Refereed Research Papers

  1. A. Perez, K. Gaalswyk, C.P. Jaroniec, J.L. MacCallum. 2018. High accuracy protein structures from minimal sparse paramagnetic solid-state NMR restraints. Submitted.

  2. M. Renaud-Young, R. Mayall, M. Goledzinowski, F. Comeau, J.L. MacCallum, V.I. Birss. 2018. Ultrasensitive Electrochemical Detection of Δ9-tetrahydrocannabinol (THC) and its Metabolites by Infusion into a Carbon Paper Electrode. Submitted.

  3. J.W. Papatzimas, E. Gorobets, R. Maity, M.I. Muniyat, J.L. MacCallum, P. Neri, N.J. Bahlis, D.J. Derksen. 2018. From Inhibition to Degradation: Targeting the Anti-apoptotic Protein MCL1. Submitted.

  4. K. Gaalswyk, M.I. Muniyat, J.L. MacCallum. 2018. The emerging role of physical modeling in the future of structure determination, Curr. Opin. Struct. Biol., 49, 145–153.

  5. J.L. MacCallum, M.I. Muniyat, J.L. MacCallum, 2018. Online Optimization of Total Acceptance in Hamiltonian Replica Exchange Simulations, J. Phys. Chem. B., 122(21), 5448–5457.

  6. K.B. Pilla, K. Gaalswyk, J.L. MacCallum, 2018. Molecular modeling of biomolecules by paramagnetic NMR and computational hybrid methods. BBA Proteins and Proteomics, 1865(11B), 1654–1663.

  7. J.A. Marrone, A. Perez, J.L. MacCallum, K.A. Dill. 2017. Computed binding of peptides to proteins with MELD-accelerated molecular dynamics. J. Chem. Theo. Comp., 13(2), 870–876.

  8. A. Perez, J.A. Marrone, E. Brini, J.L. MacCallum, K.A. Dil. 2016. Blind protein structure prediction using accelerated free-energy simulations. Sci. Adv., 2(11), e1601274.

  9. A. Perez, J.L. MacCallum, E.A. Coutsias, K.A. Dill. 2015. Constraint methods that accelerate free-energy simulations of biomolecules. J. Chem. Phys. 143, 243143.

  10. A. Perez, J.L. MacCallum, K.A. Dill. 2015. Accelerating molecular simulations of proteins using Bayesian inference on weak information. Proc. Natl. Acad. Sci. USA, 112(38), 11846-11851.

  11. A. Perez, J.L. MacCallum, E. Brini, C. Simmerling, K.A. Dill. 2015. Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations. J. Chem. Theo. Comp., 11(10), 4770–4779.

  12. J.L. MacCallum, A. Perez, and K.A. Dill. 2015. Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference, Proc. Natl. Acad. Sci. USA, 112(22), 6985–6990.

  13. A. Perez, A. Roy, K. Kasavajhala, A. Wagaman, K.A. Dill, and J.L. MacCallum. 2014. Extracting representative structures from protein conformational ensembles, Proteins, 82(10), pp. 2671-2680.

  14. S. Pressé, J. Peterson, P. Elms, J.L. MacCallum, S. Marqusee, C. Bustamante, and K.A. Dill. 2014. Single molecule conformational memory extraction: P5ab RNA hairpin, J. Phys. Chem. B, 118(24), pp. 6597-6603.

  15. A. Roy, A. Perez, K.A. Dill, and J.L. MacCallum, Computing the relative stabilities and per-residue components in protein conformational changes. Structure 22(1), pp. 168-175.

  16. K.A. Dill and J.L. MacCallum. 2012. The protein folding problem: 50 years on. Science 338(5110), pp. 1042-1046.

  17. A. Perez, Zheng Yang, Ivet Bahar, Ken A. Dill, and J.L. MacCallum. 2012. FlexE: Using elastic network models to compare models of protein structureJ. Chem. Theo. Comp., 8(10), pp. 3985- 3991. 

  18. J.L. MacCallum and D.P. Tieleman. 2011. Hydrophobicity scales: a thermodynamic looking glass into lipid–protein interactionsTrends Biochem. Sci, 36, pp. 653-662.

  19. J.L. MacCallum, W.F.D. Bennet, D.P. Tieleman. 2011. Transfer of Arginine into Lipid Bilayers is Non- Additive, Biophys. J., 101, pp. 110-117.

  20. J.L. MacCallum, A. Perez, M.J. Schneiders, L. Hua, M.P. Jacobson, and K.A. Dill. 2011. Assessment of refinement in CASP9Proteins, 79(S10), pp. 74-90.

