Topological analysis and predictive modeling of amino acid structures with implications for bioinformatics and structural biology
Abstract Amino acids, as the fundamental constituents of proteins and enzymes, play a vital role in various biological processes. Amino acids such as histidine, cysteine, and methionine are known to coordinate with metal ions in proteins and enzymes, playing critical roles in their structure and fun...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-024-83697-6 |
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| author | Huili Li Anisa Naeem Shamaila Yousaf Adnan Aslam Fairouz Tchier Keneni Abera Tola |
| author_facet | Huili Li Anisa Naeem Shamaila Yousaf Adnan Aslam Fairouz Tchier Keneni Abera Tola |
| author_sort | Huili Li |
| collection | DOAJ |
| description | Abstract Amino acids, as the fundamental constituents of proteins and enzymes, play a vital role in various biological processes. Amino acids such as histidine, cysteine, and methionine are known to coordinate with metal ions in proteins and enzymes, playing critical roles in their structure and function. In metalloproteins, metal ions are often coordinated by specific amino acid residues, contributing to the protein’s stability and catalytic activity. Investigating the structural properties of amino acids is paramount to understanding the intricacies of protein function and interactions. The molecular structure of amino acid structures are examined using topological indices that are based on both distance and degree. These indices capture unique structural features of amino acids in their molecular graphs. We have developed linear, quadratic, and logarithmic regression models to estimate the five physical/chemical properties of twenty-two amino acids molecules. The findings reveal novel insights into the structural determinants of amino acid properties and present efficient predictive models for various attributes. This research contributes towards better understanding amino acid structures and offers practical applications in bioinformatics, drug design, and structural biology, enhancing the ability to manipulate and comprehend the molecular world. |
| format | Article |
| id | doaj-art-572e4d78a3014d42adfa635db9ad0550 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-572e4d78a3014d42adfa635db9ad05502025-01-05T12:19:58ZengNature PortfolioScientific Reports2045-23222025-01-0115111510.1038/s41598-024-83697-6Topological analysis and predictive modeling of amino acid structures with implications for bioinformatics and structural biologyHuili Li0Anisa Naeem1Shamaila Yousaf2Adnan Aslam3Fairouz Tchier4Keneni Abera Tola5School of Software, Pingdingshan UniversityDepartment of Mathematics, Faculty of Science, University of GujratDepartment of Mathematics, Faculty of Science, University of GujratDepartment of Natural Sciences and Humanities, University of Engineering and Technology, Lahore (RCET)Mathematics Department, College of Science, King Saud UniversityDepartment of Mathematics, College of Natural and Computational Sciences, Wollega UniversityAbstract Amino acids, as the fundamental constituents of proteins and enzymes, play a vital role in various biological processes. Amino acids such as histidine, cysteine, and methionine are known to coordinate with metal ions in proteins and enzymes, playing critical roles in their structure and function. In metalloproteins, metal ions are often coordinated by specific amino acid residues, contributing to the protein’s stability and catalytic activity. Investigating the structural properties of amino acids is paramount to understanding the intricacies of protein function and interactions. The molecular structure of amino acid structures are examined using topological indices that are based on both distance and degree. These indices capture unique structural features of amino acids in their molecular graphs. We have developed linear, quadratic, and logarithmic regression models to estimate the five physical/chemical properties of twenty-two amino acids molecules. The findings reveal novel insights into the structural determinants of amino acid properties and present efficient predictive models for various attributes. This research contributes towards better understanding amino acid structures and offers practical applications in bioinformatics, drug design, and structural biology, enhancing the ability to manipulate and comprehend the molecular world.https://doi.org/10.1038/s41598-024-83697-6Chemical graph theoryTopological indicesAmino acidQSPR models |
| spellingShingle | Huili Li Anisa Naeem Shamaila Yousaf Adnan Aslam Fairouz Tchier Keneni Abera Tola Topological analysis and predictive modeling of amino acid structures with implications for bioinformatics and structural biology Scientific Reports Chemical graph theory Topological indices Amino acid QSPR models |
| title | Topological analysis and predictive modeling of amino acid structures with implications for bioinformatics and structural biology |
| title_full | Topological analysis and predictive modeling of amino acid structures with implications for bioinformatics and structural biology |
| title_fullStr | Topological analysis and predictive modeling of amino acid structures with implications for bioinformatics and structural biology |
| title_full_unstemmed | Topological analysis and predictive modeling of amino acid structures with implications for bioinformatics and structural biology |
| title_short | Topological analysis and predictive modeling of amino acid structures with implications for bioinformatics and structural biology |
| title_sort | topological analysis and predictive modeling of amino acid structures with implications for bioinformatics and structural biology |
| topic | Chemical graph theory Topological indices Amino acid QSPR models |
| url | https://doi.org/10.1038/s41598-024-83697-6 |
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