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MeSH Review

Computer Simulation

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Disease relevance of Computer Simulation


Psychiatry related information on Computer Simulation


High impact information on Computer Simulation

  • Here we report the solution structures and transport mechanisms of hydrated hydroxide, which we obtained from first-principles computer simulations that explicitly treat quantum and thermal fluctuations of all nuclei [7].
  • Most computer simulations of the ocean system in a climate with increasing atmospheric greenhouse-gas concentrations predict a weakening thermohaline circulation in the North Atlantic as the subpolar seas become fresher and warmer, and it is assumed that this signal will be transferred to the deep ocean by the two overflows [8].
  • A polyamide nucleic acid (PNA) was designed by detaching the deoxyribose phosphate backbone of DNA in a computer model and replacing it with an achiral polyamide backbone [9].
  • We then applied the computer model to low-risk and high-risk men and women with total serum cholesterol levels between 5.2 and 7.8 mmol/L (200 and 300 mg/dL) and estimated that, after reducing serum cholesterol levels 5% to 33%, the average life expectancy would increase by 0.03 to 3.16 years [10].
  • Three-dimensional computer models of H-2Dds/peptide complexes, based on the crystallographic structure of the human HLA-B27/peptide complex, showed that the basic residue at position 5 was in position to form a salt bridge with aspartic acid at position 156, a polymorphic residue of the H-2Dd heavy (H) chain [11].

Chemical compound and disease context of Computer Simulation


Biological context of Computer Simulation


Anatomical context of Computer Simulation


Associations of Computer Simulation with chemical compounds

  • Three-dimensional structures for model peptide channels and for a potassium (K+) channel have been combined with computer simulations to permit rigorous exploration of structure-function relations of channels [27].
  • The use of [(13)C]-sodium formate and computer simulations of the spectra identified the 12-line spectrum as arising from the POBN/carbon dioxide anion radical adduct [28].
  • Observation of the size distribution of transient cavities in computer simulations of water, n-hexane, and n-dodecane under benchtop conditions shows that the sizes of cavities are more sharply defined in liquid water but the most-probable-size cavities are about the same size in each of these liquids [29].
  • The observed quinidine APD restitution curve was fitted with a biexponential equation, and computer simulation using the fitted restitution curve reproduced the aperiodic APD seen in the quinidine toxic cells during periodic stimulation [30].
  • However, according to computer simulations of the observed electron paramagnetic resonance spectra, which yield best fits for semiquinone-semiquinone interaction, the possibility that ubi- or flavin semiquinone is the interaction partner appears more likely at this time [31].

Gene context of Computer Simulation

  • Pretest prediction of BRCA1 or BRCA2 mutation by risk counselors and the computer model BRCAPRO [32].
  • Pretest prediction of BRCA1 or BRCA2 mutation by risk counselors and the computer model BRCAPRO [33].
  • A series of computer models based on the RANTES/CCL5 promoter were generated to represent the organization of these functional elements [34].
  • According to the computer model, Arg78, Arg130, and Arg257 may be important for SULT1A1 catalytic activity [35].
  • Moreover, a computer model of M195 was used to identify several framework amino acids that are likely to interact with the complementarity-determining regions, and these residues were also retained in the humanized antibodies [36].

