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Article
A consensual machine-learning-assisted QSAR model for effective bioactivity prediction of xanthine oxidase inhibitors using molecular fingerprints
Xanthine oxidase inhibitors (XOIs) have been widely studied due to the promising potential as safe and effective therapeutics in hyperuricemia and gout. Currently, available XOI molecules have been developed f...
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Article
Open AccessUltra-fast triplet-triplet-annihilation-mediated high-lying reverse intersystem crossing triggered by participation of nπ*-featured excited states
The harvesting of ‘hot’ triplet excitons through high-lying reverse intersystem crossing mechanism has emerged as a hot research issue in the field of organic light-emitting diodes. However, if high-lying reve...
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Article
Open AccessCoupling complementary strategy to flexible graph neural network for quick discovery of coformer in diverse co-crystal materials
Cocrystal engineering have been widely applied in pharmaceutical, chemistry and material fields. However, how to effectively choose coformer has been a challenging task on experiments. Here we develop a graph ...
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Article
Open AccessUncovering the prognostic gene signatures for the improvement of risk stratification in cancers by using deep learning algorithm coupled with wavelet transform
The aim of gene expression-based clinical modelling in tumorigenesis is not only to accurately predict the clinical endpoints, but also to reveal the genome characteristics for downstream analysis for the purp...
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Article
Individually double minimum-distance definition of protein–RNA binding residues and application to structure-based prediction
Identifying protein–RNA binding residues is essential for understanding the mechanism of protein–RNA interactions. So far, rigid distance thresholds are commonly used to define protein–RNA binding residues. Ho...
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Article
Open AccessShining Light on Molecular Mechanism for Odor-selectivity of CNT-immobilized Olfactory Receptor
Olfactory receptor (OR)-based bioelectronic nose is a new type of bio-affinity sensor applied for detecting numerous odorant molecules. In order to elucidate the effect of the adsorption of nanomaterial carrie...
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Article
Distinguishing the disease-associated SNPs based on composition frequency analysis
Single-nucleotide polymorphism (SNP) is a basical variation in genome. When SNPs occur at the binding sites of microRNA, they can influence the binding efficiency, cause a fluctuation of the mRNA in vivo, and ...
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Article
Effective prediction of bacterial type IV secreted effectors by combined features of both C-termini and N-termini
Various bacterial pathogens can deliver their secreted substrates also called as effectors through type IV secretion systems (T4SSs) into host cells and cause diseases. Since T4SS secreted effectors (T4SEs) pl...
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Article
Open AccessFunctional dissection of human targets for KSHV-encoded miRNAs using network analysis
Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi’s sarcoma, primary effusion lymphoma and multicentric Castleman’s disease, etc. In this study, we firstly systematically constr...
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Article
Open AccessExploring functions of long noncoding RNAs across multiple cancers through co-expression network
In contrast to protein-coding genes, long-noncoding RNAs (lncRNAs) are much less well understood, despite increasing evidence indicating a wide range of their biological functions, and possible roles in variou...
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Article
Open AccessMolecular mechanism of carbon nanotube to activate Subtilisin Carlsberg in polar and non-polar organic media
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 s...
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Article
Open AccessDissecting the regulation rules of cancer-related miRNAs based on network analysis
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 e...
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Article
Open AccessUnfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model
Thrombin-binding aptamer (TBA) with the sequence 5′GGTTGGTGTGGTTGG3′ could fold into G-quadruplex, which correlates with functionally important genomic regionsis. However, unfolding mechanism involved in the s...
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Article
Open AccessA Combination of Chemometrics and Quantum Mechanics Methods Applied to Analysis of Femtosecond Transient Absorption Spectrum of Ortho-Nitroaniline
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 transie...
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Article
A comparative study of family-specific protein–ligand complex affinity prediction based on random forest approach
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 me...
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Article
Open AccessProbing Immobilization Mechanism of alpha-chymotrypsin onto Carbon Nanotube in Organic Media by Molecular Dynamics Simulation
The enzyme immobilization has been adopted to enhance the activity and stability of enzymes in non-aqueous enzymatic catalysis. However, the activation and stabilization mechanism has been poorly understood on...
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Article
Understanding the effects on constitutive activation and drug binding of a D130N mutation in the β2 adrenergic receptor via molecular dynamics simulation
G-protein-coupled receptors (GPCRs) are currently one of the largest families of drug targets. The constitutive activation induced by mutation of key GPCR residues is associated closely with various diseases. ...
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Article
Effects of organic solvents and substrate binding on trypsin in acetonitrile and hexane media
In this work, we used molecular dynamic (MD) simulation to study trypsin with and without a six-amino-acid peptide bound in three different solvents (water, acetonitrile and hexane) in order to provide molecul...
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Article
Effects of water content on the tetrahedral intermediate of chymotrypsin - trifluoromethylketone in polar and non-polar media: observations from molecular dynamics simulation
The work uses MD simulation to study effects of five water contents (3 %, 10 %, 20 %, 50 %, 100 % v/v) on the tetrahedral intermediate of chymotrypsin - trifluoromethyl ketone in polar acetonitrile and non-pol...
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Article
Synthesis and photovoltaic properties of conjugated copolymers bearing planar acenaphtho[1,2-b]quinoxaline moiety with deep HOMO level
A series of alternating copolymers (PC-AQx, PT-DTAQx, PC-DTAQx, PF-DTAQx, and PBDT-DTAQx) bearing novel planar acenaphtho[1,2-b]quinoxaline (AQx) or 8,11-di(thiophen- 2-yl)acenaphtho[1,2-b]quinoxaline (DTAQx)-acc...
