ; Yueying ZHU ; Huahai QIU ; Bengong ZHANG ; Guo-Wei WEI
Journal of Pharmaceutical Analysis 2025;15(6):101081-101081
Transformer models have emerged as pivotal tools within the realm of drug discovery, distinguished by their unique architectural features and exceptional performance in managing intricate data landscapes. Leveraging the innate capabilities of transformer architectures to comprehend intricate hierarchical dependencies inherent in sequential data, these models showcase remarkable efficacy across various tasks, including new drug design and drug target identification. The adaptability of pre-trained transformer-based models renders them indispensable assets for driving data-centric advancements in drug discovery, chemistry, and biology, furnishing a robust framework that expedites innovation and discovery within these domains. Beyond their technical prowess, the success of transformer-based models in drug discovery, chemistry, and biology extends to their interdisciplinary potential, seamlessly combining biological, physical, chemical, and pharmacological insights to bridge gaps across diverse disciplines. This integrative approach not only enhances the depth and breadth of research endeavors but also fosters synergistic collaborations and exchange of ideas among disparate fields. In our review, we elucidate the myriad applications of transformers in drug discovery, as well as chemistry and biology, spanning from protein design and protein engineering, to molecular dynamics (MD), drug target identification, transformer-enabled drug virtual screening (VS), drug lead optimization, drug addiction, small data set challenges, chemical and biological image analysis, chemical language understanding, and single cell data. Finally, we conclude the survey by deliberating on promising trends in transformer models within the context of drug discovery and other sciences.
2.Clinical analysis of six cases of neonatal hand-foot-mouth disease
Yanyu CHEN ; Lili QIU ; Huahai FENG ; Yanyi DENG
Chinese Journal of Neonatology 2017;32(3):217-219
Objective To study the clinical features of hand-foot-mouth disease(HFMD) in neonates.Method From April 2015 to May 2016,the clinical manifestations,laboratory examinations,treatments and prognosis of neonates with HFMD in our hospital were retrospectively analyzed.Result A total of 6 cases of neonatal HFMD were included,with 4 males and 2 females.The ages of 2 patients were ≤7 days and the other 4 patients 8 ~ 28 days.5 patients developed this disease during April to July,while the other one in January.2 cases had a definite contract history of HFMD.4 cases presented with fever and rashes in hand and foot,one case with fever,rash and oral ulcer,and one case with rash in hip and oral ulcer without fever.The nucleic acid test of enterovirus were positive in 4 cases.The symptoms of these neonatal HFMD were mild and recovered after symptom-relieving treatment.Conclusion HFMD in neonates with fever and/or rash should be considered during the HFMD epidemic period.
3.Effect of alteplase intra- arterial thrombolysis combined with continuous monitoring of transcranial Doppler in patients with acute cerebral infarction
Shaohui LUO ; Yukai WANG ; Pu DU ; Huahai FENG ; Xingzhen DENG
Chinese Journal of Postgraduates of Medicine 2016;39(12):1068-1071
Objective To observe the effect of alteplase intra-arterial thrombolysis combined with continuous monitoring of transcranial Doppler (TCD) in patients with acute cerebral infarction. Methods Fifty-four patients with acute cerebral infarction were divided into TCD group and control group by random digits table method. The patients of 2 groups were given alteplase intra-arterial thrombolysis, and the patients of TCD groups were combined with continuous monitoring of TCD. The degree of clinical neurologic impairment was evaluated by National Institutes of Health stroke scale (NIHSS) and Barthel index (BI). The condition of vascular recanalization was evaluated by the change of blood flow signal of TCD. CT was performed within 1 d after thrombolysis to detect intracranial hemorrhage and other adverse reaction. The degree of clinical neurologic impairment, blood vessel recanalization rate after thrombolysis and recanalization time and incidence of intracranial hemorrhage and other adverse reaction were compared between 2 groups. Results There were no statistical difference in NIHSS score before thrombolysis and 1 h after thrombolysis between 2 groups (P>0.05). The NIHSS scores 7 and 30 d after thrombolysis in TCD group were significantly lower than those in control group:(8.1 ± 4.9) scores vs. (12.1 ± 4.2) scores and (6.9 ± 3.1) scores vs. (10.9 ± 3.9) scores, there were statistical differences (P<0.05). The BI scores 7 and 30 d after thrombolysis in TCD group were significantly higher than those in control group: (78.5 ± 13.8) scores vs. (60.8 ± 12.4) scores and (82.6 ± 13.5) scores vs. (63.2 ± 12.9) scores, and there were statistical differences (P<0.05). The blood vessel recanalization rate 24 h after thrombolysis in TCD group was significantly higher than that in control group: 70.4% (19/27) vs. 44.4% (12/27), the recanalization time after thrombolysis was significantly shorter than that in control group: (36.4 ± 9.5) min vs. (58.5 ± 12.4) min, and there were statistical differences (P<0.05). No adverse reaction like intracranial hemorrhage and so on was found by CT detection within 1 d after thrombolysis in the 2 groups. Conclusions Alteplase intra-arterial thrombolysis combined with continuous monitoring of TCD in acute cerebral infarction has good curative effect, and no obvious adverse reaction.
