The Janus-faced E-values of HMMER2: extreme value distribution or logistic function? [0.03%]
HMMER2的Janus值:E值的极值分布还是逻辑回归函数？
Wing-Cheong Wong,Sebastian Maurer-Stroh,Frank Eisenhaber
Wing-Cheong Wong
E-value guided extrapolation of protein domain annotation from libraries such as Pfam with the HMMER suite is indispensable for hypothesizing about the function of experimentally uncharacterized protein sequences. Since the recent release o...
Comparative Study
Journal of bioinformatics and computational biology. 2011 Feb;9(1):179-206. DOI: 2011
Jiangning Song,Hao Tan,Sarah E Boyd et al.
Jiangning Song et al.
Proteases have central roles in "life and death" processes due to their important ability to catalytically hydrolyze protein substrates, usually altering the function and/or activity of the target in the process. Knowledge of the substrate ...
Siling Wang,Yuhang Wang,Yang Xie et al.
Siling Wang et al.
DNA copy number (DCN) is the number of copies of DNA at a region of a genome. The alterations of DCN are highly associated with the development of different tumors. Recently, microarray technologies are being employed to detect DCN changes ...
Enhancing biological relevance of a weighted gene co-expression network for functional module identification [0.03%]
改进加权基因共表达网络的生物相关性以识别功能模块
Santitham Prom-On,Atthawut Chanthaphan,Jonathan Hoyin Chan et al.
Santitham Prom-On et al.
Relationships among gene expression levels may be associated with the mechanisms of the disease. While identifying a direct association such as a difference in expression levels between case and control groups links genes to disease mechani...
William Taylor,Zoe Katsimitsoulia,Alexei Poliakov
William Taylor
A mechanical model of cell motion was developed that reproduced the behaviour of cells in 2-dimensional culture. Cell adhesion was modelled with inter-cellular cross-links that attached for different times giving a range of adhesion strengt...
Kanaka Durga Kedarisetti,Marcin J Mizianty,Scott Dick et al.
Kanaka Durga Kedarisetti et al.
Accurate identification of strand residues aids prediction and analysis of numerous structural and functional aspects of proteins. We propose a sequence-based predictor, BETArPRED, which improves prediction of strand residues and β-strand ...
Prediction of the exposure status of transmembrane beta barrel residues from protein sequence [0.03%]
基于蛋白质序列预测膜蛋白β Barrel跨膜区残基暴露状态
Sikander Hayat,Peter Walter,Yungki Park et al.
Sikander Hayat et al.
We present BTMX (Beta barrel TransMembrane eXposure), a computational method to predict the exposure status (i.e. exposed to the bilayer or hidden in the protein structure) of transmembrane residues in transmembrane beta barrel proteins (TM...
Error tolerant NMR backbone resonance assignment and automated structure generation [0.03%]
容错的NMR主链共振指派及自动化结构生成
Babak Alipanahi,Xin Gao,Emre Karakoc et al.
Babak Alipanahi et al.
Error tolerant backbone resonance assignment is the cornerstone of the NMR structure determination process. Although a variety of assignment approaches have been developed, none works sufficiently well on noisy fully automatically picked pe...
Jianxiu Guo,Nini Rao
Jianxiu Guo
Predicting protein folding rate from amino acid sequence is an important challenge in computational and molecular biology. Over the past few years, many methods have been developed to reflect the correlation between the folding rates and pr...
Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq [0.03%]
异构体丰富度推断可更准确估计RNA测序中的基因表达水平
Xi Wang,Zhengpeng Wu,Xuegong Zhang
Xi Wang
Due to its unprecedented high-resolution and detailed information, RNA-seq technology based on next-generation high-throughput sequencing significantly boosts the ability to study transcriptomes. The estimation of genes' transcript abundanc...