List of publications J.A.C. Rullmann

1. W.F. van Gunsteren, H.J.C. Berendsen and J.A.C. Rullmann,
   Inclusion of reaction fields in molecular dynamics: application to liquid water,
   Faraday Disc. Chem. Soc. 66, 58-70 (1978)
   

2. W.F. van Gunsteren, H.J.C. Berendsen and J.A.C. Rullmann,
   Stochastic dynamics for molecules with constraints; Brownian dynamics of n-alkanes,
   Mol. Phys. 44, 69-95 (1981)
   

3. J.B.W. Morsink, J.A.C. Rullmann and D.A. Wiersma,
   Laser-induced energy transfer in solids,
   J. Luminescence 24/25, 767-772 (1981)
   

4. J.A.C. Rullmann and P.Th. van Duijnen,
   Analysis of discrete and continuum dielectric models; application to the calculation of protonation energies in solution,
   Mol. Phys. 61, 293-311 (1987)
   

5. J.A.C. Rullmann and P.Th. van Duijnen,
   A polarizable water model for calculation of hydration energies,
   Mol. Phys. 63, 451-475 (1988); erratum: 64, 557 (1988)
   

6. R. Boelens, R.M.J.N. Lamerichs, J.A.C. Rullmann, J.H. van Boom and R. Kaptein,
   The interaction of lac repressor headpiece with its operator: an NMR view,
   Protein Seq. Data Anal. 1, 487-498 (1988).
   

7. J.A.C. Rullmann,
   Modelling molecular interactions in proteins and water; between quantum chemistry and classical electrostatics,
   Doctoral thesis, University of Groningen (1988).
   

8. J.A.C. Rullmann,
   Recente ontwikkelingen in Computational Chemistry,
   Chemisch Magazine, pp. 754-755 (1988).
   

9. J.A.C. Rullmann, M.N. Bellido and P.Th. van Duijnen,
   The active site of papain: all-atom study of interactions with protein matrix and solvent,
   J. Mol. Biol. 206, 101-118 (1989).
   

10. M.N. Bellido and J.A.C. Rullmann,
    Atomic charge models for polypeptides derived from ab initio calculations,
    J. Comp. Chem. 10, 479-487 (1989).
    

11. J.A.C. Rullmann, R. Boelens and R. Kaptein,
    NMR based docking studies of lac repressor headpiece on a lac operator fragment,
    in: DNA-Protein Interactions in Transcription, UCLA Symposia on Molecular and Cellular Biology, new series, volume 95, J. Gralla (ed.), Alan R. Liss, Inc., New York, pp. 11-24 (1989).
    

12. R. Kaptein, R. Boelens and J.A.C. Rullmann,
    Biomolecular structures from NMR: Computational aspects,
    in: Computer Simulation of Biomolecular Systems, W.F. van Gunsteren and P.K. Weiner (eds.), Escom Science Publishers, Leiden, pp. 194-216 (1989).
    

13. J.A.C. Rullmann, R. Boelens, R.M.J.N. Lamerichs, G.W. Vuister and R. Kaptein,
    NMR studies of proteins and protein-DNA interactions,
    in: Modelling of Molecular Structures and Properties (Proceedings of the 44th International Meeting of Physical Chemistry, Nancy), Studies in Physical and Theoretical Chemistry, vol. 71, J.-L. Rivail (ed.), Elsevier, pp. 661-678 (1990).
    

14. J.A.C. Rullmann, R.M.J.N. Lamerichs, C. Gonzalez, T.M.G. Koning, R. Boelens and R. Kaptein,
    Structure determination from NMR using a relaxation matrix approach; application to the solution structure of crambin,
    in: Modelling of Molecular Structures and Properties (Proceedings of the 44th International Meeting of Physical Chemistry, Nancy), Studies in Physical and Theoretical Chemistry, vol. 71, J.-L. Rivail (ed.), Elsevier, pp. 703-710 (1990).
    

15. R.Kaptein, R.M.J.N. Lamerichs, R. Boelens and J.A.C. Rullmann,
    Two-dimensional NMR study of a protein-DNA complex. Lac repressor headpiece - operator interaction,
    Biochemical Pharmacology 40, 89-96 (1990).
    

16. J.A.C. Rullmann, R. Boelens en R. Kaptein,
    "De struktuur van een eiwit-DNA complex in oplossing. De nieuwe mogelijkheden van NMR",
    Chemisch Magazine, pp. 131-133 (1990).
    

17. J.A.C. Rullmann and P.Th. van Duijnen,
    Potential energy models of biological macromolecules: a case for ab initio quantum chemistry,
    Reports in Molecular Theory 1, 1-21 (1990).
    

18. P.Th. van Duijnen and J.A.C. Rullmann,
    Intermolecular interactions with the Direct Reaction Field method,
    Int. J. Quant. Chem. 38, 181-189 (1990).
    

19. C. Gonzalez, J.A.C. Rullmann, A.M.J.J. Bonvin, R. Boelens and R. Kaptein,
    Towards an NMR R-factor,
    J. Magn. Reson. 91, 659-664 (1991).
    

20. J.A.C. Rullmann,
    Light-produkten: een hele last minder?,
    Biotekst 3, nr. 11, pp. 12-14 (1992).
    

21. J.A.C. Rullmann, A.M.J.J. Bonvin, R. Boelens and R. Kaptein,
    Structure determination from NMR - application to crambin,
    in: "Computation of biomolecular structures: achievements, problems and perspectives", D.M. Soumpasis and T.M. Jovin (eds.), Springer-Verlag, Berlin, pp. 1-14 (1993).
    

