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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)
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)
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)
Scoring functions are widely applied to the evaluation of protein-ligand binding in structure-based drug design. We have conducted a comparative assessment of 16 popular scoring functions implemented in main-stream commercial software or released by academic research groups. A set of 195 diverse protein-ligand complexes with high-resolution crystal(More)
Many molecular docking programs are available nowadays, and thus it is of great practical value to evaluate and compare their performance. We have conducted an extensive evaluation of four popular commercial molecular docking programs, including Glide, GOLD, LigandFit, and Surflex. Our test set consists of 195 protein-ligand complexes with high-resolution(More)
MOTIVATION Molecular recognition between biological macromolecules and organic small molecules plays an important role in various life processes. Both structural information and binding data of biomolecular complexes are indispensable for depicting the underlying mechanism in such an event. The PDBbind database was created to collect experimentally measured(More)
Our comparative assessment of scoring functions (CASF) benchmark is created to provide an objective evaluation of current scoring functions. The key idea of CASF is to compare the general performance of scoring functions on a diverse set of protein-ligand complexes. In order to avoid testing scoring functions in the context of molecular docking, the scoring(More)
We have performed a comprehensive analysis of water molecules at the protein-ligand interfaces observed in 392 high-resolution crystal structures. There are a total of 1829 ligand-bound water molecules in these 392 complexes; 18% are surface water molecules, and 72% are interfacial water molecules. The number of ligand-bound water molecules in each complex(More)