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Biomolecular energy calculations using transputer technology

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We report an application of current parallel processing transputer technology which has readily achieved a 25-fold reduction in computational time of peptide-solvent interactions.

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  1. Blaney JM, Weiner PK, Dearing A, Kollman PA, Jorgensen EC, Oatley SJ, Burridge JM, Blake CCF (1982) Molecular mechanics simulation of protein-ligand interactions: Binding of thyroid hormone analogues to prealbumin. J Am Chem Soc 104:6424–6434

  2. Goodfellow JM, Thanki N, Thornton JM (1989) Preliminary analysis of water molecule distributions in proteins. Mol Simul 3:167–182

  3. Hockney RW, Jesshope CR (1988) Parallel computers 2 architecture, programming and algorithms. Adam Hilger, Bristol

  4. Jones G, Goldsmith M (1988) Programming in Occam 2. Prentice Hall, Hemel Hempstead

  5. Levitt M (1974) Energy refinement of hen egg-white lysozyme. J Mol Biol 82:393–420

  6. Levitt M (1978) How many base-pairs per turn does DNA have in solution and in Chromatin? Some theoretical calculation. Proc Natl Acad Sci USA 75:640–644

  7. Powell MJD (1964) An efficient method for finding the minimum of a function of several variables without calculating derivatives. Comput J 7:155–163

  8. Thanki N, Thornton JM, Goodfellow JM (1988) Distributions of water around amino acid residues in proteins. J Mol Biol 202:637–659

  9. Vovelle F, Goodfellow JM (1986) The effect of different force fields on the probable hydration sites of urea. In: Sarma RH, Sarma MH (eds) Biomolecular stereodynamics III. Adenine Press, New York

  10. Vovelle F, Goodfellow JM (1989) Modelling of DNA interactions. In: Beveridge DL, Lavery R (eds) Theoretical chemistry and molecular biophysics: A comprehensive survey. Adenine Press, New York

  11. Vovelle F, Elliott RJ, Goodfellow JM (1989) Solvent bridging sites in A- and B-DNA helices. Int J Biol Macromol 11: 39–42

  12. Weiner SJ, Kollman PA, Nguyen DT, Case DA (1986) An all atom force field for simulation of proteins and nucleic acids. J Comp Chem 7:230–252

  13. Wipff G, Dearing A, Weiner PK, Blaney JM, Kollman PA (1983) Molecular mechanics studies of enzyme-substrate interactions: The interaction of L- and D-N-Acetyltryptophanamide with α-chymotrypsin. J Am Chem Soc 105:997–1010

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Goodfellow, J.M., Vovelle, F. Biomolecular energy calculations using transputer technology. Eur Biophys J 17, 167–172 (1989). https://doi.org/10.1007/BF00254771

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Key words

  • Transputer
  • Occam 2
  • tyrosine
  • peptide
  • energy
  • minimisation