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Article
Open AccessPhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection
Protein phosphorylation is a major form of post-translational modification (PTM) that regulates diverse cellular processes. In silico methods for phosphorylation site prediction can provide a useful and complemen...
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Article
Open AccessKnowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites
Matrix Metalloproteases (MMPs) are an important family of proteases that play crucial roles in key cellular and disease processes. Therefore, MMPs constitute important targets for drug design, development and ...
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Article
Structure-based engineering of a pectate lyase with improved specific activity for ramie degumming
Biotechnological applications of microbial pectate lyases (Pels) in plant fiber processing are promising, eco-friendly substitutes for conventional chemical degumming processes. However, to potentiate the enzy...
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Article
Open AccessHIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency
Measuring the altered gene expression level and identifying differentially expressed genes/proteins during HIV infection, replication and latency is fundamental for broadening our understanding of the mechanis...
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Article
Open AccessStaged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences
The broad heterogeneity of antigen-antibody interactions brings tremendous challenges to the design of a widely applicable learning algorithm to identify conformational B-cell epitopes. Besides the intrinsic h...
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Article
Open AccessSecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems
Bacteria translocate effector molecules to host cells through highly evolved secretion systems. By definition, the function of these effector proteins is to manipulate host cell biology and the sequence, struc...
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Inference Method for Develo** Mathematical Models of Cell Signaling Pathways Using Proteomic Datasets
The progress in proteomics technologies has led to a rapid accumulation of large-scale proteomic datasets in recent years, which provides an unprecedented opportunity and valuable resources to understand how l...
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Article
A highly Conserved Aspartic Acid Residue of the Chitosanase from Bacillus Sp. TS Is Involved in the Substrate Binding
The chitosanase from Bacillus sp. TS (CsnTS) is an enzyme belonging to the glycoside hydrolase family 8. The sequence of CsnTS shares 98 % identity with the chitosanase from Bacillus sp. K17. Crystallography anal...
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Article
Open AccessGlycoMinestruct: a new bioinformatics tool for highly accurate map** of the human N-linked and O-linked glycoproteomes by incorporating structural features
Glycosylation plays an important role in cell-cell adhesion, ligand-binding and subcellular recognition. Current approaches for predicting protein glycosylation are primarily based on sequence-derived features...
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Article
SPAR: a random forest-based predictor for self-interacting proteins with fine-grained domain information
Protein self-interaction, i.e. the interaction between two or more identical proteins expressed by one gene, plays an important role in the regulation of cellular functions. Considering the limitations of expe...
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Article
Anthelmintic closantel enhances bacterial killing of polymyxin B against multidrug-resistant Acinetobacter baumannii
Polymyxins, an old class of antibiotics, are currently used as the last resort for the treatment of multidrug-resistant (MDR) Acinetobacter baumannii. However, recent pharmacokinetic and pharmacodynamic data indi...
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Article
Open AccessDephosSite: a machine learning approach for discovering phosphotase-specific dephosphorylation sites
Protein dephosphorylation, which is an inverse process of phosphorylation, plays a crucial role in a myriad of cellular processes, including mitotic cycle, proliferation, differentiation and cell growth. Compa...
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Article
Open AccessPeriscope: quantitative prediction of soluble protein expression in the periplasm of Escherichia coli
Periplasmic expression of soluble proteins in Escherichia coli not only offers a much-simplified downstream purification process, but also enhances the probability of obtaining correctly folded and biologically a...
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Article
Open AccessGlobal metabolic analyses identify key differences in metabolite levels between polymyxin-susceptible and polymyxin-resistant Acinetobacter baumannii
Multidrug-resistant Acinetobacter baumannii presents a global medical crisis and polymyxins are used as the last-line therapy. This study aimed to identify metabolic differences between polymyxin-susceptible and ...
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Article
Open AccessCrysalis: an integrated server for computational analysis and design of protein crystallization
The failure of multi-step experimental procedures to yield diffraction-quality crystals is a major bottleneck in protein structure determination. Accordingly, several bioinformatics methods have been successfu...
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Article
Open AccessUsing contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes
Most protein complex detection methods utilize unsupervised techniques to cluster densely connected nodes in a protein-protein interaction (PPI) network, in spite of the fact that many true complexes are not d...
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Article
Open AccessThe exploration of network motifs as potential drug targets from post-translational regulatory networks
Phosphorylation and proteolysis are among the most common post-translational modifications (PTMs), and play critical roles in various biological processes. More recent discoveries imply that the crosstalks bet...
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Article
Extracellular Overexpression of Chitosanase from Bacillus sp. TS in Escherichia coli
The chitosanase gene from a Bacillus sp. strain isolated from soil in East China was cloned and expressed in Escherichia coli. The gene had 1224 nucleotides and encoded a mature protein of 407 amino acid residues...
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Article
Open AccessAccurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features
Lysine acetylation is a reversible post-translational modification, playing an important role in cytokine signaling, transcriptional regulation and apoptosis. To fully understand acetylation mechanisms, identi...
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Article
Open AccessCloning, expression and characterization of a pectate lyase from Paenibacillus sp. 0602 in recombinant Escherichia coli
Biotechnological applications of microbial pectate lyases (Pels) in plant fiber processing are considered as environmentally friendly. As such, they become promising substitutes for conventional chemical degum...
