Nucleic acids modelling

AR Banerjee, A Berzal-Heii anz, J Bond, S Butcher, JA Esteban, JE Heckman, B Sargueil, N Walter, JM Burke. Mol Modeling Nucleic Acids 682 360-368, 1998. 

C Zwieb, K Gowda, N Larsen, E Muller. Mol Modeling Nucleic Acids 682 405-413, 1998. TJ Macke, DA Case. Mol Modeling Nucleic Acids 682 379-392, 1998. 

Qaude, J. B., Suhre, K., Notredame, C., Qaverie, J. M., and Abergel, C. (2004) CaspR a web server for automated molecular replacement using homology modelling. Nucleic Acids Res. 32, W606-609. 

Bisant, D. Maizd, J. (1995). Identification of ribosome binding sites in Escherichia coli using neural network models. Nucleic Acids Res 23,1632-9. 

Five-Membered Unsaturated Heterocycles 1151 Structures of Pyrrole, Furan, and Thiophene 1152 Electrophilic Substitution Reactions of Pyrrole, Furan, and Thiophene 1153 Pyridine, a Six-Membered Heterocycle Electrophilic Substitution of Pyridine Nucleophilic Substitution of Pyridine Fused-Ring Heterocycles 1158 Nucleic Acids and Nucleotides 1160 Structure of Nucleic Acids 1163 Base Pairing in DNA The Watson-Crick Model Nucleic Acids and Heredity 1166 Replication of DNA 1167... 

While this sensor employed only a model nucleic acid probe (poly(A)), it demonstrates the principle of detection of the complementary sequence, the analyte poly(U). Figure 7.9(a) shows that a frequency decrease of 600 Hz was observed following the hybridization step, Step 3, and that this decrease was not observed with a control sensor that did not possess surface-bound poly(A). The sensor exhibits a relatively small frequency change that is superimposed on a large initial resonance frequency (9 MHz), and so S/N is low in addition, difficulties associated with ex situ measurements at constant humidity preclude the use of this device for practical DNA or RNA detection. 

E. Wittenstein, A. Sali. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res. 2000, 28, 250-253. 

Peltoia, H., H. Soderlund, and E. Ukkonen. SEQAID A DNA sequence assembling program based on a mathematical model. Nucleic Acids Res. 1984, 12, 307-321. 

Drysdale, R. A., M. A. Crosby, W. Gelbart, K. Campbell, D. Emmert, B. Matthews, S. Russo, et al. 2005. FlyBase Genes and gene models. Nucleic Acids Res 33, Database Issue D390-5. 

Atha, D., Kasprzak, W., O Connell, C., etal.. Prediction of DNA single-strand conformation polymorphism Analysis by capillary electrophoresis and computerized DNA modeling. Nucleic Acids Res, 29, 4643, 2001. 

Tanaka, K. et al (2013) Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model. Nucleic Acids Res.,... 

W.M. Rockey, F.J. Hernandez, S.Y. Huang, S. Cao, C.A. Howell, Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling, Nucleic Acid Ther. 21 (5) (2011) 299-314. 

Czaudema F, Santel A, Hinz M, Fechtner M, Durieux B, Fisch G, Leenders F, Arnold W, Giese K, Klippel A et al. (2003) Inducible shRNA expression for application in a prostate cancer mouse model. Nucleic Acids Res 31 el27. 

Empirical Approaches to Modeling Nucleic Acid Structure and Dynamics... 

In modeling nucleic acids, physics and chemistry encounter biology. Nucleic acids are molecules and require the mediods of physics and chemistry to understand their structures and dynamics. But one cannot fcs get that nucleic adds are the product of biological evolution and contain within their sequences and in their 3D structures a molecular record of the evolutionary history of the organism in which they are found 113). It is through application of the methods and thought-patterns of all three sciplines that flir er progress can be antidpated. 

Sakakibara, Y. Brown, M. Hughey, R. Mian, I.S. Sjblander, K. Underwood, R.C. Haussler, D. (1994). Stochastic context-free grammars for tRNA modeling. Nucleic Acids Res., Vol. 22, pp. 5112-5120. 

Salzbeig SL, Delcher AL, Kasif S, et al. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 1998 26 544-8. doi 10.1093/nar/26.2.544. 

CO theories have been applied to VCD spectra of model nucleic acids. The NECO theory has been applied to the prediction of the VCD spectra of nucleic acids, using vibrational electric dipole moments derived from semiempirical calculations on the individual nucleic acid bases. The method was successfully applied to the analysis of... 

In 1991 Veal and Wilson reported a specialized molecular mechanics force field for modeling nucleic acids and their complexes with cationic ligands without explicit solvent and... 

Relationships in Modeling Nucleic Acid Ligand Interactions. 

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