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BACKGROUND A good scoring function is essential for molecular docking computations. In conventional scoring functions, energy terms modeling pairwise interactions are cumulatively summed, and the best docking solution is selected. Here, we propose to transform protein-ligand interactions into three-dimensional geometric networks, from which recurring(More)
MOTIVATION Knowledge about the site at which a ligand binds provides an important clue for predicting the function of a protein and is also often a prerequisite for performing docking computations in virtual drug design and screening. We have previously shown that certain ligand-interacting triangles of protein atoms, called protein triangles, tend to occur(More)
LISE is a web server for a novel method for predicting small molecule binding sites on proteins. It differs from a number of servers currently available for such predictions in two aspects. First, rather than relying on knowledge of similar protein structures, identification of surface cavities or estimation of binding energy, LISE computes a score by(More)
The physical interactions between proteins constitute the basis of protein quaternary structures. They dominate many biological processes in living cells. Deciphering the structural features of interacting proteins is essential to understand their cellular functions. Similar to the space of protein tertiary structures in which discrete patterns are clearly(More)
The ligand-binding of membrane receptors on cell surfaces initiates the dynamic process of cross-membrane signal transduction. It is an indispensable part of the signaling network for cells to communicate with external environments. Recent experiments revealed that molecular components in signal transduction are not randomly mixed, but spatially organized(More)
The prediction of β-turn, despite the observation that one out of four residues in protein belongs to this structure element, has attracted considerably less attention comparing to secondary structure predictions. Neural network machine learning is a popular approach to address such a problem of structural bioinformatics. In this paper, we describe a new(More)
Wnt signaling and cadherin-mediated adhesion have been implicated in both processes of embryonic development and the progression of carcinomas. Recent experimental studies revealed that Wnt signaling and cadherin-mediated cell adhesion have close crosstalk with each other. A comprehensive model that investigates the dynamic balance of β-catenins in Wnt(More)
Protein-protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to(More)
The three-dimensional structures of proteins play an essential role in regulating binding between proteins and their partners, offering a direct relationship between structures and functions of proteins. It is widely accepted that the function of a protein can be determined if its structure is similar to other proteins whose functions are known. However, it(More)
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