  21. J.L. MacCallum, L. Hua, M.J. Schneiders, V.S. Pande, M.P. Jacobson, and K.A. Dill. 2009. Assessment of the protein-structure refinement category in CASP8.  Proteins, 77, pp. 66-80.

  22. W.F.D. Bennett, J.L. MacCallum, M.J. Hinner, S.J .Marrink, and D.P. Tieleman. 2009. Molecular View of Cholesterol Flip-Flop and Chemical Potential in Different Membrane Environments, J. Am. Chem. Soc. 131, pp. 12714-12720.

  23. W.F.D. Bennett, J.L. MacCallum, D.P. Tieleman. 2009. Thermodynamic analysis of the effect of choles- terol on dipalmitoylphosphatidylcholine lipid membranes, J. Am. Chem. Soc. 131, pp. 1972-1978.

  24. J.L.MacCallum, W.F.D. Bennett, and D.P. Tieleman. 2008. Distribution of amino acids in a lipid bilayer from computer simulationsBiophys. J. 94, pp. 3393-3404.

  25. J.L. MacCallum, W.F.D. Bennett, and D.P. Tieleman. 2007. Perspective: Partitioning of amino acid side chains into bilayers: results from computer simulation and comparison to experimentJ. Gen. Physiol. 129, pp. 371-377.

  26. J.L. MacCallum, M.S. Moghaddam, H.S. Chan, and D.P. Tieleman. 2007. Hydrophobic association of α-helices: Steric de-wetting and enthalpic barriers to protein foldingProc. Natl. Acad. Sci. USA 104, pp. 6206-6210.

  27. D.P. Tieleman, J.L. MacCallum, W.L. Ash, C. Kandt, Z. Xu, and L. Monticelli. 2006. Membrane protein simulations with a united atom lipid and all atom protein model: side chain transfer free energies and model proteins. J. Phys. Cond. Matt. 18, pp. S1221-S1234.

  28. J.L. MacCallum, D.P. Tieleman. 2006. Computer Simulation of the Distribution of Hexane in a Lipid Bilayer: Spatially Resolved Free Energy, Entropy, and Enthalpy Profiles. J. Am. Chem. Soc. 28, pp. 125-130.

  29. D.P. Tieleman, K.M. Robertson, J.L. MacCallum, L. Monticelli. 2004. Computer simulations of the voltage gated potassium channel KvAP. Int. J. Quant. Chem. 100(6), pp. 1071-1078.

  30. L. Monticelli, K.M. Robertson, J.L. MacCallum, D.P. Tieleman. 2004. Computer simulation of the KvAP voltage-gated potassium channel: steered molecular dynamics of the voltage sensor. FEBS Lett. 564, pp. 325-332.

  31. T. Stockner, W.L. Ash, J.L. MacCallum, D.P. Tieleman. 2004. Direct simulation of transmembrane helix association: role of asparagines. Biophys. J. 87(3), pp. 1650-1656.

  32. W.L. Ash, T. Stockner, J.L. MacCallum, D.P. Tieleman. 2004. Computer modeling of polyleucine- based coiled coil dimers in a realistic membrane environment: insight into helix-helix interactions. Biochemistry 43(28), pp. 9050-9060.

  33. M.P. Aliste, J.L. MacCallum, and D.P. Tieleman. 2003. Molecular dynamics simulations of pentapep- tides at interfaces: salt-bridge and cation-pi interactionsBiochemistry 42, pp. 8976-8987.

  34. J.L. MacCallum, D.P. Tieleman. 2003. Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field, J. Comp. Chem. 24, pp. 1930-1935.

  35. J.L. MacCallum, D.P. Tieleman. 2002. Structure of neat and hydrated 1-octanol from computer simulations. J. Am. Chem. Soc. 124, pp. 15085-15093.

 

Book Chapters

  1. J.L. MacCallum, and D.P. Tieleman. 2008. Interactions between small molecules and lipid bilayers, in Current Topics in Membranes and Transport 60, pp. 227-256, Editor: S.E. Feller.

 

Conference Proceedings

  1. D.P. Tieleman, W.F.D. Bennett, and J.L. MacCallum. 2007. Molecular dynamics simulations of biological membranes. Chem. Phys. Lipids 149, Suppl. S, S4.

  2. J.L. MacCallum, P. Mukhopadhyay, H. Luo, and D.P. Tieleman. 2003. Large scale molecular dynamics simulations of lipid-drug interactions, in Proceedings of the 17th Annual International Symposium on High Performance Computing Systems and Applications and the OSCAR Symposium, Editor: David Senechal, NRC Research Press, Ottawa, Canada.