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New empirical scoring functions have been developed to estimate the binding affinity of a given protein-ligand complex with known three-dimensional structure. These scoring functions include terms accounting for van der Waals interaction, hydrogen bonding, deformation penalty, and hydrophobic effect. A special feature is that three different algorithms have(More)
A new method is presented for the calculation of partition coefficients of solutes in octanol/water. Our algorithm, XLOGP, is based on the summation of atomic contributions and includes correction factors for some intramolecular interactions. Using this method, we calculate the log P of 1831 organic compounds and analyze the derived parameters by(More)
Biomolecular networks have to perform their functions robustly. A robust function may have preferences in the topological structures of the underlying network. We carried out an exhaustive computational analysis on network topologies in relation to a patterning function in Drosophila embryogenesis. We found that whereas the vast majority of topologies can(More)
WRKY proteins, defined by the conserved WRKYGQK sequence, are comprised of a large superfamily of transcription factors identified specifically from the plant kingdom. This superfamily plays important roles in plant disease resistance, abiotic stress, senescence as well as in some developmental processes. In this study, the Arabidopsis WRKY1 was shown to be(More)
A new atom-additive method is presented for calculating octanol/water partition coefficient (log P) of organic compounds. The method, XLOGP v2.0, gives log P values by summing the contributions of component atoms and correction factors. Altogether 90 atom types are used to classify carbon, nitrogen, oxygen, sulfur, phosphorus and halogen atoms, and 10(More)
Drug molecules not only interact with specific targets, but also alter the state and function of the associated biological network. How to design drugs and evaluate their functions at the systems level becomes a key issue in highly efficient and low-side-effect drug design. The arachidonic acid metabolic network is the network that produces inflammatory(More)
BACKGROUND During the past decades, research and development in drug discovery have attracted much attention and efforts. However, only 324 drug targets are known for clinical drugs up to now. Identifying potential drug targets is the first step in the process of modern drug discovery for developing novel therapeutic agents. Therefore, the identification(More)
We have developed a new version (2.0) of the de novo drug design program LigBuilder. With LigBuilder 2.0, the synthesis accessibility of designed compounds can be analyzed, and a cavity detection procedure is implemented to detect the positions and shapes of the binding sites on the surface of a given protein structure and to quantitatively estimate(More)
Trypsin and chymotrypsin are both serine proteases with high sequence and structural similarities, but with different substrate specificity. Previous experiments have demonstrated the critical role of the two loops outside the binding pocket in controlling the specificity of the two enzymes. To understand the mechanism of such a control of specificity by(More)
Elucidating kinetic processes of protein-protein interactions (PPI) helps to understand how basic building blocks affect overall behavior of living systems. In this study, we used structure-based properties to build predictive models for kinetic constants of PPI. A highly diverse PPI dataset, protein-protein kinetic interaction data and structures (PPKIDS),(More)