Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction [0.03%]
基于对接模型的异二聚体互作面分类及复合物结构预测打分函数的构建
Yuko Tsuchiya,Eiji Kanamori,Haruki Nakamura et al.
Yuko Tsuchiya et al.
Protein-protein docking simulations can provide the predicted complex structural models. In a docking simulation, several putative structural models are selected by scoring functions from an ensemble of many complex models. Scoring function...
Evaluating the efficacy of a structure-derived amino acid substitution matrix in detecting protein homologs by BLAST and PSI-BLAST [0.03%]
评估结构衍生氨基酸替换矩阵在BLAST和PSI-BLAST中检测蛋白质同源物方面的有效性
Nalin Cw Goonesekere
Nalin Cw Goonesekere
The large numbers of protein sequences generated by whole genome sequencing projects require rapid and accurate methods of annotation. The detection of homology through computational sequence analysis is a powerful tool in determining the c...
Performance of PLS regression coefficients in selecting variables for each response of a multivariate PLS for omics-type data [0.03%]
基于PLS回归系数的多变量PLS在选择omics型数据每个响应变量中的性能评估
Giuseppe Palermo,Paolo Piraino,Hans-Dieter Zucht
Giuseppe Palermo
Multivariate partial least square (PLS) regression allows the modeling of complex biological events, by considering different factors at the same time. It is unaffected by data collinearity, representing a valuable method for modeling high-...
Yuanyou Tan,John M Bush,Weijiu Liu et al.
Yuanyou Tan et al.
Identification of genes involved in the aging process is critical for understanding the mechanisms of age-dependent diseases such as cancer and diabetes. Measuring the mutant gene lifespan, each missing one gene, is traditionally employed t...
Junfeng Liu,Liang Chen,Hongyu Zhao et al.
Junfeng Liu et al.
Probabilistic DNA sequence models have been intensively applied to genome research. Within the evolutionary biology framework, this article investigates the feasibility for rigorously estimating the probability of a set of orthologous DNA s...
Tun-Wen Pai,Chien-Ming Chen,Meng-Chang Hsiao et al.
Tun-Wen Pai et al.
Simple sequence repeats (SSRs) play important roles in gene regulation and genome evolution. Although there exist several online resources for SSR mining, most of them only extract general SSR patterns without providing functional informati...
Lingsheng Dong,Andrew J Bard,William G Richards et al.
Lingsheng Dong et al.
Purpose: Bladder cancer is relatively common but early detection techniques such as cystoscopy and cytology are somewhat limited. We developed a broadly applicable, platform-independent and clinically relevant method base...
The development of an affinity evaluation and prediction system by using protein-protein docking simulations and parameter tuning [0.03%]
基于蛋白质对接模拟和参数调节的亲和力评价及预测系统的发展
Koki Tsukamoto,Tatsuya Yoshikawa,Kiyonobu Yokota et al.
Koki Tsukamoto et al.
A system was developed to evaluate and predict the interaction between protein pairs by using the widely used shape complementarity search method as the algorithm for docking simulations between the proteins. We used this system, which we c...
A simple method for assessing the strength of evidence for association at the level of the whole gene [0.03%]
一种简单评价基因水平上关联证据强度的方法
David Curtis,Anna E Vine,Jo Knight
David Curtis
Introduction: It is expected that different markers may show different patterns of association with different pathogenic variants within a given gene. It would be helpful to combine the evidence implicating association at...
Yuko Tsuchiya,Haruki Nakamura,Kengo Kinoshita
Yuko Tsuchiya
A discrimination method between biologically relevant interfaces and artificial crystal-packing contacts in crystal structures was constructed. The method evaluates protein-protein interfaces in terms of complementarities for hydrophobicity...