Xuemei Pu

Learn More
In this study, we focus on different types of Gram-negative bacterial secreted proteins, and try to analyze the relationships and differences among them. Through an extensive literature search, 1612 secreted proteins have been collected as a standard data set from three data sources, including Swiss-Prot, TrEMBL and RefSeq. To explore the relationships(More)
BACKGROUND Protein-protein interactions (PPIs) are crucial for almost all cellular processes, including metabolic cycles, DNA transcription and replication, and signaling cascades. Given the importance of PPIs, several methods have been developed to detect them. Since the experimental methods are time-consuming and expensive, developing computational(More)
Signal peptides play a crucial role in various biological processes, such as localization of cell surface receptors, translocation of secreted proteins and cell-cell communication. However, the amino acid mutation in signal peptides, also called non-synonymous single nucleotide polymorphisms (nsSNPs or SAPs) may lead to the loss of their functions. In the(More)
The assessment of binding affinity between ligands and the target proteins plays an essential role in drug discovery and design process. As an alternative to widely used scoring approaches, machine learning methods have also been proposed for fast prediction of the binding affinity with promising results, but most of them were developed as all-purpose(More)
BACKGROUND Type III secretion systems (T3SSs) are central to the pathogenesis and specifically deliver their secreted substrates (type III secreted proteins, T3SPs) into host cells. Since T3SPs play a crucial role in pathogen-host interactions, identifying them is crucial to our understanding of the pathogenic mechanisms of T3SSs. This study reports a novel(More)
Flavin mono-nucleotide (FMN) closely evolves in many biological processes. In this study, a computational method was proposed to identify FMN binding sites based on amino acid sequences of proteins only. A modified Position Specific Score Matrix was used to characterize the local environmental sequence information, and a visible improvement of performance(More)
In the work, we mainly used molecular dynamics (MD) simulation and protein structure network (PSN) to study subtilisin Carlsberg (SC) immobilized onto carbon nanotube (CNT) in water, acetonitrile and heptane solvents, in order to explore activation mechanism of enzymes in non-aqueous media. The result indicates that the affinity of SC with CNT follows the(More)
A combination of the advanced chemometrics method with quantum mechanics calculation was for the first time applied to explore a facile yet efficient analysis strategy to thoroughly resolve femtosecond transient absorption spectroscopy of ortho-nitroaniline (ONA), served as a model compound of important nitroaromatics and explosives. The result revealed(More)
G-protein-coupled receptors (GPCRs) are important drug targets and generally activated by ligands. However, some experiments found that GPCRs also give rise to constitutive activity through some mutations (viz., CAM), which are usually associated with different kinds of diseases. However, the mechanisms of CAMs and their roles in interactions with(More)
miRNAs (microRNAs) are a set of endogenous and small non-coding RNAs which specifically induce degradation of target mRNAs or inhibit protein translation to control gene expression. Obviously, aberrant miRNA expression in human cells will lead to a serious of changes in protein-protein interaction network (PPIN), thus to activate or inactivate some pathways(More)