SCOWLP classification: Structural comparison and analysis of protein binding regions

Teyra, Joan; Paszkowski‐Rogacz, Maciej; Anders, Gerd; Pisabarro, M. Teresa

doi:10.1186/1471-2105-9-9

Cited by 56 publications

(67 citation statements)

References 16 publications

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“…Modeling of 3D structure templates was performed with the SWISS-MODEL Workspace (http://swissmodel.expasy.org) and ElliPro (http://tools.immuneepitope.org/tools) [51, 52]. Templates were acquired for M. bovis proteins by modeling their sequences in the FASTA format.…”

Section: Methodsmentioning

confidence: 99%

Immunoproteomic identification of MbovP579, a promising diagnostic biomarker for serological detection of Mycoplasma bovis infection

et al. 2016

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A lack of knowledge regarding the antigenic properties of Mycoplasma bovis proteins prevents the effective control of bovine infections using immunological approaches. In this study, we detected and characterized a specific and sensitive M. bovis diagnostic biomarker. After M. bovis total proteins and membrane fractions were separated with two dimensional gel electrophoresis, proteins reacting with antiserawere detected using MALDI-TOF MS. Thirty-nine proteins were identified, 32 of which were previously unreported. Among them, immunoinformatics predicted eight antigens, encoded by Mbov_0106, 0116, 0126, 0212, 0275, 0579, 0739, and 0789, to have high immunological value. These genes were expressed in E. coli after mutagenesis of UGA to UGG using overlap extension PCR. A lipoprotein, MbovP579, encoded by a functionally unknown gene, was a sensitive and specific antigen for detection of antibodies in sera from both M. bovis-infected and vaccinated cattle. The specificity of MbovP579 was confirmed by its lack of cross-reactivity with other mycoplasmas, including Mycoplasma agalactiae. An iELISA based on rMbovP579 detected seroconversion 7 days post-infection (dpi). The ELISA had sensitivity of 90.2% (95% CI: 83.7%, 94.3%) and a specificity of 97.8% (95% CI: 88.7%, 99.6%) with clinical samples. Additional comparative studies showed that both diagnostic and analytic sensitivities of the ELISA were higher than those of a commercially available kit (p<0.01). We have thus detected and characterized the novel antigen, MbovP579, and established an rMbovP579-based ELISA as a highly sensitive and specific method for the early diagnosis of M. bovis infection.

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Section: Methodsmentioning

confidence: 99%

Immunoproteomic identification of MbovP579, a promising diagnostic biomarker for serological detection of Mycoplasma bovis infection

et al. 2016

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“…Binding sites were mapped onto the surfaces of each hub template structure by means of a multiple alignment, and clustered into mutually exclusive interfaces using an agglomerative hierarchical algorithm [30], following several steps:…”

Section: Mapping Of Binding Sitesmentioning

confidence: 99%

Energetic determinants of protein binding specificity: Insights into protein interaction networks

2009

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One of the challenges of the postgenomic era is to provide a more realistic representation of cellular processes by combining a systems biology description of functional networks with information on their interacting components. Here we carried out a systematic large-scale computational study on a structural protein-protein interaction network dataset in order to dissect thermodynamic characteristics of binding determining the interplay between protein affinity and specificity. As expected, interactions involving specific binding sites display higher affinities than those of promiscuous binding sites. Next, in order to investigate a possible role of modular distribution of hot spots in binding specificity, we divided binding sites into modules previously shown to be energetically independent. In general, hot spots that interact with different partners are located in different modules. We further observed that common hot spots tend to interact with partners exhibiting common binding motifs, whereas different hot spots tend to interact with partners with different motifs. Thus, energetic properties of binding sites provide insights into the way proteins modulate interactions with different partners. Knowledge of those factors playing a role in protein specificity is important for understanding how proteins acquire additional partners during evolution. It should also be useful in drug design.

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“…With that corpus, we could identify informative key phrases for classification and exploit them through hot-spot techniques [10,11,21]. For some categories, we could also train sequence labeling models that automatically annotate evidence phrases [28]. …”

Section: Discussionmentioning

confidence: 99%

Risk factor detection for heart disease by applying text analytics in electronic medical records

Torii

Fan

Yang

et al. 2015

Journal of Biomedical Informatics

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In the United States, about 600,000 people die of heart disease every year. The annual cost of care services, medications, and lost productivity reportedly exceeds 108.9 billion dollars. Effective disease risk assessment is critical to prevention, care, and treatment planning. Recent advancements in text analytics have opened up new possibilities of using the rich information in electronic medical records (EMRs) to identify relevant risk factors. The 2014 i2b2/UTHealth Challenge brought together researchers and practitioners of clinical natural language processing (NLP) to tackle the identification of heart disease risk factors reported in EMRs. We participated in this track and developed an NLP system by leveraging existing tools and resources, both public and proprietary. Our system was a hybrid of several machine-learning and rule-based components. The system achieved an overall F1 score of 0.9185, with a recall of 0.9409 and a precision of 0.8972.

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SCOWLP classification: Structural comparison and analysis of protein binding regions

Cited by 56 publications

References 16 publications

Immunoproteomic identification of MbovP579, a promising diagnostic biomarker for serological detection of Mycoplasma bovis infection

Immunoproteomic identification of MbovP579, a promising diagnostic biomarker for serological detection of Mycoplasma bovis infection

Energetic determinants of protein binding specificity: Insights into protein interaction networks

Risk factor detection for heart disease by applying text analytics in electronic medical records

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