A simple and efficient method for predicting protein-protein interaction sites

Higa, R. H.; Tozzi, Clésio Luis

doi:10.4238/vol7-3x-meeting07

Cited by 5 publications

(1 citation statement)

References 44 publications

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“…The radius of the sphere is typically chosen to be between 8 and 14 Å. Contact number has been used in enhancing protein fold recognition [20] and predicting protein-protein interaction sites [21]. Also, Martin reconstructed protein structure from contact number information using the tabu search [22].…”

Section: Introductionmentioning

confidence: 99%

QSE: A new 3‐D solvent exposure measure for the analysis of protein structure

Pok

Jung

et al. 2011

Proteomics

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Solvent exposure of amino acids measures how deep residues are buried in tertiary structure of proteins, and hence it provides important information for analyzing and predicting protein structure and functions. Existing methods of calculating solvent exposure such as accessible surface area, relative accessible surface area, residue depth, contact number, and half-sphere exposure still have some limitations. In this article, we propose a novel solvent exposure measure named quadrant-sphere exposure (QSE) based on eight quadrants derived from spherical neighborhood. The proposed measure forms a microenvironment around Cα atom as a sphere with a radius of 13 Å, and subdivides it into eight quadrants according to a rectangular coordinate system constructed based on geometric relationships of backbone atoms. The number of neighboring Cα atoms whose labels are the same is given as the QSE value of the center Cα atom at hand. As evidenced by histograms that show very different distributions for different structure configurations, the proposed measure captures local properties that are characteristic for a residue's eight-directional neighborhood within a sphere. Compared with other measures, QSE provides a different view of solvent exposure, and provides information that is specific for different tertiary structure. As the experimental results show, QSE measure can potentially be used in protein structure analysis and predictions.

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Section: Introductionmentioning

confidence: 99%

QSE: A new 3‐D solvent exposure measure for the analysis of protein structure

Pok

Jung

et al. 2011

Proteomics

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Prediction of protein–protein interaction sites using patch-based residue characterization

Qiu

Wang

2012

Journal of Theoretical Biology

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Progress and challenges in predicting protein interfaces

Esmaielbeiki¹,

Krawczyk²,

Knapp³

et al. 2015

Brief Bioinform

128

122

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The majority of biological processes are mediated via protein–protein interactions. Determination of residues participating in such interactions improves our understanding of molecular mechanisms and facilitates the development of therapeutics. Experimental approaches to identifying interacting residues, such as mutagenesis, are costly and time-consuming and thus, computational methods for this purpose could streamline conventional pipelines. Here we review the field of computational protein interface prediction. We make a distinction between methods which address proteins in general and those targeted at antibodies, owing to the radically different binding mechanism of antibodies. We organize the multitude of currently available methods hierarchically based on required input and prediction principles to provide an overview of the field.

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A simple and efficient method for predicting protein-protein interaction sites

Cited by 5 publications

References 44 publications

QSE: A new 3‐D solvent exposure measure for the analysis of protein structure

QSE: A new 3‐D solvent exposure measure for the analysis of protein structure

Prediction of protein–protein interaction sites using patch-based residue characterization

Progress and challenges in predicting protein interfaces

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