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Structure-based screening using fully flexible docking is still too slow for large molecular libraries. High quality docking of a million molecule library can take days even on a cluster with hundreds of CPUs. This performance issue prohibits the use of fully flexible docking in the design of large combinatorial libraries. We have developed a fast(More)
MOTIVATION The identification of the change of gene expression in multifactorial diseases, such as breast cancer is a major goal of DNA microarray experiments. Here we present a new data mining strategy to better analyze the marginal difference in gene expression between microarray samples. The idea is based on the notion that the consideration of gene's(More)
Motivation: Numerous methods for predicting β-turns in proteins have been developed based on various computational schemes. Here, we introduce a new method of β-turn prediction that uses the support vector machine (SVM) algorithm together with predicted secondary structure information. Various parameters from the SVM have been adjusted to achieve optimal(More)
Receptor flexibility is a critical issue in structure-based virtual screening methods. Although a multiple-receptor conformation docking is an efficient way to account for receptor flexibility, it is still too slow for large molecular libraries. It was reported that a fast ligand-centric, shape-based virtual screening was more consistent for hit enrichment(More)
Docking and scoring are critical issues in virtual drug screening methods. Fast and reliable methods are required for the prediction of binding affinity especially when applied to a large library of compounds. The implementation of receptor flexibility and refinement of scoring functions for this purpose are extremely challenging in terms of computational(More)
The calculation of contact-dependent secondary structure propensity (CSSP) is a unique and sensitive method that detects non-native secondary structure propensities in protein sequences. This method has applications in predicting local conformational change, which typically is observed in core sequences of protein aggregation and amyloid fibril formation.(More)
Somatic mutation is a major cause of cancer progression and varied responses of tumors against anticancer agents. Thus, we must obtain and characterize genome-wide mutational profiles in individual cancer subtypes. The Cancer Genome Atlas database includes large amounts of sequencing and omics data generated from diverse human cancer tissues. In the present(More)
We developed a user-friendly, interactive program to simultaneously cluster and visualize omics data, such as DNA and protein array profiles. This program provides diverse algorithms for the hierarchical clustering of two-dimensional data. The clustering results can be interactively visualized and optimized on a heatmap. The present tool does not require(More)
MOTIVATION It is expected that individual genes have intrinsically different variability in the global expressional trend among them. Thus, the consideration of gene-specific expressional properties will help us to distinguish target-selective gene expression over non-selective over-expression. RESULTS The re-standardization and integration of(More)
Unexpected drug efficacy or resistance is poorly understood in cancers because of the lack of systematic analyses of drug response profiles in cancer tissues of various genotypic backgrounds. The recent development of high‑throughput technologies has allowed massive screening of chemicals and drugs against panels of heterogeneous cancer cell lines. In(More)