22. A.M.J.J. Bonvin, J.A.C. Rullmann, R.M.J.N. Lamerichs, R. Boelens and R. Kaptein,
    "'Ensemble' Iterative Relaxation Matrix Approach: a new NMR refinement protocol applied to the solution structure of crambin",
    Proteins 15, 385-400 (1993).
    

23. V.P. Chuprina, J.A.C. Rullmann, R.M.J.N. Lamerichs, J.H. van Boom, R. Boelens and R. Kaptein,
    "Structure of the Complex of lac Repressor Headpiece and an 11 Base Pair Half-Operator determined by NMR Spectroscopy and Restrained Molecular Dynamics",
    J. Mol. Biol. 234, 446-462 (1993).
    

24. R.M.A. Knegtel, J.A.C. Rullmann, R. Boelens and R. Kaptein,
    "MONTY: A Monte Carlo approach to protein-DNA recognition",
    J. Mol. Biol. 235, 318-324 (1994).
    

25. R. Kaptein, R. Boelens, V.P. Chuprina and J.A.C. Rullmann,
    "NMR Studies of Protein-Nucleic Acid Interaction: The Lac Operon",
    in: "NMR of Biological Macromolecules", C.I. Stassinopoulou (ed.), Nato ASI Series, Vol. H 87, Springer-Verlag, Berlin, pp. 323-333 (1994).
    

26. A.H. de Vries, P.Th. van Duijnen, A.H. Juffer, J.A.C. Rullmann, J.P. Dijkman, H. Merenga and B.T. Thole,
    "Implementation of Reaction Field Methods in Quantum Chemistry Computer Codes",
    J. Comp. Chem. 16, 37-55 (1995); erratum: 16, 1445-1446 (1995).
    

27. R. Kaptein, R. Boelens, V.P. Chuprina, J.A.C. Rullmann and M. Slijper,
    "NMR and nucleic acid-protein interaction: the lac repressor operator system",
    Methods in Enzymology 261, 513-524 (1995).
    

28. R. Kaptein, M. Slijper, V.P. Chuprina, J.A.C. Rullmann, R.M.A. Knegtel and R. Boelens,
    "Protein-DNA interaction from NMR and Monte Carlo Docking",
    in: "NMR as a Structural Tool for Macromolecules; Current and Future Directions", Nageswara Rao, B.D. and Kemple, M.D. (eds.), Plenum Press, New York, pp. 175-187 (1996).
    

29. R. Kaptein, M. Slijper, J.A.C. Rullmann and R. Boelens,
    "A bright look at Protein-DNA Complexes",
    Chemisch Magazine, p. 104 (1996).
    

30. R.A. Laskowski, J.A.C. Rullmann, M.W. MacArthur, R. Kaptein and J.M. Thornton,
    "AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR",
    J. Biomol. NMR 8, 477-486 (1996).
    

31. J.F. Doreleijers, J.P.M. Langedijk, K. Hård, R. Boelens, J.A.C. Rullmann, W.M. Schaaper, J.T. van Oirschot and R. Kaptein,
    "Solution Structure of the Immunodominant Region of Protein G of Bovine Respiratory Syncytial Virus",
    Biochemistry 35, 14684-14688 (1996).
    

32. K.S. Wilson, S. Butterworth, Z. Dauter, V.S. Lamzin, M. Walsh, S. Wodak, J. Pontius, J. Richelle, A. Vaguine, C. Sander, R.W.W. Hooft, G. Vriend, J.M. Thornton, R.A. Laskowski, M.W. MacArthur, E.J. Dodson, G. Murshudov, T.J. Oldfield, R. Kaptein and J.A.C. Rullmann,
    "Who checks the checkers? Four validation tools applied to eight atomic resolution structures",
    J. Mol. Biol. 276, 417-436 (1998).
    

33. J.F. Doreleijers, J.A.C. Rullmann and R. Kaptein,
    "Quality Assessment of NMR Structures: a Statistical Survey",
    J. Mol. Biol. 281, 149-164 (1998).
    

34. J.F. Doreleijers, M.L. Raves, J.A.C. Rullmann and R. Kaptein,
    "Completeness of NOEs in Protein Structures, a Statistical Analysis of NMR Data",
    J. Biomol. NMR 14, 123-132 (1999).
    

35. B.T. Alako, A. Veldhoven, S. van Baal, R. Jelier, S. Verhoeven, T. Rullmann, J. Polman and G. Jenster,
    "CoPub Mapper: mining MEDLINE based on search term co-publication",
    BMC Bioinformatics 6, 51 (2005).

36. J.A.C. Rullmann, H. Struemper, N.A. Defranoux, S. Ramanujan, C.M.L. Meeuwisse and A. van Elsas,
    "Systems biology for battling rheumatoid arthritis: Application of the Entelos PhysioLab platform",
    IEE Proc. Syst. Biol. 152, 256-262 (2005).

37. Wynand Alkema, Ton Rullmann and Andrea van Elsas,
    "Target validation in silico: does the virtual patient cure the pharma pipeline?",
    Expert Opinion on Therapeutic Targets 10, 635-638 (2006).