ArticleProtein science : a publication of the Protein Society2005
The effect of long-range interactions on the secondary structure formation of proteins.
Article in Protein science : a publication of the Protein Society, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed.
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- Comprehensive assessment of AlphaFold's predictions of secondary structure and solvent accessibility at the amino acid-level in eukaryotic, bacterial and archaeal proteins.Computational and structural biotechnology journal · 2025Article
- Wavelet coherence phase analysis decodes the universal switching mechanism of Ras GTPase superfamily.iScience · 2023Article
- Secondary structure specific simpler prediction models for protein backbone angles.BMC bioinformatics · 2022Article
- Information quantity for secondary structure propensities of protein subsequences in the Protein Data Bank.Biophysics and physicobiology · 2022Article
- Enhancing protein backbone angle prediction by using simpler models of deep neural networks.Scientific reports · 2020Article
- How accurate is circular dichroism-based model validation?European biophysics journal : EBJ · 2020Article
- Sixty-five years of the long march in protein secondary structure prediction: the final stretch?Briefings in bioinformatics · 2018Article
- GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison.Scientific reports · 2017Article
- Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach.BMC bioinformatics · 2016Article
- Protein structure prediction using residue- and fragment-environment potentials in CASP11.Proteins · 2016Article
- Logistic regression models to predict solvent accessible residues using sequence- and homology-based qualitative and quantitative descriptors applied to a domain-complete X-ray structure learning set.Journal of applied crystallography · 2015Article
- DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment.BMC bioinformatics · 2015Article
- Prediction of structural features and application to outer membrane protein identification.Scientific reports · 2015Article
- Detecting local residue environment similarity for recognizing near-native structure models.Proteins · 2014Article
- From local structure to a global framework: recognition of protein folds.Journal of the Royal Society, Interface · 2014Review
- Distributions of amino acids suggest that certain residue types more effectively determine protein secondary structure.Journal of molecular modeling · 2013Article
- The loop hypothesis: contribution of early formed specific non-local interactions to the determination of protein folding pathways.Biophysical reviews · 2013Review
- Effective inter-residue contact definitions for accurate protein fold recognition.BMC bioinformatics · 2012Article
- Fast learning optimized prediction methodology (FLOPRED) for protein secondary structure prediction.Journal of molecular modeling · 2012Article
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Abstract
The influence of long-range residue interactions on defining secondary structure in a protein has long been discussed and is often cited as the current limitation to accurate secondary structure prediction. There are several experimental examples where a local sequence alone is not sufficient to determine its secondary structure, but a comprehensive survey on a large data set has not yet been done. Interestingly, some earlier studies denied the negative effect of long-range interactions on secondary structure prediction accuracy. Here, we have introduced the residue contact order (RCO), which directly indicates the separation of contacting residues in terms of the position in the sequence, and examined the relationship between the RCO and the prediction accuracy. A large data set of 2777 nonhomologous proteins was used in our analysis. Unlike previous studies, we do find that prediction accuracy drops as residues have contacts with more distant residues. Moreover, this negative correlation between the RCO and the prediction accuracy was found not only for beta-strands, but also for alpha-helices. The prediction accuracy of beta-strands is lower if residues have a high RCO or a low RCO, which corresponds to the situation that a beta-sheet is formed by beta-strands from different chains in a protein complex. The reason why the current study draws the opposite conclusion from the previous studies is examined. The implication for protein folding is also discussed.
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