MehNet: a vigesimal-based model by amino acid melting points generates unique ID numbers for protein sequences

Abstract

The amino acid encoding plays a pivotal role in machine learning-based methods for predicting protein structure and function, as well as in protein mapping techniques. Additionally, the classification of protein sequences presents its own challenges. The current study aims to assign a constant value to each amino acid, thereby creating distinctions among protein sequences. The datasets used in this study were obtained from the UniProt Knowledgebase. Subsequently, these datasets underwent preprocessing steps, and identical sequences were categorized under the same headings. Each amino acid was ranked based on its respective melting point and was assigned a vigesimal digit. These generated vigesimal digits were subsequently converted to decimal values. The centerpiece of this methodology was the melting point hashing table, which was given the name ‘MehNet’. Ultimately, each protein sequence was assigned a unique identification number. This approach successfully digitized protein sequences. Notably, experiments involving randomly distributed vigesimal digits for amino acids did not yield results as promising as those achieved with MehNet. The model’s classification phase, which utilizes a k-nearest neighbors (kNN) classifier, demonstrates exceptional performance in miscellaneous viral sequences. It achieves high accuracy rates, with an overall accuracy of 99.75%. Notably, it achieves an outstanding accuracy of 99.92% for the Influenza C class, highlighting its ability to distinguish closely related viral sequences.

Communicated by Ramaswamy H. Sarma

Keywords:

• MehNet
• melting points
• vigesimal digits
• protein ID numbers

Acknowledgments

The author wishes to thank Serpil Erten, Şengül Doğan, and Türker Tuncer for their supports during this study.

Disclosure statement

The author has no relevant financial or non-financial interests to disclose.

Data and code availability

The data and source code that support the findings of this study are openly available in Mendeley Data repository at http://doi.org/10.17632/24x9hdckx5.1, titled "MehNet Source Code and IDs" (Erten, 2024).