Ligand-K Sequence Elimination: A NovelAlgorithm for Ensemble-Based Redesignof Receptor-Ligand Binding

Shen Q.; Tian H.; Tang D.; Yao W.; Gao X.

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Ligand-K Sequence Elimination: A NovelAlgorithm for Ensemble-Based Redesignof Receptor-Ligand Binding

机译：配体-K序列消除：基于新的基于算法的受体-配体结合重新设计算法

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摘要

K* is rotamerically ensemble-based approach to compute the binding constant. However, its time-consuming feature limited its application. We present a novel algorithm that not only computes the partition function efficiently, but also avoids the exponential growth of execution time by iteratively pruning the sequence space until the sequence with highest affinity is identified.

机译：K *是基于旋转系综的方法来计算绑定常数。但是，其耗时的功能限制了其应用。我们提出了一种新颖的算法，该算法不仅可以有效地计算分区函数，而且还可以通过迭代修剪序列空间直到识别出具有最高亲和力的序列来避免执行时间的指数增长。

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《Computational Biology and Bioinformatics, IEEE/ACM Transactions on》 |2014年第3期|573-578|共6页
作者
Shen Q.; Tian H.; Tang D.; Yao W.; Gao X.;
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作者单位

College of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, Jiangsu, China|c|;

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原文格式 PDF
正文语种 eng
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关键词
Ensemble; K* algorithm; protein redesign; sequence elimination;

机译：集成;K *算法;蛋白质重新设计;序列消除;

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专利

1. BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces [J] . Adegoke A. Ojewole, Jonathan D. Jou, Vance G. Fowler, Journal of computational biology . 2018,第7期

机译：BBK *（K *上的分支和边界）：一种可验证且有效的基于集合的蛋白质设计算法，可优化大序列空间上的稳定性和结合亲和力
2. BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces [J] . Ojewole Adegoke A., Jou Jonathan D., Fowler Vance G., Journal of computational biology: A journal of computational molecular cell biology . 2018,第7期

机译：BBK *（分支和k *绑定）：一种可提供高效的基于合奏的蛋白质设计算法，可优化在大序列空间上的稳定性和结合亲和力
3. Multiparametric Homogeneous Method for Identification of Ligand Binding to G Protein-Coupled Receptors: Receptor-Ligand Binding and β-Arrestin Assay [J] . Kari Kopra, Markus Kainulainen, Piia Mikkonen, Analytical chemistry . 2013,第4期

机译：用于鉴定配体与G蛋白偶联受体结合的多参数均相方法：受体-配体结合和β-arrestin分析
4. BBK~* (Branch and Bound over K*): A Provable and Efficient Ensemble-Based Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces [C] . Adegoke A. Ojewole, Jonathan D. Jou, Vance G. Fowler, Annual international conference on research in computational molecular biology . 2017

机译：BBK〜*（K *上的分支和边界）：一种可验证且有效的基于集合的算法，可在较大序列空间上优化稳定性和绑定亲和力
5. Investigation of transcription factor binding sequences and target genes using protein binding microarrays. [D] . Bolotin, Eugene Leonidovich. 2010

机译：使用蛋白质结合微阵列研究转录因子结合序列和靶基因。
6. BBK* (Branch and Bound Over K*): A Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces [O] . Adegoke A. Ojewole, Jonathan D. Jou, Vance G. Fowler, -1

机译：BBK *（在K *上分支和绑定）：一种可验证且有效的基于集合体的蛋白质设计算法可优化大序列空间上的稳定性和结合亲和力
7. Receptor-ligand interaction: a new method for determining binding parameters without a priori assumptions on non-specific binding. [O] . van Zoelen, E J 1989

机译：受体-配体相互作用：一种无需先验假设就可以确定结合参数的新方法，无需进行非特异性结合。

Ligand-K Sequence Elimination: A NovelAlgorithm for Ensemble-Based Redesignof Receptor-Ligand Binding

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