ArticleJournal of cheminformatics2019
Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis.
Article in Journal of cheminformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 13 citations in OpenAlex.
- A Rational Framework to Estimate the Chiroptical Activity of [6]Helicene Derivatives.The journal of physical chemistry. A · 2025Article
- Factors Influencing the Binding of HIV-1 Protease Inhibitors: Insights from Machine Learning Models.ChemMedChem · 2025Article
- CSM Software: Continuous Symmetry and Chirality Measures for Quantitative Structural Analysis.Journal of chemical information and modeling · 2024Article
- Continuous symmetry and chirality measures: approximate algorithms for large molecular structures.Journal of cheminformatics · 2023Article
- The near-symmetry of protein oligomers: NMR-derived structures.Scientific reports · 2020Article
- Optimizing the refinement of merohedrally twinned P6Acta crystallographica. Section D, Structural biology · 2020Article
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Authors and funding
2 authors at 1 institution in 1 country.
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Abstract
Symmetry of proteins, an important source of their elegant structure and unique functions, is not as perfect as it may seem. In the framework of continuous symmetry, in which symmetry is no longer a binary yes/no property, such imperfections can be quantified and used as a global descriptor of the three-dimensional structure. We present an improved algorithm for calculating the continuous symmetry measure for proteins that takes into account their complete set of atoms including all side chains. Our method takes advantage of the protein sequence and the division into peptides in order to improve the accuracy and efficiency of the calculation over previous methods. The Hungarian algorithm is applied to solve the assignment problem and find the permutation that defines the symmetry operation. Analysis of the symmetry of several sets of protein homomers, with various degrees of rotational symmetry is presented. The new methodology lays the foundations for accurate, efficient and reliable large scale symmetry analysis of protein structure and can be used as a collective variable that describes changes of the protein geometry along various processes, both at the backbone level and for the complete protein structure.
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