What is X-Score? X-Score is a "scoring function", which has its major applications to structure-based drug design studies. It computes a binding score for a given protein-ligand complex structure, and this binding score correlates to experimental binding constants well. Three individual empirical scoring functions have been implemented in this program, which are named as HPScore, HMScore, and HSScore, respectively.
What is XLOGP3? We have developed a new method, i.e. XLOGP3, for the fast calculation of logP. Its predecessor, XLOGP and XLOGP2 (ref. 1 and 2), which are atom-additive methods with well-defined correction factors, have already gained their popularity in this field for their applicability and fair accuracy. As the latest release of this series, XLOGP3 has implemented an optimized atom typing scheme and is calibrated on a much larger training set.
What is KGS2? KGS2 is a software patch of scoring functions, which has its objective to improve the prediction accuracy of scoring functions. Our basic assumption is that molecular systems with similar structures have similar properties, a strategy that has been applied successfully to the computation of some physicochemical properties such as partition coefficient and water solubility. Accordingly, the unknown binding affinity of a given complex can be estimated more reliably from the known binding affinity of a reference complex, which shares a similar pattern of protein-ligand interactions with the query complex.
What is PredHydSite? PredHydSite is used to predict potential water molecules in the protein binding pocket. It contains two modules, wsite and wsiteGen. The former uses the bound ligand to set the grid box in the binding pocket. It can used to predict water molecules in the pocket, with or without the ligand. The latter uses a known point (x, y, z) or a bound ligand to set the grid box around the binding pocket.
What is I-interpert? I-interpret is an efficient "interpreter" of chemical structures, which can automatically interpret the chemical structure of a given organic molecule merely from its essential structural information, including element identities and three-dimensional coordinates of its component atoms. I-interpret was tested on thousands of small organic molecules and achieved a high success rate in interpreting their correct chemical structures. It can serve as a valuable tool for processing chemical structures in various molecular modeling studies, especially for high-throughput projects such as processing large databases of organic molecules.
What is XLOGS? A new method called XLOGS for logS computation is developed. It predicts the logS of a query compound by using the known logS of appropriate reference compound as a starting point. The difference in the logS of the query compound and the reference compound is then estimated by an additive model. A total of 83 atom/group types and three correction factors are as descriptors in XLOGS.
What is AutoT&T? The Automatic Tailoring and Transplanting (AutoT&T) method is developed as a versatile computational tool for lead optimization as well as lead discovery in molecular-targeted drug design. This method detects suitable fragments on reference molecules, e.g. outputs of a virtual screening job in prior, and then transplants them onto the given lead compound to generate new ligand molecules. Then, binding affinities, synthetic feasibilities and drug-likeness properties are evaluated to select the promising candidates for further consideration.
What is AutoCIP? Protein–protein interactions are observed in various biological processes. They are important for understanding the underlying molecular mechanisms and can be potential targets for developing small-molecule regulators of such processes. Previous studies suggest that certain residues on protein–protein binding interfaces are "hot spots". As an extension to this concept, we have developed a residue-based method to identify the characteristic interaction patterns (CIPs) on protein–protein binding interfaces, in which each pattern is a cluster of four contacting residues.
What is X-ToolBox? X-ToolBox consists of some tool programs, e.g. predicting protonation status, fix PDB file of protein, fix Mol2 and SDF file of small ligand.
What is PDBbind-CN database? The aim of the PDBbind database is to provide a comprehensive collection of the experimentally measured binding affinity data for all types of biomolecular complexes deposited in the Protein Data Bank (PDB). It thus provides an essential linkage between energetic and structural information of these complexes, which is helpful for various computational and statistical studies on molecular recognition occurred in biological systems.

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