کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
4497725 | 1318948 | 2010 | 9 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Prediction of the parallel/antiparallel orientation of beta-strands using amino acid pairing preferences and support vector machines
دانلود مقاله + سفارش ترجمه
دانلود مقاله ISI انگلیسی
رایگان برای ایرانیان
موضوعات مرتبط
علوم زیستی و بیوفناوری
علوم کشاورزی و بیولوژیک
علوم کشاورزی و بیولوژیک (عمومی)
پیش نمایش صفحه اول مقاله
![عکس صفحه اول مقاله: Prediction of the parallel/antiparallel orientation of beta-strands using amino acid pairing preferences and support vector machines Prediction of the parallel/antiparallel orientation of beta-strands using amino acid pairing preferences and support vector machines](/preview/png/4497725.png)
چکیده انگلیسی
In principle, structural information of protein sequences with no detectable homology to a protein of known structure could be obtained by predicting the arrangement of their secondary structural elements. Although some ab initio methods for protein structure prediction have been reported, the long-range interactions required to accurately predict tertiary structures of β-sheet containing proteins are still difficult to simulate. To remedy this problem and facilitate de novo prediction of β-sheet containing protein structures, we developed a support vector machine (SVM) approach that classified parallel and antiparallel orientation of β-strands by using the information of interstrand amino acid pairing preferences. Based on a second-order statistics on the relative frequencies of each possible interstrand amino acid pair, we defined an average amino acid pairing encoding matrix (APEM) for encoding β-strands as input in the prediction model. As a result, a prediction accuracy of 86.89% and a Matthew's correlation coefficient value of 0.71 have been achieved through 7-fold cross-validation on a non-redundant protein dataset from PISCES. Although several issues still remain to be studied, the method presented here to some extent could indicate the important contribution of the amino acid pairs to the β-strand orientation, and provide a possible way to further be combined with other algorithms making a full 'identification' of β-strands.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Theoretical Biology - Volume 263, Issue 3, 7 April 2010, Pages 360-368
Journal: Journal of Theoretical Biology - Volume 263, Issue 3, 7 April 2010, Pages 360-368
نویسندگان
Ning Zhang, Guangyou Duan, Shan Gao, Jishou Ruan, Tao Zhang,