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Molecular dynamics (MD) simulations for Zif268 (a zinc-finger-protein binding specifically to the GC-rich DNA)-d(A(1) G(2) C(3) G(4) T(5) G(6) G(7) G(8) C(9) A(10) C(11) )(2) and TATA(ZF) (a zinc-finger-protein recognizing the AT-rich DNA)-d(A(1) C(2) G(3) C(4) T(5) A(6) T(7) A(8) A(9) A(10) A(11) G(12) G(13) )(2) complexes have been performed for(More)
Two artificial water oxidation catalysts, the blue dimer and the Llobet catalyst, have been studied using hybrid DFT methods. The results are compared to those for water oxidation in the natural photosystem II enzyme. Studies on the latter system have now reached a high level of understanding, at present much higher than the one for the artificial systems.(More)
Antifreeze proteins (AFPs) help many organisms protect themselves from freezing in subzero temperatures. The most active AFPs found to date are those from insects, which possess exceptionally regular beta-helical structures. On the ice-binding surface of these proteins, regularly arrayed water molecules are observed within the repeating Thr-Xxx-Thr motif,(More)
The circadian locomotor output cycles kaput (CLOCK), and brain and muscle ARNT-like 1 (BMAL1) proteins are important transcriptional factors of the endogenous circadian clock. The CLOCK and BMAL1 proteins can regulate the transcription-translation activities of the clock-related genes through the DNA binding. The hetero-/homo-dimerization and DNA(More)
Because of their remarkable ability to depress the freezing point of aqueous solutions, antifreeze proteins (AFPs) play a critical role in helping many organisms survive subzero temperatures. The beta-helical insect AFP structures solved to date, consisting of multiple repeating circular loops or coils, are perhaps the most regular protein structures(More)
We have studied the conformational transition of the calmodulin binding domains (CBD) in several calmodulin-binding kinases, in which CBD changes from the disordered state to the ordered state when binding with calmodulin (CaM). Targeted molecular dynamics simulation was used to investigate the binding process of CaM and CBD of CaM-dependent kinase I(More)
The DNA binding and cross-linking modes of a trinuclear platinum complex [Pt(3)Cl(3)(hptab)][ClO(4)](3) (1; hptab = N,N,N',N',N'',N''-hexakis(2-pyridylmethyl)-1,3,5-tris(aminomethyl)benzene) and its dinuclear analogue [Pt(2)Cl(2)(m-tpxa)]Cl(2) (2; m-tpxa = N,N,N',N'-tetra(2-pyridylmethyl)-m-xylylene diamine) are reported and compared. The adducts of 1 and 2(More)
Neural Network (NN) ensemble approach has been an appealing topic in the field of analog circuit fault diagnosis lately. In this paper, a new method for fault diagnosis of analog circuits with tolerance based on NN ensemble method with cross-validation is proposed. Firstly, bias-variance decomposition shows the theoretical guide on how to choose the(More)
Feature extraction is the key process in any pattern recognition issues. There is no exception in analog circuit fault diagnosis, because fault diagnosis is equivalent to pattern recognition issue in nature. In this paper, several feature extraction approaches in the field of analog circuits fault diagnosis are summed up. Newly appeared entropy-based,(More)
The positive cooperativity of the Kemptide substrate or the ATP molecule with the PKA catalytic subunit has been studied by dynamics simulations and free energy calculations on a series of binary and ternary models. The results revealed that the first ATP binding to the PKA catalytic subunit is energetically favorable for the successive Kemptide binding,(More)