ArticleBMC evolutionary biology2005
Structural similarity of loops in protein families: toward the understanding of protein evolution.
Article in BMC evolutionary biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Synthesis, Characterization, and Biological Evaluation of Novel Azo-Based Imidazo[1,2‑ACS omega · 2025Article
- Physicochemical, functional, and evolutionary characteristics of protein loop regions in human andBiophysics and physicobiology · 2025Article
- Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency.Briefings in bioinformatics · 2023Article
- Accurate Prediction of Enzyme Thermostabilization with Rosetta Using AlphaFold Ensembles.Journal of chemical information and modeling · 2023Article
- Benchmarking the Accuracy of AlphaFold 2 in Loop Structure Prediction.Biomolecules · 2022Article
- Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations.Journal of chemical theory and computation · 2021Article
- Determination of B- and T- cell epitopes for Helicobacter pylori cagPAI: An in silico approach.The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology · 2020Article
- Simple Selection Procedure to Distinguish between Static and Flexible Loops.International journal of molecular sciences · 2020Article
- Salivary Scavenger and Agglutinin (SALSA) Is Expressed in Mucosal Epithelial Cells and Decreased in Bronchial Epithelium of Asthmatic Horses.Frontiers in veterinary science · 2019Article
- Detecting transitions in protein dynamics using a recurrence quantification analysis based bootstrap method.BMC bioinformatics · 2017Article
- Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY-DNA (W-Box) Complex Interaction in Tomato (Frontiers in plant science · 2017Article
- Why reinvent the wheel? Building new proteins based on ready-made parts.Protein science : a publication of the Protein Society · 2016Review
- Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.PLoS computational biology · 2015Article
- Conformational sampling in template-free protein loop structure modeling: an overview.Computational and structural biotechnology journal · 2013Review
- The importance of slow motions for protein functional loops.Physical biology · 2012Article
- Deciphering the preference and predicting the viability of circular permutations in proteins.PloS one · 2012Article
- Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.BMC bioinformatics · 2011Article
- The combined effects of amino acid substitutions and indels on the evolution of structure within protein families.PloS one · 2010Article
- Models to Approximate the Motions of Protein Loops.Journal of chemical theory and computation · 2010Article
- The nature of protein domain evolution: shaping the interaction network.Current genomics · 2010Article
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2 authors.
Funding
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Abstract
backgroundProtein evolution and protein classification are usually inferred by comparing protein cores in their conserved aligned parts. Structurally aligned protein regions are separated by less conserved loop regions, where sequence and structure locally deviate from each other and do not superimpose well.
resultsOur results indicate that even longer protein loops can not be viewed as "random coils" and for the majority of protein families in our test set there exists a linear correlation between the measures of sequence similarity and loop structural similarity. Results suggest that distance matrices derived from the loop (dis)similarity measure may produce in some cases more reliable cluster trees compared to the distance matrices based on the conventional measures of sequence and structural (dis)similarity.
conclusionsWe show that by considering "dissimilar" loop regions rather than only conserved core regions it is possible to improve our understanding of protein evolution.
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