1.VenusMutHub: A systematic evaluation of protein mutation effect predictors on small-scale experimental data.
Liang ZHANG ; Hua PANG ; Chenghao ZHANG ; Song LI ; Yang TAN ; Fan JIANG ; Mingchen LI ; Yuanxi YU ; Ziyi ZHOU ; Banghao WU ; Bingxin ZHOU ; Hao LIU ; Pan TAN ; Liang HONG
Acta Pharmaceutica Sinica B 2025;15(5):2454-2467
In protein engineering, while computational models are increasingly used to predict mutation effects, their evaluations primarily rely on high-throughput deep mutational scanning (DMS) experiments that use surrogate readouts, which may not adequately capture the complex biochemical properties of interest. Many proteins and their functions cannot be assessed through high-throughput methods due to technical limitations or the nature of the desired properties, and this is particularly true for the real industrial application scenario. Therefore, the desired testing datasets, will be small-size (∼10-100) experimental data for each protein, and involve as many proteins as possible and as many properties as possible, which is, however, lacking. Here, we present VenusMutHub, a comprehensive benchmark study using 905 small-scale experimental datasets curated from published literature and public databases, spanning 527 proteins across diverse functional properties including stability, activity, binding affinity, and selectivity. These datasets feature direct biochemical measurements rather than surrogate readouts, providing a more rigorous assessment of model performance in predicting mutations that affect specific molecular functions. We evaluate 23 computational models across various methodological paradigms, such as sequence-based, structure-informed and evolutionary approaches. This benchmark provides practical guidance for selecting appropriate prediction methods in protein engineering applications where accurate prediction of specific functional properties is crucial.
3.Transcatheter arterial chemoembolization combined with surgical resection for the treatment of ruptured hepatocellular carcinoma
Zhiwei LI ; Yuanxi WANG ; Lie CAI ; Yu ZHENG ; Jin CHEN
Chinese Journal of Hepatobiliary Surgery 2012;18(10):777-779
ObjectiveTo study the efficacy of transcatheter arterial chemoembolization (TACE) combined with surgical resection in the treatment of ruptured hepatocellular carcinoma (HCC).MethodsThe clinical data of 26 patients who presented with ruptured HCC to our hospital from January 2008 to December 2011 were retrospectively studied. These patients received TACE (n=19),surgical resection (n=7),and surgical resection after TACE (n=8).ResultsShock in the 19 patients who received TACE was promptly corrected and the vital signs were stabilized.On subsequent CT,the tumors shrunk in size.Salvage liver resection was carried out in 8 patients 1 month after TACE.After treatment,AFP decreased or became normalized,thus the treatment results were good. A one-stage liver resection was carried out in 7 patients. One patient died after operation and peritoneal metastases occurred in 4 patients. Conclusions TACE stopped bleeding from ruptured HCC efficaciously,reduced the need for open exploration,and improved the rate of resection of HCC.TACE combined with surgical resection significantly lowered the rate of abdominal tumor metastases.
4.Studies on the antimutagenic and antitumour effects of phycobiliproteins from Gracilaria lemaneiformis
Yongyu ZHANG ; Meizhen CHEN ; Jie YU ; Yuanxi LIN
Chinese Journal of Marine Drugs 1994;0(03):-
The inhibitory effect of the crude phycoerythrin(PE) on the frequency of PCE micronucleus induced by CP and its antitumor effect on mice bearing S 180 sarcoma were studied. The result showed that the PE could decrease significantly the frequency of PCE micronucleus with a fair dose-effect relationship, and showed obvious antitumor effect on S 180 bearing mice with an inhibitory rate 44%.

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