Analytical, diagnostic and therapeutic context of Computer Simulation


  1. Evidence for a multiple random coupling mechanism in the alpha-ketoglutarate dehydrogenase multienzyme complex of Escherichia coli: a computer model analysis. Hackert, M.L., Oliver, R.M., Reed, L.J. Proc. Natl. Acad. Sci. U.S.A. (1983) [Pubmed]
  2. AMP deamination delays muscle acidification during heavy exercise and hypoxia. Korzeniewski, B. J. Biol. Chem. (2006) [Pubmed]
  3. Carbonyl carbon transverse relaxation dispersion measurements and ms-micros timescale motion in a protein hydrogen bond network. Ishima, R., Baber, J., Louis, J.M., Torchia, D.A. J. Biomol. NMR (2004) [Pubmed]
  4. Progression criteria for cancer antigen 15.3 and carcinoembryonic antigen in metastatic breast cancer compared by computer simulation of marker data. Sölétormos, G., Hyltoft Petersen, P., Dombernowsky, P. Clin. Chem. (2000) [Pubmed]
  5. Molecular basis for microbial adhesion to geochemical surfaces: computer simulation of Pseudomonas aeruginosa adhesion to goethite. Shroll, R.M., Straatsma, T.P. Biophys. J. (2003) [Pubmed]
  6. Decision-making in refractory epilepsy: an analysis based on computer simulation. Ward, C.D. J. Neurol. Neurosurg. Psychiatr. (1986) [Pubmed]
  7. The nature and transport mechanism of hydrated hydroxide ions in aqueous solution. Tuckerman, M.E., Marx, D., Parrinello, M. Nature (2002) [Pubmed]
  8. Rapid freshening of the deep North Atlantic Ocean over the past four decades. Dickson, B., Yashayaev, I., Meincke, J., Turrell, B., Dye, S., Holfort, J. Nature (2002) [Pubmed]
  9. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Nielsen, P.E., Egholm, M., Berg, R.H., Buchardt, O. Science (1991) [Pubmed]
  10. The benefits of treating hyperlipidemia to prevent coronary heart disease. Estimating changes in life expectancy and morbidity. Grover, S.A., Abrahamowicz, M., Joseph, L., Brewer, C., Coupal, L., Suissa, S. JAMA (1992) [Pubmed]
  11. H-2Dd exploits a four residue peptide binding motif. Corr, M., Boyd, L.F., Padlan, E.A., Margulies, D.H. J. Exp. Med. (1993) [Pubmed]
  12. Simulation of corneal neovascularization by inverted diffusion limited aggregation. Landini, G., Misson, G. Invest. Ophthalmol. Vis. Sci. (1993) [Pubmed]
  13. Course of acute renal failure studied by a model of creatinine kinetics. Moran, S.M., Myers, B.D. Kidney Int. (1985) [Pubmed]
  14. Control of the threonine-synthesis pathway in Escherichia coli: a theoretical and experimental approach. Chassagnole, C., Fell, D.A., Raïs, B., Kudla, B., Mazat, J.P. Biochem. J. (2001) [Pubmed]
  15. Compensatory mutations, antibiotic resistance and the population genetics of adaptive evolution in bacteria. Levin, B.R., Perrot, V., Walker, N. Genetics (2000) [Pubmed]
  16. Carbon monoxide-induced arterial wall hypoxia and atherosclerosis. Schneiderman, G., Goldstick, T.K. Atherosclerosis (1978) [Pubmed]
  17. Human genetics, animal models and computer simulations for studying hypertension. Takahashi, N., Smithies, O. Trends Genet. (2004) [Pubmed]
  18. A computer model analysis of the active-site coupling mechanism in the pyruvate dehydrogenase multienzyme complex of Escherichia coli. Hackert, M.L., Oliver, R.M., Reed, L.J. Proc. Natl. Acad. Sci. U.S.A. (1983) [Pubmed]
  19. Detection of tandem duplications and implications for linkage analysis. Matise, T.C., Chakravarti, A., Patel, P.I., Lupski, J.R., Nelis, E., Timmerman, V., Van Broeckhoven, C., Weeks, D.E. Am. J. Hum. Genet. (1994) [Pubmed]
  20. Age-dependent tetrahydrothiophenium ion formation in young children and adults receiving high-dose busulfan. Gibbs, J.P., Murray, G., Risler, L., Chien, J.Y., Dev, R., Slattery, J.T. Cancer Res. (1997) [Pubmed]
  21. On the mechanism of sodium- and potassium-activated adenosine triphosphatase. Time course of intermediary steps examined by computer simulation of transient kinetics. Mårdh, S., Lindahl, S. J. Biol. Chem. (1977) [Pubmed]
