Journal of Computer-Aided Molecular Design

, Volume 26, Issue 1, pp 103–105 | Cite as

The character of molecular modeling

  • Anthony Nicholls


In asking what progress might occur in molecular modeling in the next 25 years it is worth asking what progress has been made in the last twenty-five. In doing so it is hard to be optimistic for the future of the field unless a greater commitment is made to basic science.


Structure-based design Docking Proteins Scientific method 


  1. 1.
    Feynman RP (2001) The character of physical law (Messenger Lectures, 1964). The MIT Press, Cambridge. ISBN-10: 0262560038Google Scholar
  2. 2.
    Quine WV (1977) Natural kinds in ontological relativity and other essays. Columbia University Press, New YorkGoogle Scholar
  3. 3.
    Ericsson KA, Charness N, Feltovich PJ, Hoffman RR (eds.) (2006) The Cambridge handbook of expertise and expert performance. Cambridge University Press, Cambridge. ISBN-10: 0521600812Google Scholar
  4. 4.
    Skillman AG (ed.) (2008) Special issue: SAMPL2: tautomer ratio and solvation energy challenge, JCAMD, vol. 24, No. 4 (2010). J Med Chem 51(4):769–779Google Scholar
  5. 5.
    Nicholls A, Mobley DL, Guthrie JP, Chodera JD, Bayly CI, Cooper MD, Pande VS (2008) Predicting small-molecule solvation free energies: an informal blind test for computational chemistryGoogle Scholar
  6. 6.
    Day GM, Cooper TG, Cruz-Cabeza AJ, Hejczykm KE, Ammon HL, Boerrigter SXM, Tan JS, Della Valle RG, Venuti E, Jose J, Gadre SR, Desiraju GR, Thakur TS, van Eijck BP, Facelli JC, Bazterra VE, Ferraro MB, Hofmann DWM, Neumann MA, Leusen FJJ, Kendrick J, Price SL, Misquitta AJ, Karamertzanis PG, Welch GWA, Scheraga HA, Arnautova YA, Schmidt MU, van de Streek J, Wolf AK, Schweizerr B, Cryst A (2009) Significant progress in predicting the crystal structures of small organic molecules—a report on the fourth blind test. B65Google Scholar
  7. 7.
    Voelz VA, Bowman GR, Beauchamp K, Pande VS (2010) Molecular simulation of ab initio protein folding for a millisecond folder NTL9 (1–39). J Am Chem Soc 132(5):1526–1528CrossRefGoogle Scholar
  8. 8.
    Ucisik MN, Dashti DS, Faver JC, Merz KM Jr (2011) Pairwise additivity of energy components in protein-ligand binding: the HIV II protease-indinavir case. J Chem Phys 135:085101Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.OpenEye Scientific Software, Inc.Santa FeUSA

Personalised recommendations