ArticlePLoS computational biology2009
Four distances between pairs of amino acids provide a precise description of their interaction.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Multimodal geometric learning for antimicrobial peptide identification by leveraging alphafold2-predicted structures and surface features.Briefings in bioinformatics · 2025Article
- Structure-aware protein self-supervised learning.Bioinformatics (Oxford, England) · 2023Article
- Customized chitooligosaccharide production-controlling their lengthFrontiers in bioengineering and biotechnology · 2022Article
- Autoencoder based local T cell repertoire density can be used to classify samples and T cell receptors.PLoS computational biology · 2021Article
- PremPS: Predicting the impact of missense mutations on protein stability.PLoS computational biology · 2020Article
- Functional specialization of UDP-glycosyltransferase 73P12 in licorice to produce a sweet triterpenoid saponin, glycyrrhizin.The Plant journal : for cell and molecular biology · 2019Article
- Computational tools help improve protein stability but with a solubility tradeoff.The Journal of biological chemistry · 2017Article
- Predicting receptor functionality of signaling lymphocyte activation molecule for measles virus hemagglutinin by docking simulation.Microbiology and immunology · 2017Article
- Protein-structure-guided discovery of functional mutations across 19 cancer types.Nature genetics · 2016Article
- Identification of Amino Acid Residues in Fibroblast Growth Factor 14 (FGF14) Required for Structure-Function Interactions with Voltage-gated Sodium Channel Nav1.6.The Journal of biological chemistry · 2016Article
- Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics.International journal of molecular sciences · 2014Review
- Article
- The linear interaction energy method for the prediction of protein stability changes upon mutation.Proteins · 2012Article
- A conserved tryptophan at the membrane-water interface acts as a gatekeeper for Kir6.2/SUR1 channels and causes neonatal diabetes when mutated.The Journal of physiology · 2011Article
- NCACO-score: an effective main-chain dependent scoring function for structure modeling.BMC bioinformatics · 2011Article
- From isotropic to anisotropic side chain representations: comparison of three models for residue contact estimation.PloS one · 2011Article
- Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions.BMC bioinformatics · 2010Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The three-dimensional structures of proteins are stabilized by the interactions between amino acid residues. Here we report a method where four distances are calculated between any two side chains to provide an exact spatial definition of their bonds. The data were binned into a four-dimensional grid and compared to a random model, from which the preference for specific four-distances was calculated. A clear relation between the quality of the experimental data and the tightness of the distance distribution was observed, with crystal structure data providing far tighter distance distributions than NMR data. Since the four-distance data have higher information content than classical bond descriptions, we were able to identify many unique inter-residue features not found previously in proteins. For example, we found that the side chains of Arg, Glu, Val and Leu are not symmetrical in respect to the interactions of their head groups. The described method may be developed into a function, which computationally models accurately protein structures.
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