The Elcock Group
Molecular Simulations in Biology
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Publications
Peer-reviewed publications
Thomas, A.S., & Elcock, A.H. (2007)
Molecular dynamics simulations of hydrophobic associations in aqueous salt solutions indicate a connection between water hydrogen bonding and the Hofmeister effect.
J. Am. Chem. Soc. 129, 14887-14898.
McGuffee, S.R., & Elcock, A.H. (2006)
Atomically detailed simulations of concentrated protein solutions: the effects of salt, pH, point mutations and protein concentration in simulations of 1000-molecule systems.
J. Am. Chem. Soc. 128, 12098-12110.
Elcock, A.H. (2006)
Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome.
PLoS Comput. Biol. 2, 824-841.
Thomas, A.S., & Elcock, A.H. (2006)
Direct observation of salt effects on molecular interactions through explicit-solvent molecular dynamics simulations: differential effects on electrostatic and hydrophobic interactions and comparisons to Poisson-Boltzmann theory.
J. Am. Chem. Soc. 128, 7796-7806.
Frembgen-Kesner, T. & Elcock, A.H. (2006)
Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase.
Rockey, W.M., & Elcock, A.H. (2005)
Rapid computational identification of the targets of protein kinase inhibitors.
Thomas, A.S., & Elcock, A.H. (2004)
Molecular simulations suggest protein salt bridges are uniquely suited to life at high temperatures.
J. Am. Chem. Soc. 126, 2208-2214.
Yang, H., & Elcock, A.H. (2003)
Association lifetimes of hydrophobic amino acid pairs measured directly from molecular dynamics simulations.
J. Am. Chem. Soc. 125, 13968-13969.
Elcock, A.H. (2003)
Atomic-level observation of macromolecular crowding effects: escape of a protein from the GroEL cage.
Proc. Natl. Acad. Sci. USA 100, 2340-2344.
Rockey, W.M., & Elcock, A.H. (2002)
Progress toward virtual screening for drug side effects.
Elcock, A.H. (2002)
Atomistic simulations of competition between substrates binding to an enzyme.
Elcock, A.H. (2001)
Prediction of functionally important residues based solely on the computed energetics of protein structure.
Elcock, A.H., Sept, D., & McCammon, J.A. (2001) (feature article)
Computer simulation of protein-protein interactions.
J. Phys. Chem. B., 105, 1504-1518.
Elcock, A.H., & McCammon, J.A. (2001)
Identification of protein oligomerization states by analysis of interface conservation.
Proc. Natl. Acad. Sci. USA, 98, 2990-2994.
Elcock, A.H., & McCammon, J.A. (2001)
Calculation of weak protein-protein interactions: the pH-dependence of the second virial coefficient.
Elcock, A.H. (1999)
Realistic modeling of the denatured states of proteins allows accurate calculations of the pH-dependence of protein stability.
Elcock, A.H., Gabdoulline, R.R., Wade, R.C., & McCammon, J.A. (1999)
Computer simulation of protein-potein association: Acetylcholinesterase-Fasciculin.
Elcock, A.H. (1998)
The stability of salt bridges at high temperatures: Implications for hyperthermophilic proteins.
J. Mol. Biol. 284, 489-502.
Elcock, A.H., & McCammon, J.A. (1998)
Electrostatic contributions to the stability of halophilic proteins.
J. Mol. Biol. 280, 731-748.
Elcock, A.H., Huber, G.A., & McCammon, J.A. (1997)
Electrostatic channeling of substrates between enzyme active sites: Comparison of simulation and experiment.
Biochemistry 36, 16049-16058.
Elcock, A.H., & McCammon, J.A. (1997)
A continuum solvation model for studying protein hydration thermodynamics at high temperatures.
J. Phys. Chem. B. 101, 9624-9634.
Elcock, A.H., & McCammon, J.A. (1996)
Evidence for Electrostatic Channeling in a Fusion Protein of Citrate Synthase and Malate dehydrogenase.
Biochemistry 35, 12652-12658.
Elcock, A.H., Potter, M.J., Matthews, D.A., Knighton, D.R., & McCammon, J.A (1996)
Electrostatic Channeling in the Bifunctional Enzyme Dihydrofolate Reductase-Thymidylate Synthase.
J. Mol. Biol. 262, 370-374.
Elcock, A.H., & McCammon, J.A. (1996)
The Low Dielectric Interior of Proteins is Sufficient to Cause Major Structural Changes in DNA on Association.
J. Am. Chem. Soc. 118, 3787-3788.
Elcock, A.H., Rodger, A., & Richards, W.G. (1996)
Theoretical Studies of the Intercalation of 9-hydroxyellipticine in DNA.
Biopolymers, 39, 309-326.
Elcock, A.H., & McCammon, J.A. (1995)
Sequence-dependent Hydration of DNA: Theoretical Results.
J. Am. Chem. Soc. 117, 10161-10162.
Elcock, A.H., Lyne, P.D., Mulholland, A.J., Nandra, A., & Richards, W.G. (1995)
A Combined Quantum and Molecular Mechanical Study of DNA Cross-linking by Nitrous Acid.
J. Am. Chem. Soc. 117, 4706-4707.
Elcock, A.H., & Richards, W.G. (1993)
Relative Hydration Free Energies of the Nucleic Acid Bases.
J. Am. Chem. Soc. 115, 7930-7931.
Other publications
Rockey, W.M., & Elcock, A.H. (2006) (invited review)
Structure selection for protein kinase docking and virtual screening: homology models or crystal structures
Curr. Protein Pept. Sci. 7, 437-457.
Rockey, W.M., & Elcock, A.H. (2006) (invited review)
Rapid computational identification of the targets of protein kinase inhibitors.
Curr. Opin. Drug Discov. Dev. 9, 326-331.
Elcock, A.H. (2004) Molecular simulations of diffusion and association in multi-macromolecular systems in Numerical Computer Methods, Part D, volume 383 of Methods in Enzymology, Brand, L., & Johnson, M.L., Eds. Elsevier, Inc. San Diego, CA.
Elcock, A.H. (2002) (invited review)
Modeling supramolecular assemblages.
Curr. Opin. Struct. Biol. 12, 154-160.
Elcock, A.H., Potter, M.J., & McCammon, J.A. (1997) Application of Poisson Boltzmann solvation forces to macromolecular simulations in “Computer Simulation of Biomolecular Systems”, volume 3, Wilkinson, A.J., et al., Eds., ESCOM Science Publishers, B.V. Leiden, The Netherlands.