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Computational structure prediction, including de novo and homology modeling, is an important tool for membrane protein studies. Developing an accurate scoring function that can be used for structure discrimination and assessment remains a challenge. In our previous work, we have analyzed a set of high-resolution membrane protein structures using the network approach developed in our lab and proposed...
Membrane protein and its interaction network has become a novel research direction in bioinformatics. Multiple researches on these interactions can improve our understanding of diseases and provide the basis to revolutionize therapeutic treatments. In this paper, a novel membrane protein interaction network simulator is proposed for system biology studies by intelligent multi-agents method. We consider...
The protein folding problem is a central issue in Bioinformatics. It still represents a challenge for both Biology and Computer Science. Proteins are composed by up to hundreds of amino acids, each one with tenths of atoms. In general, a full representation of such structure and its interacting elements precludes computational simulations. This work proposes a molecular model for representing protein...
System biology is one of the leading edge cross-subjects which requires the cooperation between computer science and biological science. Abstracting complex life phenomenon, like metabolic or transcription regulation pathway, into networks to simulate these processes is one of the hotspots in System biological research. In this paper, we construct a network to simulate one of the most concerned areas...
We present an individual agent-based model of transcription factor binding to DNA. We explicitly represent every single transcription factor and every single binding site in our simulation. In order to obtain statistically significant results from our model, it is necessary to perform a large number of simulations. This has previously been hampered by the computational demands of individual agent-based...
The available data of complete ordering of genes on each chromosome of organisms is increasing thank to the research in gene hunting and annotation. Researchers like evolutionary biologists and computer scientists are greatly interested in gene order data because it make possible to resolve the ancient branches to fill the tree of life. Inversion based distance metric and the so called DCJ (double-cut-and-join)...
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