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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)
Tillering in rice (Oryza sativa) is one of the most important agronomic traits that determine grain yields. Previous studies on rice tillering mutants have shown that the outgrowth of tiller buds in rice is regulated by a carotenoid-derived MAX/RMS/D (more axillary branching) pathway, which may be conserved in higher plants. Strigolactones, a group of(More)
The recessive tall rice (Oryza sativa) mutant elongated uppermost internode (eui) is morphologically normal until its final internode elongates drastically at the heading stage. The stage-specific developmental effect of the eui mutation has been used in the breeding of hybrid rice to improve the performance of heading in male sterile cultivars. We found(More)
Eleven popular scoring functions have been tested on 100 protein-ligand complexes to evaluate their abilities to reproduce experimentally determined structures and binding affinities. They include four scoring functions implemented in the LigFit module in Cerius2 (LigScore, PLP, PMF, and LUDI), four scoring functions implemented in the CScore module in(More)
We have developed a new method, i.e., XLOGP3, for logP computation. XLOGP3 predicts the logP value of a query compound by using the known logP value of a reference compound as a starting point. The difference in the logP values of the query compound and the reference compound is then estimated by an additive model. The additive model implemented in XLOGP3(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)
The X-linked inhibitor of apoptosis protein (XIAP) is a potent cellular inhibitor of apoptosis. Designing small-molecule inhibitors that target the BIR3 domain of XIAP, where Smac/DIABLO (second mitochondria-derived activator of caspase/direct IAP-binding protein with low pI) and caspase-9 bind, is a promising strategy for inhibiting the antiapoptotic(More)
The X-linked inhibitor of apoptosis (XIAP) is a promising new molecular target for the design of novel anticancer drugs aiming at overcoming apoptosis-resistance of cancer cells to chemotherapeutic agents and radiation therapy. Recent studies demonstrated that the BIR3 domain of XIAP where caspase-9 and Smac proteins bind is an attractive site for designing(More)
This study focused on the screening of small-molecule inhibitors that target signal transducers and activators of transcription 3 (Stat3) in human breast carcinoma. The constitutive activation of Stat3 is frequently detected in human breast cancer cell lines as well as clinical breast cancer specimens and may play an important role in the oncogenesis of(More)
We have screened the entire Protein Data Bank (Release No. 103, January 2003) and identified 5671 protein-ligand complexes out of 19 621 experimental structures. A systematic examination of the primary references of these entries has led to a collection of binding affinity data (K(d), K(i), and IC(50)) for a total of 1359 complexes. The outcomes of this(More)