ArticleProtein science : a publication of the Protein Society2009
Analysis of loop boundaries using different local structure assignment methods.
Article in Protein science : a publication of the Protein Society, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Transition Dipole Strength as a Quantitative Tool for Protein Secondary Structure Analysis.The journal of physical chemistry. B · 2025Article
- Structural Space of the Duffy Antigen/Receptor for Chemokines' Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations.International journal of molecular sciences · 2023Article
- A Perspective on the (Rise and Fall of) Protein β-Turns.International journal of molecular sciences · 2022Review
- Insights into Comparative Modeling of VInternational journal of molecular sciences · 2021Article
- A look back at the molten globule state of proteins: thermodynamic aspects.Biophysical reviews · 2019Review
- Extension of the classical classification of β-turns.Scientific reports · 2016Article
- CSI 2.0: a significantly improved version of the Chemical Shift Index.Journal of biomolecular NMR · 2014Article
- From local structure to a global framework: recognition of protein folds.Journal of the Royal Society, Interface · 2014Review
- PolyprOnline: polyproline helix II and secondary structure assignment database.Database : the journal of biological databases and curation · 2014Article
- β-Bulges: extensive structural analyses of β-sheets irregularities.Protein science : a publication of the Protein Society · 2013Article
- Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program.Journal of chemical theory and computation · 2013Article
- Assignment of PolyProline II conformation and analysis of sequence--structure relationship.PloS one · 2011Article
- A short survey on protein blocks.Biophysical reviews · 2010Article
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4 authors.
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Abstract
Loops connect regular secondary structures. In many instances, they are known to play important biological roles. Analysis and prediction of loop conformations depend directly on the definition of repetitive structures. Nonetheless, the secondary structure assignment methods (SSAMs) often lead to divergent assignments. In this study, we analyzed, both structure and sequence point of views, how the divergence between different SSAMs affect boundary definitions of loops connecting regular secondary structures. The analysis of SSAMs underlines that no clear consensus between the different SSAMs can be easily found. Because these latter greatly influence the loop boundary definitions, important variations are indeed observed, that is, capping positions are shifted between different SSAMs. On the other hand, our results show that the sequence information in these capping regions are more stable than expected, and, classical and equivalent sequence patterns were found for most of the SSAMs. This is, to our knowledge, the most exhaustive survey in this field as (i) various databank have been used leading to similar results without implication of protein redundancy and (ii) the first time various SSAMs have been used. This work hence gives new insights into the difficult question of assignment of repetitive structures and addresses the issue of loop boundaries definition. Although SSAMs give very different local structure assignments capping sequence patterns remain efficiently stable.
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