Zhixiong Zhao

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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)
Scoring functions are often applied in combination with molecular docking methods to predict ligand binding poses and ligand binding affinities or to identify active compounds through virtual screening. An objective benchmark for assessing the performance of current scoring functions is expected to provide practical guidance for the users to make smart(More)
Persistent homology has been advocated as a new strategy for the topological simplification of complex data. However, it is computationally intractable for large data sets. In this work, we introduce multiresolution persistent homology for tackling large datasets. Our basic idea is to match the resolution with the scale of interest so as to create a(More)
Most of the existing literature which has entirely focused on clustering nodes in large-scale networks. To discover multi-scale overlapping communities quickly, we propose a highly efficient multi-resolution link community detection algorithm to detect the link communities in massive networks based on the idea of edge labeling. First, we will get the node(More)
We present a feature functional theory-binding predictor (FFT-BP) for the protein-ligand binding affinity prediction. The underpinning assumptions of FFT-BP are as follows: i) representability: there exists a microscopic feature vector that can uniquely characterize and distinguish one protein-ligand complex from another; ii) feature-function relationship:(More)
In the last decade, a large number of graph mining algorithms have been proposed. But there are only a few descriptions about community structure. The communities in different network have different structure, and even in the same network the communities may have different community structure. If we can't describe the community structure reasonably, it is(More)
UNLABELLED In structure-based drug design, automated de novo design methods are helpful tools for lead discovery as well as lead optimization. In a previous study ( J. Chem. Inf. MODEL 2011 , 51 , 1474 - 1491 ) we reported a new de novo design method, namely, Automatic Tailoring and Transplanting (AutoT&T). It overcomes some intrinsic problems in(More)
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