High-throughput identification of interacting protein-protein binding sites

Background  

With the advent of increasing sequence and structural data, a number of methods have been proposed to locate putative protein binding sites from protein surfaces. Therefore, methods that are able to identify whether these binding sites interact are needed.     

Variation in structural location and amino acid conservation of functional sites in protein domain families

Background  

The functional sites of a protein present important information for determining its cellular function and are fundamental in drug design. Accordingly, accurate methods for the prediction of functional sites are of immense value. Most available methods are based on a set of homologous sequences and structural or evolutionary information, and assume that functional sites are more conserved than the average. In the analysis presented here, we have investigated the conservation of location and type of amino acids at functional sites, and compared the behaviour of functional sites between different protein domains.     

Estimating the evidence of selection and the reliability of inference in unigenic evolution

Background  

Unigenic evolution is a large-scale mutagenesis experiment used to identify residues that are potentially important for protein function. Both currently-used methods for the analysis of unigenic evolution data analyze 'windows' of contiguous sites, a strategy that increases statistical power but incorrectly assumes that functionally-critical sites are contiguous. In addition, both methods require the questionable assumption of asymptotically-large sample size due to the presumption of approximate normality.     

A high-throughput pipeline for the design of real-time PCR signatures

Background  

Pathogen diagnostic assays based on polymerase chain reaction (PCR) technology provide high sensitivity and specificity. However, the design of these diagnostic assays is computationally intensive, requiring high-throughput methods to identify unique PCR signatures in the presence of an ever increasing availability of sequenced genomes.     

ResBoost: characterizing and predicting catalytic residues in enzymes

Background  

Identifying the catalytic residues in enzymes can aid in understanding the molecular basis of an enzyme's function and has significant implications for designing new drugs, identifying genetic disorders, and engineering proteins with novel functions. Since experimentally determining catalytic sites is expensive, better computational methods for identifying catalytic residues are needed.     

MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes

Background  

Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. The ability to identify them in a genome-wide manner depends on the availability of accurate models and of search methods able to detect putative regulatory elements with enhanced sensitivity and specificity.     

SeqAnt: A web service to rapidly identify and annotate DNA sequence variations

Background  

The enormous throughput and low cost of second-generation sequencing platforms now allow research and clinical geneticists to routinely perform single experiments that identify tens of thousands to millions of variant sites. Existing methods to annotate variant sites using information from publicly available databases via web browsers are too slow to be useful for the large sequencing datasets being routinely generated by geneticists. Because sequence annotation of variant sites is required before functional characterization can proceed, the lack of a high-throughput pipeline to efficiently annotate variant sites can act as a significant bottleneck in genetics research.     

Relating destabilizing regions to known functional sites in proteins

Background  

Most methods for predicting functional sites in protein 3D structures, rely on information on related proteins and cannot be applied to proteins with no known relatives. Another limitation of these methods is the lack of a well annotated set of functional sites to use as benchmark for validating their predictions. Experimental findings and theoretical considerations suggest that residues involved in function often contribute unfavorably to the native state stability. We examine the possibility of systematically exploiting this intrinsic property to identify functional sites using an original procedure that detects destabilizing regions in protein structures. In addition, to relate destabilizing regions to known functional sites, a novel benchmark consisting of a diverse set of hand-curated protein functional sites is derived.     

Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes

Background  

Computational prediction methods are currently used to identify genes in prokaryote genomes. However, identification of the correct translation initiation sites remains a difficult task. Accurate translation initiation sites (TISs) are important not only for the annotation of unknown proteins but also for the prediction of operons, promoters, and small non-coding RNA genes, as this typically makes use of the intergenic distance. A further problem is that most existing methods are optimized for Escherichia coli data sets; applying these methods to newly sequenced bacterial genomes may not result in an equivalent level of accuracy.     

A protein domain interaction interface database: InterPare

Background  

Most proteins function by interacting with other molecules. Their interaction interfaces are highly conserved throughout evolution to avoid undesirable interactions that lead to fatal disorders in cells. Rational drug discovery includes computational methods to identify the interaction sites of lead compounds to the target molecules. Identifying and classifying protein interaction interfaces on a large scale can help researchers discover drug targets more efficiently.     

Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins

Background  

While occurring enzymatically in biological systems, O-linked glycosylation affects protein folding, localization and trafficking, protein solubility, antigenicity, biological activity, as well as cell-cell interactions on membrane proteins. Catalytic enzymes involve glycotransferases, sugar-transferring enzymes and glycosidases which trim specific monosaccharides from precursors to form intermediate structures. Due to the difficulty of experimental identification, several works have used computational methods to identify glycosylation sites.     

An Alternative Approach for Estimating the Accuracy of Colposcopy in Detecting Cervical Precancer

Introduction

Since colposcopy helps to detect cervical cancer in its precancerous stages, as new strategies and technologies are developed for the clinical management of cervical neoplasia, precisely determining the accuracy of colposcopy is important for characterizing its continued role. Our objective was to employ a more precise methodology to estimate of the accuracy of colposcopy to better reflect clinical practice.

Study design

For each patient, we compared the worst histology result among colposcopically positive sites to the worst histology result among all sites biopsied, thereby more accurately determining the number of patients that would have been underdiagnosed by colposcopy than previously estimated.

Materials and Methods

We utilized data from a clinical trial in which 850 diagnostic patients had been enrolled. Seven hundred and ninety-eight of the 850 patients had been examined by colposcopy, and biopsy samples were taken at colposcopically normal and abnormal sites. Our endpoints of interest were the percentages of patients underdiagnosed, and sensitivity and specificity of colposcopy.

Results

With the threshold of low-grade squamous intraepithelial lesions for positive colposcopy and histology diagnoses, the sensitivity of colposcopy decreased from our previous assessment of 87.0% to 74.0%, while specificity remained the same. The drop in sensitivity was the result of histologically positive sites that were diagnosed as negative by colposcopy. Thus, 28.4% of the 798 patients in this diagnostic group would have had their condition underdiagnosed by colposcopy in the clinic.

Conclusions

In utilizing biopsies at multiple sites of the cervix, we present a more precise methodology for determining the accuracy of colposcopy. The true accuracy of colposcopy is lower than previously estimated. Nevertheless, our results reinforce previous conclusions that colposcopy has an important role in the diagnosis of cervical precancer.     

Sequence based residue depth prediction using evolutionary information and predicted secondary structure

Background  

Residue depth allows determining how deeply a given residue is buried, in contrast to the solvent accessibility that differentiates between buried and solvent-exposed residues. When compared with the solvent accessibility, the depth allows studying deep-level structures and functional sites, and formation of the protein folding nucleus. Accurate prediction of residue depth would provide valuable information for fold recognition, prediction of functional sites, and protein design.