  22. Relative activity of structural analogues of amsacrine against human leukemia cell lines containing amsacrine-sensitive or -resistant forms of topoisomerase II: use of computer simulations in new drug development. Zwelling, L.A., Mitchell, M.J., Satitpunwaycha, P., Mayes, J., Altschuler, E., Hinds, M., Baguley, B.C. Cancer Res. (1992) [Pubmed]
  23. The simple model of adipocyte hexose transport. Kinetic features, effect of insulin, and network thermodynamic computer simulations. May, J.M., Mikulecky, D.C. J. Biol. Chem. (1982) [Pubmed]
  24. Sensory gating in a computer model of the CA3 neural network of the hippocampus. Flach, K.A., Adler, L.E., Gerhardt, G.A., Miller, C., Bickford, P., MacGregor, R.J. Biol. Psychiatry (1996) [Pubmed]
  25. 13C n.m.r. isotopomer and computer-simulation studies of the non-oxidative pentose phosphate pathway of human erythrocytes. Berthon, H.A., Bubb, W.A., Kuchel, P.W. Biochem. J. (1993) [Pubmed]
  26. Quantification of glucose transport and phosphorylation in human skeletal muscle using FDG PET. Reinhardt, M., Beu, M., Vosberg, H., Herzog, H., Hübinger, A., Reinauer, H., Müller-Gärtner, H.W. J. Nucl. Med. (1999) [Pubmed]
  27. Simulations of ion channels--watching ions and water move. Sansom, M.S., Shrivastava, I.H., Ranatunga, K.M., Smith, G.R. Trends Biochem. Sci. (2000) [Pubmed]
  28. An in vivo ESR spin-trapping study: free radical generation in rats from formate intoxication--role of the Fenton reaction. Dikalova, A.E., Kadiiska, M.B., Mason, R.P. Proc. Natl. Acad. Sci. U.S.A. (2001) [Pubmed]
  29. Theory of hydrophobicity: transient cavities in molecular liquids. Pratt, L.R., Pohorille, A. Proc. Natl. Acad. Sci. U.S.A. (1992) [Pubmed]
  30. Action potential alternans and irregular dynamics in quinidine-intoxicated ventricular muscle cells. Implications for ventricular proarrhythmia. Karagueuzian, H.S., Khan, S.S., Hong, K., Kobayashi, Y., Denton, T., Mandel, W.J., Diamond, G.A. Circulation (1993) [Pubmed]
  31. Interaction of ubisemiquinone with a paramagnetic component in heart tissue. Ruzicka, F.J., Beinert, H., Schepler, K.L., Dunham, W.R., Sands, R.H. Proc. Natl. Acad. Sci. U.S.A. (1975) [Pubmed]
  32. Pretest prediction of BRCA1 or BRCA2 mutation by risk counselors and the computer model BRCAPRO. Euhus, D.M., Smith, K.C., Robinson, L., Stucky, A., Olopade, O.I., Cummings, S., Garber, J.E., Chittenden, A., Mills, G.B., Rieger, P., Esserman, L., Crawford, B., Hughes, K.S., Roche, C.A., Ganz, P.A., Seldon, J., Fabian, C.J., Klemp, J., Tomlinson, G. J. Natl. Cancer Inst. (2002) [Pubmed]
  33. Pretest prediction of BRCA1 or BRCA2 mutation by risk counselors and the computer model BRCAPRO. Bonadona, V., Sinilnikova, O.M., Lenoir, G.M., Lasset, C. J. Natl. Cancer Inst. (2002) [Pubmed]
  34. Molecular and in silico characterization of a promoter module and C/EBP element that mediate LPS-induced RANTES/CCL5 expression in monocytic cells. Fessele, S., Boehlk, S., Mojaat, A., Miyamoto, N.G., Werner, T., Nelson, E.L., Schlondorff, D., Nelson, P.J. FASEB J. (2001) [Pubmed]
  35. Arginine residues in the active site of human phenol sulfotransferase (SULT1A1). Chen, G., Chen, X. J. Biol. Chem. (2003) [Pubmed]
  36. Chimeric and humanized antibodies with specificity for the CD33 antigen. Co, M.S., Avdalovic, N.M., Caron, P.C., Avdalovic, M.V., Scheinberg, D.A., Queen, C. J. Immunol. (1992) [Pubmed]
  37. Strategies for hematopoietic stem cell gene therapy: insights from computer simulation studies. Abkowitz, J.L., Catlin, S.N., Guttorp, P. Blood (1997) [Pubmed]
  38. Structure of tuberoinfundibular peptide of 39 residues. Piserchio, A., Usdin, T., Mierke, D.F. J. Biol. Chem. (2000) [Pubmed]
  39. Neutron diffraction and computer simulation studies of D-xylose. Mason, P.E., Neilson, G.W., Enderby, J.E., Saboungi, M.L., Brady, J.W. J. Am. Chem. Soc. (2005) [Pubmed]
  40. Gallamine disposition in open-heart surgery involving cardiopulmonary bypass. Shanks, C.A., Ramzan, I.M., Walker, J.S., Brown, K.F. Clin. Pharmacol. Ther. (1983) [Pubmed]
  41. Oxidative titrations of reduced cytochrome aa3: influence of cytochrome c and carbon monoxide on the midpoint potential values. Schroedl, N.A., Hartzell, C.R. Biochemistry (1977) [Pubmed]
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