4.Correlation analysis of uric albumin/uric creatinine ratio with NEW-TOAST different types in acute cerebral infarction
Jingjuan CHEN ; Chengguo ZHANG ; Guode LI ; Guanglun ZENG ; Piao DU ; Guohua ZHANG ; Huahai FENG
Chinese Journal of Neuromedicine 2014;13(8):799-802
Objective To detect the urinary albumin level and urinary albumin/urine creatinine ratio in patients with acute cerebral infarction and explore their relations with NEW-TOAST typing.Methods One hundred and sixty-eight patients with acute cerebral infarction,admitted to our hospital from March 2011 to March 201,were chosen in our study; and other 45 healthy subjects were used as controls; according to NEW-TOAST typing,the patients were divided into different subgroups.Their clinical data were retrospectively analyzed; the 24 hour urinary albumin level and urinary albumin/urine creatinine ratio were detected and their relation was analyzed between patient group and controls,and between patients of different subtypes; besides,the correlation of neurologic impairment (NIHSS) scores with urinary albumin/urine creatinine ratio was analyzed.Results The 24 hour urinary albumin level and urinary albumin/urine creatinine ratio was positively correlated (r=0.301,P=0.001); according to the NEW-TOAST subtypes,patients with large artery atherosclerosis and small artery occlusion had significantly higher level of 24 hour urinary albumin level and urinary albumin/urine creatinine ratio (P<0.05).NIHSS scores and urinary albumin/creatinine ratio in patient group were positively correlated (r=0.215,P=0.001).Conclusion Acute cerebral infarction and kidney disease are closely correlated;both 24 hour urinary albumin level and urinary albumin/urine creatinine ratio can be the predictor of acute cerebral infarction and influence the prognosis.
5.Protective effect of tiopronin supplemented with chemotherapy in treating advanced breast cancer
Huanwei CHEN ; Xiaoqiong ZHAO ; Xianming FENG ; Huahai LIN
Chinese Journal of Primary Medicine and Pharmacy 2008;15(11):1825-1826
Objective To observe the efficacy and safety of tiopronin supplemented with chemotherapy in treating advanced breast cancer.Methods Sixty patients with advanced breast cancer were randomly divided into two groups:treatment group(n = 28) and control group (n = 32).Two groups were treated the same of NVB + DDP,the treatment group was supplemented with tiopronin,given for 10 days.Efficacy,toxicity in two groups were compared.Results The effective rate in the treatment group and the control group were 46.4% and 46.9% respectively, with no significant difference between the two groups ,P > 0.05.But the improved quality of life of patients in the treatment group was higher than that in the control group, P < 0.05.The rate of adverse reaction in liver function damaged (9.4%)and leucocyte lassitude(46.4%) were apparent lower than those in the control group(31.2% ,81.2% ),with significant difference between the two groups(P < 0.05, P < 0.01).Conclusion Tiopronin supplemented with chemotherapy show apparent effect in decreasing the adverse reaction of chemotherapy,improving the quality of life and not influence efficacy in advanced breast cancer.So tiopronln may act as protective drug for chemotherapy and deserve further testing in the clinic.

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