Proteins can exhibit sequence level identity/similarity and also structure level identity. These are the most common aspects of a protein that are used to identify homologous proteins/regions. However, the structure and thus function of a protein is determined by the physicochemical properties that each amino acid possesses. We have found that two physicochemical properties when combined in the right manner can be used along with dynamic time warping to identify similarity among proteins that better transcends the twilight zone than sequence based analyses. Additionally, this method may have advantages over structure based approaches which are generally expensive in terms of time, computing power and money.
The pertinent publications for this method are as follows:
• Dixson, J. D. and R. K. Azad. 2021. A Novel Predictor of ACE2-Binding Ability Among Betacoronaviruses. Evolution, Medicine and Public Health 9(1):360-373.
• Dixson, J. D., Vumma, L. and R. K. Azad. 2024. An Analysis of Combined Molecular Weight and Hydrophobicity Similarity between the Amino Acid Sequences of Spike Protein Receptor Binding Domains of Betacoronaviruses and Functionally Similar Sequences from Other Virus Families. Microorganisms 12(10), 2021. https://doi.org/10.3390/microorganisms12102021
• Dixson, J. D. and R. K. Azad. 2024. Physicochemical Evaluation of Remote Homology in the Twilight Zone. Proteins. https://doi.org/10.1002/prot.26742
Please use these citation when using this method or any derivative of it. This method is copyrighted by Jamie Dixson and Rajeev Azad in all forms and for all uses except educational and non-profit use. If you wish to use this method or any derivative of it in a commercial or for profit capacity you must seek and obtain permission from both copyright owners.
The contact information for the copyright owners are as follows:
Jamie [email protected]
Rajeev [email protected]
All technical questions regarding implementation of the MWHP PCDTW algorithms should be directed to Jamie Dixson.
Despite the main code being written by Jamie Dixson and the concept being conceived by Jamie Dixson, this repository contains some code that was partially written by Ambarish Kumar. Ambarish Kumar is permitted to use and alter the code within this repository for the duration and extent of his doctorate research and publication and you may contact him directly regarding his branch within this repository. His email address is [email protected]