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To study traditional Chinese medicines and exchange related information through the worldwide Web, we developed a traditional Chinese medicine database and a program for searching and displaying data in the database on the Web. In this paper, the traditional Chinese medicine database is briefly introduced; the methods used in developing the program,(More)
After new human transmissible H1N1 (swine flu) viruses were reported in Mexico and the United States in April 2009, the World Health Organization (WHO) announced the emergence of a novel influenza A virus. Most governments in the world have been alerted and are monitoring the situation closely. As one of the official responses to the H1N1 pandemic, the(More)
Solvation energy calculation is one of the main difficulties for the estimation of protein-ligand binding free energy and the correct scoring in docking studies. We have developed a new solvation energy estimation method for protein-ligand binding based on atomic solvation parameter (ASP), which has been shown to improve the power of protein-ligand binding(More)
Traditional Chinese drugs (TCDs) have played a key role for Chinese people in the treatment of diseases since ancient times. The use of TCDs has generated a great amount of information in the past thousand years about the relationship between natural products and the human body. However, up to now, our understanding on the mode of action of the TCD is still(More)
Histone deacetylases (HDACs) play a critical role in gene transcription and have become a novel target for the discovery of drugs against cancer and other diseases. During the past several years there have been extensive efforts in the identification and optimization of histone deacetylase inhibitors (HDACIs) as novel anticancer drugs. Here we report a(More)
A set of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors was investigated with the aim of developing 3D-QSAR models using the Flexible Atom Receptor Model (FLARM) method. Some 3D-QSAR models were built with high correlation coefficients, and the FLARM method predicted the biological activities of compounds in test set well. The FLARM(More)
Eigenvalue analysis (EVA) was conducted on a series of potent agonists of peroxisome proliferator-activated receptor gamma (PPARgamma). Predictive EVA quantitative structure-activity relationship (QSAR) models were established using the SYBYL package, which had conventional r2 and cross-validated coefficient (q2) values up to 0.920 and 0.587 for the AM1(More)
To address the problems associated with molecular conformations and alignments in the 3D-QSAR studies, we have developed the Flexible Ligand - Atomic Receptor Model (FLARM) 2.0 method. The FLARM 2.0 method has three unique features as compared to other pseudoreceptor model methods: (1) the training ligands are flexibly optimized inside the receptors to(More)
Since benzodiazepines have been used widely in the treatment of anxiety, sleeplessness, and epilepsy, the receptor sites for the benzodiazepine are of prime importance. Quantitative structure-activity relationship (QSAR) studies and receptor modeling via Flexible Atom Receptor Model (FLARM) for the binding affinities of a series of imidazobenzodiazepines at(More)