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Validating protein structure using kernel density estimates

Author

Listed:
  • Charles C. Taylor
  • Kanti V. Mardia
  • Marco Di Marzio
  • Agnese Panzera

Abstract

Measuring the quality of determined protein structures is a very important problem in bioinformatics. Kernel density estimation is a well-known nonparametric method which is often used for exploratory data analysis. Recent advances, which have extended previous linear methods to multi-dimensional circular data, give a sound basis for the analysis of conformational angles of protein backbones, which lie on the torus. By using an energy test, which is based on interpoint distances, we initially investigate the dependence of the angles on the amino acid type. Then, by computing tail probabilities which are based on amino-acid conditional density estimates, a method is proposed which permits inference on a test set of data. This can be used, for example, to validate protein structures, choose between possible protein predictions and highlight unusual residue angles.

Suggested Citation

  • Charles C. Taylor & Kanti V. Mardia & Marco Di Marzio & Agnese Panzera, 2012. "Validating protein structure using kernel density estimates," Journal of Applied Statistics, Taylor & Francis Journals, vol. 39(11), pages 2379-2388, July.
    • Handle: RePEc:taf:japsta:v:39:y:2012:i:11:p:2379-2388
    DOI: 10.1080/02664763.2012.710898
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    References listed on IDEAS

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    1. Taylor, Charles C., 2008. "Automatic bandwidth selection for circular density estimation," Computational Statistics & Data Analysis, Elsevier, vol. 52(7), pages 3493-3500, March.
    2. Di Marzio, Marco & Panzera, Agnese & Taylor, Charles C., 2009. "Local polynomial regression for circular predictors," Statistics & Probability Letters, Elsevier, vol. 79(19), pages 2066-2075, October.
    3. Bai, Z. D. & Rao, C. Radhakrishna & Zhao, L. C., 1988. "Kernel estimators of density function of directional data," Journal of Multivariate Analysis, Elsevier, vol. 27(1), pages 24-39, October.
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    1. Marco Marzio & Stefania Fensore & Agnese Panzera & Charles C. Taylor, 2018. "Circular local likelihood," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 27(4), pages 921-945, December.
    2. Bedouhene Kahina & Zougab Nabil, 2020. "A Bayesian procedure for bandwidth selection in circular kernel density estimation," Monte Carlo Methods and Applications, De Gruyter, vol. 26(1), pages 69-82, March.

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