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)
Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with(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)
Autophagy, a conserved catabolic process in eukaryotes, mediates the nutrient and energy homeostasis via the degradation of intracellular cytoplasmic materials and organelles by lysosomal machinery. It serves as a recycling mechanism for the rejuvenation of cell contents, which is known to be critical in various biological events, such as starvation(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)
In this work, a systematic protocol is proposed to automatically parametrize the non-polar part of implicit solvent models with polar and non-polar components. The proposed protocol utilizes either the classical Poisson model or the Kohn-Sham density functional theory based polarizable Poisson model for modeling polar solvation free energies. Four sets of(More)
The Diels-Alder [4 + 2] cycloaddition reaction is one of the most powerful and elegant organic synthesis methods for forming 6-membered molecules and has been known for nearly a century. However, whether and how enzymes catalyze this type of reaction is still not completely clear. Here we focus on PyrI4, an enzyme found in the biosynthetic pathway of(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)