Qisheng Pan

LDLR Variant Classification Through Activity-Normalized Prime Editing Screening

Yu Tian, Vojislav Gligorovski, Nicolas Mathis, Jing Zhao et autres

Abstract Background Inherited variants in the LDL receptor ( LDLR ) gene are the most common cause of familial hypercholesterolemia (FH), significantly increasing coronary artery disease risk. Early identification of pathogenic LDLR variants enables prompt intervention with lipid-lowering therapies; however, the majority …

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CharacTERT: A Machine Learning Tool for Classifying hTERT Missense Variants

Georgina Becerra Parra, Qisheng Pan, Yoochan Myung, Stephanie Portelli et autres

Abstract Missense mutations in TERT , the gene encoding the human telomerase catalytic subunit hTERT, are associated with Telomere Biology Disorders (TBDs). Experimentally elucidating the effects of all possible missense variants would be time-consuming and technically challenging. Moreover, current computational predictors are …

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Systematic evaluation of computational tools to predict the effects of mutations on protein-ligand binding affinity in the absence of experimental structures

Qisheng Pan, Stephanie Portelli, Thanh Binh Nguyen, David B. Ascher

Drug resistance caused by mutations is a significant global health concern. One way to better understand this phenomenon is by studying changes in protein-ligand binding affinity upon mutation. While recent advances in protein modelling, such as AlphaFold2 and AlphaFold3, have transformed structural …

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Harnessing AlphaFold and explainable AI to better characterise human missense variants and diseases

Qisheng Pan

AlzDiscovery : A computational tool to identify Alzheimer's disease‐causing missense mutations using protein structure information

Qisheng Pan, Georgina Becerra Parra, Yoochan Myung, Stephanie Portelli et autres

Alzheimer's disease (AD) is one of the most common forms of dementia and neurodegenerative diseases, characterized by the formation of neuritic plaques and neurofibrillary tangles. Many different proteins participate in this complicated pathogenic mechanism, and missense mutations can alter the folding and …

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Characterization on the oncogenic effect of the missense mutations of p53 via machine learning

Qisheng Pan, Stephanie Portelli, Thanh Nguyen, David B. Ascher

Dysfunctions caused by missense mutations in the tumour suppressor p53 have been extensively shown to be a leading driver of many cancers. Unfortunately, it is time-consuming and labour-intensive to experimentally elucidate the effects of all possible missense variants. Recent works presented a …

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Characterizing and predicting ccRCC-causing missense mutations in Von Hippel-Lindau disease

Adam Serghini, Stephanie Portelli, Guillaume Troadec, Catherine Song et autres

BACKGROUND: Mutations within the Von Hippel-Lindau (VHL) tumor suppressor gene are known to cause VHL disease, which is characterized by the formation of cysts and tumors in multiple organs of the body, particularly clear cell renal cell carcinoma (ccRCC). A major challenge …

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Identifying the Molecular Drivers of Pathogenic Aldehyde Dehydrogenase Missense Mutations in Cancer and Non-Cancer Diseases

Dana Jessen-Howard, Qisheng Pan, David B. Ascher

Human aldehyde dehydrogenases (ALDHs) comprising 19 isoenzymes play a vital role on both endogenous and exogenous aldehyde metabolism. This NAD(P)-dependent catalytic process relies on the intact structural and functional activity of the cofactor binding, substrate interaction, and the oligomerization of ALDHs. Disruptions …

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DDMut: predicting effects of mutations on protein stability using deep learning

Yunzhuo Zhou, Qisheng Pan, Douglas E. V. Pires, Carlos H. M. Rodrigues et autres

Understanding the effects of mutations on protein stability is crucial for variant interpretation and prioritisation, protein engineering, and biotechnology. Despite significant efforts, community assessments of predictive tools have highlighted ongoing limitations, including computational time, low predictive power, and biased predictions towards destabilising …

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A bias of Asparagine to Lysine mutations in SARS-CoV-2 outside the receptor binding domain affects protein flexibility

Jennifer C. Boer, Qisheng Pan, Jessica K. Holien, Thanh Nguyen et autres

Introduction: COVID-19 pandemic has been threatening public health and economic development worldwide for over two years. Compared with the original SARS-CoV-2 strain reported in 2019, the Omicron variant (B.1.1.529.1) is more transmissible. This variant has 34 mutations in its Spike protein, 15 …

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Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures

Qisheng Pan, Thanh Nguyen, David B. Ascher, Douglas E. V. Pires

Changes in protein sequence can have dramatic effects on how proteins fold, their stability and dynamics. Over the last 20 years, pioneering methods have been developed to try to estimate the effects of missense mutations on protein stability, leveraging growing availability of …

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