کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
5417528 | 1506925 | 2009 | 11 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Combining a genetic algorithm with a linear scaling semiempirical method for protein-ligand docking
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کلمات کلیدی
موضوعات مرتبط
مهندسی و علوم پایه
شیمی
شیمی تئوریک و عملی
پیش نمایش صفحه اول مقاله
چکیده انگلیسی
In the search for more energetically precise docking methods and to avoid the problem of defining suitable ligand force fields, we have built a software to perform rigid molecular docking by combining a genetic algorithm with a linear scaling semiempirical program. The resulting AlgoGen-DivCon software uses the Divide and Conquer linear scaling methodology to evaluate protein-ligand interaction energies using quantum semiempirical hamiltonians while conformational search is performed by a genetic algorithm which optimizes the position of a mobile ligand relative to a fixed protein system. Tests have been performed to assess the performance of AlgoGen-DivCon. Our results on the docking of 8-azaxanthine, oxonic acid and uric acid in a 700 atom Urate Oxidase model are structurally very similar to known crystallographic structures and prove that it is now possible to perform in a reasonable amount of time molecular dockings of relatively large protein-ligand complexes using a quantum description of the interaction energy.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Molecular Structure: THEOCHEM - Volume 898, Issues 1â3, 30 March 2009, Pages 31-41
Journal: Journal of Molecular Structure: THEOCHEM - Volume 898, Issues 1â3, 30 March 2009, Pages 31-41
نویسندگان
Eddy Thiriot, Gerald Monard,