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iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations
Abstract
Summary: We have developed a web server, iPTREE-STAB for discriminating the stability of proteins (stabilizing or destabilizing) and predicting their stability changes (ΔΔG) upon single amino acid substitutions from amino acid sequence. The discrimination and prediction are mainly based on decision tree coupled with adaptive boosting algorithm, and classification and regression tree, respectively, using three neighboring residues of the mutant site along N- and C-terminals. Our method showed an accuracy of 82% for discriminating the stabilizing and destabilizing mutants, and a correlation of 0.70 for predicting protein stability changes upon mutations. Availability: http://bioinformatics.myweb.hinet.net/iptree.htm Contact: michael-gromiha@aist.go.jp Supplementary information: Dataset and other details are given.
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A decision-theoretic generalization of on-line learning and an application to boosting
Freund, Y., & Schapire, R. E. (1997) · Journal of Computer and System Sciences · doi:10.1006/jcss.1997.1504 · Cited by 20,466
Guerois, R., Nielsen, J. E., & Serrano, L. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00442-4 · Cited by 1,728
Cited by
Stability effects of mutations and protein evolvability
Tokuriki, N., & Tawfik, D. S. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.08.003 · Cited by 834
INPS-MD: a web server to predict stability of protein variants from sequence and structure
Savojardo, C., Fariselli, P., Martelli, P. L., & Casadio, R. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw192 · Cited by 290
Montanucci, L., Capriotti, E., Frank, Y., Ben-Tal, N., & Fariselli, P. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2923-1 · Cited by 167
Learning Optimal and Fair Decision Trees for Non-Discriminative Decision-Making
Aghaei, S., Azizi, M. J., & Vayanos, P. (2019) · Proceedings of the AAAI Conference on Artificial Intelligence · doi:10.1609/aaai.v33i01.33011418 · Cited by 135
Lv, X., Chen, J., Lu, Y., Chen, Z., Xiao, N., & Yang, Y. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00064 · Cited by 26
Metadata
- Authors
- Huang, L.-T., Gromiha, M. M., & Ho, S.-Y.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-03-22
- Volume
- 23
- Issue
- 10
- Pages
- 1292-1293
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2120949690
- Cited by
- 159
- References
- 2
- FWCI
- 4.07
- Type
- journal article
- Language
- en
- Open access
- closed
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- Huang, L.-T., Gromiha, M. M., & Ho, S.-Y. (2007). iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations. Bioinformatics. https://doi.org/10.1093/bioinformatics/btm100
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