Computer Algorithms for Discriminating Protein Folds and Predicting Protein Folding Rates Based on Contact Information

机译：基于联系信息的蛋白质折叠识别和蛋白质折叠速率预测的计算机算法

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Inter-residue interactions play an important role in governing the folding and stability of protein structures. In this work, we have analyzed the contacts between amino acid residues in different folding types of globular proteins and various ranges of folding rates. Based on amino acid contacts a novel parameter, multiple contact index has been developed for understanding protein folding rates. We have computed short, medium and long-range contacts in proteins of different folding types and rates from their sequences and structures. Utilizing the information, we have developed models for recognizing protein folds and predicting their folding rates, using machine learning techniques. Our methods showed an accuracy of 55% for discriminating 1612 globular proteins belonging to 30 different folds and an accuracy of 96% to distinguish the fast and slow folding proteins using 5-fold cross-validation method.

机译：残基间相互作用在控制蛋白质结构的折叠和稳定性中起重要作用。在这项工作中，我们分析了不同折叠类型的球状蛋白质中氨基酸残基之间的接触以及各种折叠速率。基于氨基酸接触的新参数，已开发出多种接触指数以了解蛋白质折叠速率。我们已经从它们的序列和结构计算了不同折叠类型和比率的蛋白质中的短，中和远距离接触。利用这些信息，我们使用机器学习技术开发了识别蛋白质折叠并预测其折叠速率的模型。我们的方法显示出使用5倍交叉验证方法区分16种1230个不同折叠形式的球状蛋白的准确度为55％，对快慢折叠蛋白质进行区分的准确度为96％。

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《Computer Science and Information Technology - Spring Conference, 2009. IACSITSC '09》|2009年|581-585|共5页
会议地点 Singapore(SG);Singapore(SG)
作者
Gromiha M.M.;
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Comput. Biol. Res. Center, AIST, Tokyo, Japan;

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bioinformatics; learning (artificial intelligence); molecular biophysics; proteins; computer algorithm; contact information; interresidue interactions; machine learning; protein folding; fold recognition; long-range order; machine learning techniques; multiple contact index; protein folding rates;

机译：生物信息学;学习（人工智能）;分子生物物理学;蛋白质;计算机算法;接触信息;残基间相互作用;机器学习;蛋白质折叠;折叠识别;远程顺序;机器学习技术;多种接触指数;蛋白质折叠率;

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专利

1. Machine Learning Algorithms for Predicting Protein Folding Rates and Stability of Mutant Proteins: Comparison with Statistical Methods [J] . M. Michael Gromiha, Liang-Tsung Huang Current Protein and Peptide Science . 2011,第6期

机译：预测折叠率和突变蛋白稳定性的机器学习算法：与统计方法的比较
2. Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: Application of long-range order to folding rate prediction [J] . Gromiha MM., Selvaraj S. Journal of Molecular Biology . 2001,第1期

机译：确定两种状态蛋白质折叠速率时长程相互作用和接触顺序之间的比较：长程顺序在折叠速率预测中的应用
3. Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts [J] . Zhu Jianwei, Zhang Haicang, Li Shuai Cheng, Bioinformatics . 2017,第23期

机译：通过从预测残留物触点中提取折叠特征来改善蛋白质折叠识别
4. Computer algorithms for discriminating protein folds and predicting protein folding rates based on contact information [C] . M. Michael Gromiha International Association of Computer Science and Information Technology Conference . 2009

机译：基于联系信息辨别蛋白折叠和预测蛋白质折叠率的计算机算法
5. The (Un)Folding of Multidomain Proteins Through the Lens of Single-molecule Force-spectroscopy and Computer Simulation. [D] . Scholl, Zackary N. 2016

机译：通过单分子力谱和计算机模拟的透镜对多域蛋白的（非）折叠。
6. Folding simulation of protein models on the structure-based cubo-octahedral lattice with the Contact Interactions algorithm. [O] . L. Toma, S. Toma 1999

机译：使用接触相互作用算法在基于结构的立方八面体晶格上蛋白质模型的折叠模拟。
7. Protein Folding Implementation of Stochastic and Deterministic Algorithms using the two-dimensionalHP Model for Computer Simulation of the Protein Folding Process [O] . Andersson Simon, Hammar Tor, Radway Alexander, 2014

机译：利用二维Hp模型进行蛋白质折叠过程计算机模拟的随机和确定性算法的蛋白质折叠实现

Computer Algorithms for Discriminating Protein Folds and Predicting Protein Folding Rates Based on Contact Information

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