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We developed a method for fast decoy clustering by using reference root-mean-squared distance (rRMSD) rather than commonly used pairwise RMSD (pRMSD) values. For 41 proteins with 2000 decoys each, the computing efficiency increases nine times without a significant change in the accuracy of near-native selections. Tests on additional protein decoys based on different reference conformations confirmed this result. Further analysis indicates that the pRMSD and rRMSD values are highly correlated (with an average correlation coefficient of 0.82) and the clusters obtained from pRMSD and rRMSD values are highly similar (the representative structures of the top five largest clusters from the two methods are 74% identical). SCUD (Structure ClUstering of Decoys) with an automatic cutoff value is available at http://theory.med.buffalo.edu. 相似文献
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Frontispiece: Whole‐Cell Biotransformation of Benzene to Phenol Catalysed by Intracellular Cytochrome P450BM3 Activated by External Additives 下载免费PDF全文
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Md Tamjidul Hoque Yuedong Yang Avdesh Mishra Yaoqi Zhou 《Journal of computational chemistry》2016,37(12):1119-1124
An important unsolved problem in molecular and structural biology is the protein folding and structure prediction problem. One major bottleneck for solving this is the lack of an accurate energy to discriminate near‐native conformations against other possible conformations. Here we have developed sDFIRE energy function, which is an optimized linear combination of DFIRE (the Distance‐scaled Finite Ideal gas Reference state based Energy), the orientation dependent (polar‐polar and polar‐nonpolar) statistical potentials, and the matching scores between predicted and model structural properties including predicted main‐chain torsion angles and solvent accessible surface area. The weights for these scoring terms are optimized by three widely used decoy sets consisting of a total of 134 proteins. Independent tests on CASP8 and CASP9 decoy sets indicate that sDFIRE outperforms other state‐of‐the‐art energy functions in selecting near native structures and in the Pearson's correlation coefficient between the energy score and structural accuracy of the model (measured by TM‐score). © 2016 Wiley Periodicals, Inc. 相似文献
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脉冲多普勒(PD)雷达由于其优越的性能在机载雷达中得到广泛应用。对PD雷达的信号特征进行了分析,探讨了可能的干扰途径,研究了噪声压制干扰、距离欺骗干扰、速度欺骗干扰及假目标干扰对PD雷达的作用机理,提出了干扰PD雷达的工程实现方法。 相似文献
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