Local Protein Structures

Offmann, Bernard; Tyagi, Manoj; Brevern, Akexandre G. de

doi:10.2174/157489307781662105

Cited by 81 publications

(92 citation statements)

References 405 publications

(515 reference statements)

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“…The distance criteria will be noted with the value of in superscript to facilitate the reading, e.g. for the C distance, a value of threshold equal to 8 Å will be noted C 8 . The threshold varies, in this study, between 4 and 20 Å.…”

Section: Datasetmentioning

confidence: 99%

“…To assess the relevance of this observation, we have computed the difference between rf for C 8 and rf for C 20 , and evaluated if the differences are correlated with the initial values of rf of C 8 . It is also possible to simply compute the correlation between rf for C 8 and rf for C 20 . Nonetheless, the first approach allows looking at the contacts that are specifically found at distance more than 8 Å.…”

Section: Various Thresholds ( For Various Distance Types Precedent Amentioning

confidence: 99%

“…helix and sheet, which compose only a part of protein backbones. The absence of assignment for an important proportion of residues has led to the emergence of new approaches based on local protein structure libraries called structural alphabets able to approximate all local protein structures [8][9][10][11][12][13][14]. This kind of approach has proven its relevance by enabling local structure prediction [13,15], structural alignments [16][17][18] and the discovery of functional local structural motifs [19].…”

Section: Introductionmentioning

confidence: 99%

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Protein contacts, inter-residue interactions and side-chain modelling

Faure¹,

Bornot²,

Brevern³

2008

Biochimie

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To cite this version:Guilhem Faure, Aurélie Bornot, Alexandre De Brevern. Protein contacts, inter-residue interactions and side-chain modelling.: protein contacts. Biochimie, Elsevier, 2008, 90 (4) AbstractThree-dimensional structures of proteins are the support of their biological functions.Their folds are stabilized by contacts between residues. Inner protein contacts are generally described through direct atomic contacts, i.e. interactions between side-chain atoms, while contact prediction methods mainly used inter-C distances. In this paper, we have analyzed the protein contacts on a recent high quality non-redundant databank using different criteria.First, we have studied the average number of contacts depending on the distance threshold to define a contact. Preferential contacts between types of amino acids have been highlighted.Detailed analyses have been done concerning the proximity of contacts in the sequence, the size of the proteins and fold classes. The strongest differences have been extracted, highlighting important residues.Then, we studied the influence of five different side-chain conformation prediction methods (SCWRL, IRECS, SCAP, SCATD and SSCOMP) on the distribution of contacts.The prediction rates of these different methods are quite similar. However, using a distance criterion between side-chains, the results are quite different, e.g. SCAP predicts 50% more contacts than observed, unlike other methods that predict fewer contacts than observed.Contacts deduced are quite distinct from one method to another with at most 75% contacts in common. Moreover, distributions of amino acid preferential contacts present unexpected behaviors distinct from previously observed in the X-ray structures, especially at the surface of proteins. For instance, the interactions involving Tryptophan greatly decrease.

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Section: Datasetmentioning

confidence: 99%

Section: Various Thresholds ( For Various Distance Types Precedent Amentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Protein contacts, inter-residue interactions and side-chain modelling

Faure¹,

Bornot²,

Brevern³

2008

Biochimie

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“…These methods are based on libraries of local backbone structures that represent the frequently occurring regular backbone conformations. With the premise that the secondary structure description in terms of α-helix and β-strands covers only about 50% of all local conformations, several studies attempted to characterize most or all of the backbone structure [22,23]. A library of local backbone conformations that can be used to abstract a complete protein backbone is called as a Structural Alphabet (SA).…”

Section: Introductionmentioning

confidence: 99%

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies

2012

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Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a 1D sequence string.A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition.Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods.3

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“…The complete set of local structure prototypes defines a structural alphabet Offmann et al, 2007). The number of prototypes in a library is important for characterizing the local fold (Hunter and Subramaniam, 2003;Martin et al, 2008;Sander et al, 2006;Tung et al, 2007;Unger et al, 1989).…”

Section: Introductionmentioning

confidence: 99%

Species specific amino acid sequence–protein local structure relationships: An analysis in the light of a structural alphabet

Brevern

Joseph

2011

Journal of Theoretical Biology

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To cite this version:Alexandre De Brevern, Agnel Praveen Joseph. Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet.: species sequence -structure relationship. Journal of Theoretical Biology, Elsevier, 2011, 276 (1) AbstractProtein structure analysis and prediction methods are based on non-redundant data extracted from the available protein structures, regardless of the species from which the protein originates. Hence, these datasets represent the global knowledge on protein folds, which constitutes a generic distribution of amino acid sequence -protein structure (AAS-PS) relationships. In this study, we try to elucidate whether the AAS-PS relationship could possess specificities depending on the specie.For this purpose, we have chosen three different species: Saccharomyces cerevisiae, Plasmodium falciparum and Arabidopsis thaliana. We analyzed the AAS-PS behaviors of the proteins from these three species and compared it to the "expected" distribution of a classical non-redundant databank. With the classical secondary structure description, only slight differences in amino acid preferences could be observed. With a more precise description of local protein structures (Protein Blocks), significant changes could be highlighted.Saccharomyces cerevisiae's AAS-PS relationship is close to the general distribution, while striking differences are observed in the case of Arabidopsis thaliana. Plasmodium falciparum is the most distant one.This study presents some interesting view-points on AAS-PS relationship. Certain species exhibit unique preferences for amino acids to be associated with protein local structural elements. Thus, AAS-PS relationships are species dependant. These results can give useful insights for improving prediction methodologies which take the species specific information into account.

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Local Protein Structures

Cited by 81 publications

References 405 publications

Protein contacts, inter-residue interactions and side-chain modelling

Protein contacts, inter-residue interactions and side-chain modelling

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies

Species specific amino acid sequence–protein local structure relationships: An analysis in the light of a structural alphabet

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