ArticleNucleic acids research2014
ArchDB 2014: structural classification of loops in proteins.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
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- Revisiting Eck and Dayhoff's Building Block Model of Ferredoxin Evolution on Dayhoff's 100th Birthday.Journal of molecular evolution · 2026Article
- Automated Engineering Protein Dynamics via Loop Grafting: ImprovingACS catalysis · 2025Article
- Tracing the birth and intrinsic disorder of loops and domains in protein evolution.Biophysical reviews · 2024Review
- On Protein Loops, Prior Molecular States and Common Ancestors of Life.Journal of molecular evolution · 2024Review
- Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment.Viruses · 2024Review
- Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency.Briefings in bioinformatics · 2023Article
- Evolution of Intrinsic Disorder in Protein Loops.Life (Basel, Switzerland) · 2023Article
- SBILib: a handle for protein modeling and engineering.Bioinformatics (Oxford, England) · 2023Article
- Tracing the birth of structural domains from loops during protein evolution.Scientific reports · 2023Article
- Benchmarking the Accuracy of AlphaFold 2 in Loop Structure Prediction.Biomolecules · 2022Article
- On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction.NAR genomics and bioinformatics · 2021Article
- On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures.Bioinformatics (Oxford, England) · 2018Article
- Using feature optimization-based support vector machine method to recognize the β-hairpin motifs in enzymes.Saudi journal of biological sciences · 2017Article
- Known unknowns of cardiolipin signaling: The best is yet to come.Biochimica et biophysica acta. Molecular and cell biology of lipids · 2017Review
- Extension of the classical classification of β-turns.Scientific reports · 2016Article
- Using Local States To Drive the Sampling of Global Conformations in Proteins.Journal of chemical theory and computation · 2016Article
- Engineered Domain Swapping as an On/Off Switch for Protein Function.Chemistry & biology · 2015Article
- Cardiolipin Interactions with Proteins.Biophysical journal · 2015Article
- Conformational sampling and structure prediction of multiple interacting loops in soluble and β-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method.Bioinformatics (Oxford, England) · 2015Article
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6 authors.
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Abstract
The function of a protein is determined by its three-dimensional structure, which is formed by regular (i.e. β-strands and α-helices) and non-periodic structural units such as loops. Compared to regular structural elements, non-periodic, non-repetitive conformational units enclose a much higher degree of variability--raising difficulties in the identification of regularities, and yet represent an important part of the structure of a protein. Indeed, loops often play a pivotal role in the function of a protein and different aspects of protein folding and dynamics. Therefore, the structural classification of protein loops is an important subject with clear applications in homology modelling, protein structure prediction, protein design (e.g. enzyme design and catalytic loops) and function prediction. ArchDB, the database presented here (freely available at http://sbi.imim.es/archdb), represents such a resource and has been an important asset for the scientific community throughout the years. In this article, we present a completely reworked and updated version of ArchDB. The new version of ArchDB features a novel, fast and user-friendly web-based interface, and a novel graph-based, computationally efficient, clustering algorithm. The current version of ArchDB classifies 149,134 loops in 5739 classes and 9608 subclasses.
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