研究领域

theoretical, physical

My lab studies protein structure and biomolecular recognition using a combination of computational modeling and biophysical experiments. We aim to understand basic driving forces and to use this knowledge for practical applications, including new approaches to structure determination and the design of new biomolecules. Our focus is on the development and application of powerful computational modeling tools, which we validate and improve through complementary experimental studies. Current efforts in the lab focus on two main directions: (1) alternative approaches to structure determination and (2) design of protein-protein and protein-peptide interactions using physical modeling and free energy simulations.

近期论文

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J.L. MacCallum, A. Perez, and K.A. Dill, Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference, Proc. Natl. Acad. Sci. USA, in press. 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. 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. 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. K.A. Dill and J.L. MacCallum. 2012. The protein folding problem: 50 years on. Science 338(5110), pp. 1042-1046. A. Perez, Zheng Yang, Ivet Bahar, Ken A. Dill, and J.L. MacCallum. 2012. FlexE: Using elastic network models to compare models of protein structure. J. Chem. Theo. Comp., 8(10), pp. 3985- 3991. J.L. MacCallum and D.P. Tieleman. 2011. Hydrophobicity scales: a thermodynamic looking glass into lipid–protein interactions. Trends Biochem. Sci, 36, pp. 653-662. 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. J.L. MacCallum, A. Perez, M.J. Schneiders, L. Hua, M.P. Jacobson, and K.A. Dill. 2011. Assessment of refinement in CASP9. Proteins, 79(S10), pp. 74-90. 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. 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. 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. J.L.MacCallum, W.F.D. Bennett, and D.P. Tieleman. 2008. Distribution of amino acids in a lipid bilayer from computer simulations. Biophys. J. 94, pp. 3393-3404. 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 experiment. J. Gen. Physiol. 129, pp. 371-377. 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 folding. Proc. Natl. Acad. Sci. USA 104, pp. 6206-6210. 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. 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. 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. 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. 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.