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Protein Peeling 2: a web server to convert protein structures into series of protein units

Autor: S. Hazout, A.G. de Brevern, Jean-Christophe Gelly, Catherine Etchebest

Publikováno v: Nucleic Acids Research
Nucleic Acids Research, Oxford University Press, 2006, 34 (Web Server issue), pp.W75-8. ⟨10.1093/nar/gkl292⟩
Nucleic Acids Research, 2006, 34 (Web Server issue), pp.W75-8. ⟨10.1093/nar/gkl292⟩

Protein Peeling 2 (PP2) is a web server for the automatic identification of protein units (PUs) given the 3D coordinates of a protein. PUs are an intermediate level of protein structure description between protein domains and secondary structures. It

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2f4ccb7e2f0780d2e1391cf557f6aaf7
https://doi.org/10.1093/nar/gkl292

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Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms

Autor: Pierre Vincens, Gaëlle Lelandais, Claude Jacq, S. Hazout, Stéphane Vialette, Anne Badel-Chagnon

Publikováno v: Bioinformatics
Bioinformatics, Oxford University Press (OUP), 2006, 22, pp.1359-1366

Motivation: Molecular evolution, which is classically assessed by comparison of individual proteins or genes between species, can now be studied by comparing co-expressed functional groups of genes. This approach, which better reflects the functional

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4b9959432cf344fb94e45fc1e9c43c55
https://doi.org/10.1093/bioinformatics/btl087

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Predicting the disulfide bonding state of cysteines using protein descriptors

Autor: S. Hazout, Pierre Tufféry, M.H. Mucchielli-Giorgi

Publikováno v: Proteins: Structure, Function, and Bioinformatics. 46:243-249

Knowledge of the disulfide bonding state of the cysteines of proteins is of major interest in designing numerous molecular biology experiments, or in predicting their three-dimensional structure. Previous methods using the information gained from ali

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::e1d8206a610c936a00c48198ac3c55db
https://doi.org/10.1002/prot.10047

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Compacting local protein folds with a 'hybrid protein model'

Autor: S. Hazout, A.G. de Brevern

Publikováno v: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 106:36-47

The “hybrid protein model” is a fuzzy model for compacting local protein structures. It learns a nonredundant database encoded in a previously defined structural alphabet composed of 16 protein blocks (PBs). The hybrid protein is composed of a se

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::76b274b5800c18bb0d6d7e1685c6932b
https://doi.org/10.1007/s002140000227

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Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks

Autor: A.G. de Brevern, S. Hazout, Catherine Etchebest

Publikováno v: Proteins: Structure, Function, and Genetics. 41:271-287

By using an unsupervised cluster analyzer, we have identified a local structural alpha- bet composed of 16 folding patterns of five consecu- tive C a ("protein blocks"). The dependence that exists between successive blocks is explicitly taken into ac

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::b4024397a4ce5a9cb9aa06cc24af336b
https://doi.org/10.1002/1097-0134(20001115)41:3<271::aid-prot10>3.0.co

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Hidden Markov model approach for identifying the modular framework of the protein backbone

Autor: J. F. Boisvieux, S. Hazout, J.P. Chevrolat, Pierre Tufféry, Anne-Claude Camproux

Publikováno v: Protein Engineering, Design and Selection. 12:1063-1073

3 To whom correspondence should be addressed The hidden Markov model (HMM) was used to identify recurrent short 3D structural building blocks (SBBs) describing protein backbones, independently of any a priori knowledge. Polypeptide chains are decompo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::047d61282f822ede7939a50b67215e2b
https://doi.org/10.1093/protein/12.12.1063

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Analyzing patterns between regular secondary structures using short structural building blocks defined by a hidden Markov model

Autor: C. André, S. Hazout, J. F. Boisvieux, Pierre Tufféry, L. Buffat, Anne-Claude Camproux

Publikováno v: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 101:33-40

Hidden Markov models were used to identify recurrent short 3D structural building blocks (SSBBs) describing protein backbones. Polypeptide chains were broken down into successive short segments defined by their inter-alpha-carbon distances. Fitting t

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::7e6a197d627f80c13ca93019b1584409
https://doi.org/10.1007/s002140050402

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Prediction of solvent accessibility of amino acid residues: critical aspects

Autor: Pierre Tufféry, S. Hazout, Marie-Hélène Mucchielli-Giorgi

Publikováno v: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 101:186-193

For predicting solvent accessibility from the sequence of amino acids in proteins, we use a logistic function trained on a non-redundant protein database. Using a principal component analysis, we find that the prediction can be considered, in a good

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::1c1bbb1faffb787365e1582994d8c2e9
https://doi.org/10.1007/s002140050428

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