دورية أكاديمية
A benchmark of optimally folded protein structures using integer programming and the 3D-HP-SC model.
| العنوان: | A benchmark of optimally folded protein structures using integer programming and the 3D-HP-SC model. |
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| المؤلفون: | Hattori LT; Bioinformatics and Computational Intelligence Laboratory, Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba (PR), Brazil. Electronic address: lthattori@gmail.com., Gutoski M; Bioinformatics and Computational Intelligence Laboratory, Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba (PR), Brazil., Vargas Benítez CM; Bioinformatics and Computational Intelligence Laboratory, Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba (PR), Brazil., Nunes LF; Bioinformatics and Computational Intelligence Laboratory, Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba (PR), Brazil. Electronic address: nunes@utfpr.edu.br., Lopes HS; Bioinformatics and Computational Intelligence Laboratory, Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba (PR), Brazil. Electronic address: hslopes@utfpr.edu.br. |
| المصدر: | Computational biology and chemistry [Comput Biol Chem] 2020 Feb; Vol. 84, pp. 107192. Date of Electronic Publication: 2019 Dec 23. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Elsevier Country of Publication: England NLM ID: 101157394 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-928X (Electronic) Linking ISSN: 14769271 NLM ISO Abbreviation: Comput Biol Chem Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: Oxford : Elsevier Original Publication: Oxford : Pergamon, c2003- |
| مواضيع طبية MeSH: | Computational Biology/*methods , Proteins/*chemistry, Databases, Protein/statistics & numerical data ; Models, Chemical ; Models, Molecular ; Protein Structure, Tertiary ; Software |
| مستخلص: | The Protein Structure Prediction (PSP) problem comprises, among other issues, forecasting the three-dimensional native structure of proteins using only their primary structure information. Most computational studies in this area use synthetic data instead of real biological data. However, the closer to the real-world, the more the impact of results and their applicability. This work presents 17 real protein sequences extracted from the Protein Data Bank for a benchmark to the PSP problem using the tri-dimensional Hydrophobic-Polar with Side-Chains model (3D-HP-SC). The native structure of these proteins was found by maximizing the number of hydrophobic contacts between the side-chains of amino acids. The problem was treated as an optimization problem and solved by means of an Integer Programming approach. Although the method optimally solves the problem, the processing time has an exponential trend. Therefore, due to computational limitations, the method is a proof-of-concept and it is not applicable to large sequences. For unknown sequences, an upper bound of the number of hydrophobic contacts (using this model) can be found, due to a linear relationship with the number of hydrophobic residues. The comparison between the predicted and the biological structures showed that the highest similarity between them was found with distance thresholds around 5.2-8.2 Å. Both the dataset and the programs developed will be freely available to foster further research in the area. (Copyright © 2019. Published by Elsevier Ltd.) |
| فهرسة مساهمة: | Keywords: Biological sequences; Hydrophobic-polar model; Integer programming; Protein structure problem |
| المشرفين على المادة: | 0 (Proteins) |
| تواريخ الأحداث: | Date Created: 20200110 Date Completed: 20200225 Latest Revision: 20200225 |
| رمز التحديث: | 20240628 |
| DOI: | 10.1016/j.compbiolchem.2019.107192 |
| PMID: | 31918170 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1476-928X |
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| DOI: | 10.1016/j.compbiolchem.2019.107192 |