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is produced in cells (mastocides) from the histidine amino acid. The γ-amino oil acid AC is produced in the brain substance and probably plays a role of the mediator or inhibitor of pulses. Many biomolecules (BM) are composed not only by hydrophilic, but also by hydrophobic groups, in the vicinity of which the water-water (or blood plasma) interaction is expected to be present even in the zeroth approximation. We present results of the Monte-Carlo calculating the cluster consisting of the serotonine ST (histamine HM) molecules and 100 molecules of water. All relevant interaction potentials are obtained by means of quantum calculation [1]. The water-water interaction potential was found by Matsouka etal by CI method. The BM-water interaction potential was obtained in the SCF approximation Calculation is carried out at T=300K; All molecules are treated as rigid. The results for interaction energies are given below in table: Potential, kJmol-1 Neutral molecule zwitterion Water-water -27.7 ± 0.8 -27.2 ± 0.7 ST-water -59.5 ±2.0 -348.5 ± 15.0 HM-water -37,8 ±2.0 -178,4 ± 15.0 The zwitterion appears as expected to be strongly favoured with respect to neutral molecule. The HM in the “zwitterion” more intensively (on the order) catalyses the gastric juice secretion and secretion from other endocrine glands. The similar situation is with action of the HM in the inflammatory and allergic reactions with further increasing vessel walls permeability and action of the ST with further blood-vessel narrowing in places of the trombocites decay [2]. We at first consider the possibilities of laser and neutron capture action on different of molecules, including an analysis of Szilard-Chalmers (n,γ), (n,n), Mössbauer and GM [2] effects. Some new bio-nano-technologies are analysed. References: [1] E. Clementi et al, Gazz. Chim. Ital. 108 (1978) 157-174; J. Am.Chem. Soc. 99 (1977) 5531-42 ; A.Glushkov, Journ.Struct. Chem. 34 (1993) 3-10; 31 (1990) 9-15; 32 (1992) 11-16; Rus. J. Phys. Chem. 66 (1992) 1259-76; 66 (1992) 589-596; A. Glushkov, S.Malinovskaya, Rus. J. Phys. Chem. 62 (1988) 100-106; 65 (1991) 2970-78; [2] A. Glushkov, S.Malinovskaya, In: New projects and new lines of research in nuclear physics. Eds. G.Fazio and F.Hanappe, Singapore : World Scientific.-2003.-P.242-250 ; Int.J.Quant.Chem 99 (2004) 889-896 ; 104 (2005) 496-500; Europ.Phys.Journ. 160 (2008) 195-208 ; Mol.Phys. (UK), 106 (2008) 1257-1262 ; A. Glushkov, Comput. Life Sciences (Springer), to be submitted (2009); PL-005 Understanding disease-associated amino acid mutations with computational models Shen, Bairong PL-006 Physico– chemical principles governing biological processes
Lim., Carmay Our research interests are to unravel the underlying physico–chemical principles governing biological processes, develop new methods, as required, along the way and use the above principles and methods to design molecules with potential therapeutic utility. This talk will provide an example of work in these three areas by unraveling the physical basis underlying structural and catalytic Zn−binding sites in proteins. References: 1.“Physical Basis of Structural and Catalytic Zn−binding Sites in Proteins”. Yu-Ming Lee & Carmay Lim*, J. Mol. Biol. (2008) 379:545–553. 2.“Metal Binding Affinity and Selectivity in Metalloproteins: Insights from Computational Studies”. Todor Dudev & Carmay Lim*, Annual Reviews in Biophysics. (2008) 37:97–116 3.“Effect of Carboxylate–Binding Mode on Metal Binding/Selectivity and Function in Proteins”. Todor Dudev & Carmay Lim*, Acc. Chem. Res. (2007) 40: 85−93. 4.“Principles Governing Mg, Ca, and Zn Binding and Selectivity in Proteins”. Todor Dudev* & Carmay Lim*, Chemical Reviews (2003) 103: 773–787. PL-007 A novel Locally Linear Embedding and Wavelet Transform based encoding method for prediction of MHC-II binding affinity Juan Liu 1* , Qingjiao Li 1 , Wen Zhang 1 1 School of Computer Science, Wuhan University, Wuhan 430079, China * Corresponding author The binding between peptides and MHC molecules is an important event to the cellular immunity against pathogens. The binding peptides are recognized as the epitopes, which are useful for the epitope-based vaccine design. Accurate prediction of the MHC-II binding peptides has long been a challenge in bioinformatics. Recently, most researchers are interested in predicting the binding affinity instead of categorizing peptides as “binders” or “non-binders”. In this paper, we introduced a novel encoding scheme based on Locally Linear Embedding (LLE) and Wavelet Transform (WT), in which important amino acid properties were firstly selected from all properties (described in AAindex database) by using LLE, and then amino acids of peptides were replaced with these novel properties. Further, WT was adopted to extract the frequency attributes of the numerical sequences; thereby the peptides were transformed into homogeneous-length vectors. Finally, Support Vector machine Regression (SVR) was used to make quantitative prediction models based on these numerical vectors. When applied to the 17 datasets from IEDB database, our encoding scheme produced consistently better performance than other encoding schemes, indicating that our encoding scheme is an effective tool for the prediction of MHC-II binding affinity. Keywords: Cellular immunity; Epitopes; MHC-II binding affinity; Support Vector machine Regression; Locally Linear Embedding; Wavelet Transform; Encoding method PL-008 Nakai, Kenta PL-009 Nanopolaritonics: the interaction between molecules and near-field light. Daniel Neuhauser,
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