[8] Predicting location of continuous epitopes in proteins from their primary structures

Pellequer, Jean‐Luc; Westhof, Éric; Regenmortel, M.H.V. Van

doi:10.1016/0076-6879(91)03010-e

Cited by 162 publications

(129 citation statements)

References 38 publications

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“…6). Since loops tend to be more flexible than other organized secondary structure elements (Jemmerson and Paterson, 1985;Pellequer et al, 1991), these results suggest that epitopes are relatively flexible.…”

Section: Epitopes Secondary Structurementioning

confidence: 86%

Computational characterization of B-cell epitopes

Rubinstein

Mayrose

Halperin

et al. 2008

Molecular Immunology

209

231

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Characterizing B-cell epitopes is a fundamental step for understanding the immunological basis of bio-recognition. To date, epitope analyses have either been based on limited structural data, or sequence data alone. In this study, our null hypothesis was that the surface of the antigen is homogeneously antigenic. To test this hypothesis, a large dataset of antibody-antigen complex structures, together with crystal structures of the native antigens, has been compiled. Computational methods were developed and applied to detect and extract physico-chemical, structural, and geometrical properties that may distinguish an epitope from the remaining antigen surface. Rigorous statistical inference was able to clearly reject the null hypothesis showing that epitopes are distinguished from the remaining antigen surface in properties such as amino acid preference, secondary structure composition, geometrical shape, and evolutionary conservation. Specifically, epitopes were found to be significantly enriched with tyrosine and tryptophan, and to show a general preference for charged and polar amino acids. Additionally, epitopes were found to show clear preference for residing on planar parts of the antigen that protrude from the surface, yet with a rugged surface shape at the atom level. The effects of complex formation on the structural properties of the antigen were also computationally characterized and it is shown that epitopes undergo compression upon antibody binding. This correlates with the finding that epitopes are enriched with unorganized secondary structure elements that render them flexible. Thus, this study extends the understanding of the underlying processes required for antibody binding, and reveals new aspects of the antibody-antigen interaction.

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Section: Epitopes Secondary Structurementioning

confidence: 86%

Computational characterization of B-cell epitopes

Rubinstein

Mayrose

Halperin

et al. 2008

Molecular Immunology

209

231

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show abstract

“…A full review of epitope prediction as was current for the time was presented by Pellequer et al 1991. Many of the propensity scales in use at the time were compared, Hopp included, against 9 extensively studied epitopes from 11 proteins.…”

Section: B-cell Epitope Predictionmentioning

confidence: 99%

Review of Immunoinformatic approaches to in-silico B-cell epitope prediction

Reitmaier

2007

Nature Precedings

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“…This type of analysis characterizes the probability of obtaining the given numbers of correct and wrong predictions by chance. According to [12], we interpreted the prediction as correct if the uniqueness value for a functional amino acid exceeded the average plus 0.7 x S.D., and/or the value for the non-functional amino acid was less than the average minus 0.7 x S.D. Here S.D.…”

Section: U$ = -(;Fi (Adjyimentioning

confidence: 99%

“…Results of the prediction were analyzed using2 statistics as described in [12]. This type of analysis characterizes the probability of obtaining the given numbers of correct and wrong predictions by chance.…”

Section: U$ = -(;Fi (Adjyimentioning

confidence: 99%

Residues responsible for distinct biological functions are characterized by different statistical features of sequential and spatial neighborhoods: A thermolysin example

1994

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An investigation of the functional topography of thermolysin was carried out using frequency analysis of its primary and tertiary structures. The statistical validity of this approach was estimated for the enzyme active site, the substrate-binding pocket, the inter-domain interface and calcium-binding sites' predictions. We showed that frequency analysis of primary structure could be employed to predict the localization of contiguous parts of the inter-domain interface. The same approach appears to be unsuitable to a search for conformation-dependent enzyme active sites and substrate-binding pockets. In contrast, frequency analysis of the spatial neighborhood is not effective for predicting the inter-domain interface as distinct from the active site, substrate-binding pocket and calcium-binding sites. These differences should be taken into account when investigating and understanding protein structure-function relationships.

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[8] Predicting location of continuous epitopes in proteins from their primary structures

Cited by 162 publications

References 38 publications

Computational characterization of B-cell epitopes

Computational characterization of B-cell epitopes

Review of Immunoinformatic approaches to in-silico B-cell epitope prediction

Residues responsible for distinct biological functions are characterized by different statistical features of sequential and spatial neighborhoods: A thermolysin example

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