N. Lux Fawzi, E. H. Yap, Y. Okabe, K. Kohlstedt, S. P. Brown & T. Head-Gordon (2008). Contrasting disease and non-disease protein aggregation by molecular simulation Acc. Chem. Research, submitted [doc]

N. Lux Fawzi, A. Phillips, J. Z. Ruscio, M. Doucleff, D. E. Wemmer & T. Head-Gordon (2008). Structure and dynamics of the Alzheimer’s Ab1-40 peptide from the interplay of NMR experiments and simulation J. Am. Chem. Soc. (published online)[link]

T. Head-Gordon & R. M. Lynden-Bell (2008). Hydrophobic solvation of Gay Berne particles in modified water models. J. Chem. Phys. 128 , 104506-104512. [link]

N. Lux Fawzi, K. Kohlstedt, Y. Okabe, and T. Head-Gordon (2008). Protofibril assemblies of the Arctic, Dutch, and Flemish mutants of the Alzheimer’s Ab1-40 peptide. Biophys. J. in press (published online)[link]

M. S. Lin and T. Head-Gordon (2008). Improved energy selection of native loops from loop decoys. J. Chem. Theo. Comp. (Cover article) 4 , 515-521. [link]

R. K. Murarka and T. Head-Gordon (2008). Dielectric relaxation of aqueous solutions of amphiphilic and hydrophilic peptides. J. Phys. Chem. B 112 , 179-186. [link]

R. K. Murarka and T. Head-Gordon (2007). Single particle and collective hydration dynamics of hydrophobic and hydrophilic peptides.  J. Chem. Phys. . 126, 215101-215109. [link]

M. S. Lin, N. L. Fawzi, and T. Head-Gordon (2007).  Hydrophobic potential of mean force as a solvent function for protein structure prediction.  Structure 15, 727-740. [link]

E.-H. Yap, N. Lux Fawzi & T. Head-Gordon (2007). A coarse-grained α−carbon protein model with anisotropic hydrogen-bonding. Proteins, Struct. Func. Bioinformatics 70, 626-638. [link]

M. E. Johnson, T. Head-Gordon, A. A. Louis (2007). Representability problems for coarse-grained water models. J. Chem. Phys. 126, 144509-144519. [link]

C. Malardier-Jugroot and T. Head-Gordon (2007). Separable cooperative and localized translational motions of confined water. Phys. Chem. Chem. Phys. 9, 1962-1971. [link]

T. Head-Gordon and S. Rick (2007). Consequences of chain networks on thermodynamic, dielectric and structural properties for liquid water. Phys. Chem. Chem. Phys. 8, 83-91. [link] Also see discussion in Hot Topics: [link]

N. Lux Fawzi, Y. Okabe, E.-H. Yap & T. Head-Gordon (2007). Fibril stability and elongation studies of the Alzheimer’s Aβ1-40 peptide. J. Mol. Biol. 365, 535-550. [link]

R. M. Lynden-Bell and T. Head-Gordon (2006). Solvation in modified water models: toward understanding hydrophobic solvation. Mol. Phys. 104, 3593-3605. [link]

T. Head-Gordon and ME Johnson (2006). Tetrahedral structure or chains for liquid water. Proc. Natl. Acad. Sci. 103, 7973-7977. [pdf] Also see Nature Highlight: [link]

I. Lotan and T. Head-Gordon (2006). An analytical electrostatic model for salt screened interactions between multiple proteins. J. Chem. Theory Comp. 2, 541-555 [link]

N. Marianayagam, N. Fawzi & T. Head-Gordon (2005). Protein folding by distributed computing and the denatured state ensemble. Proc. Natl. Acad. Sci. 102, 16684-16689 [pdf]

D. Russo, R. K. Murarka, J. R.D. Copley, T. Head-Gordon (2005). Molecular view of water dynamics near model peptides.  J. Phys. Chem. B 109, 12966-12975 [link]

N. Fawzi, V. Chubukov, L.A. Clark, S. Brown & T. Head-Gordon (2005). Influence of denatured and intermediate states of folding on protein aggregation. Protein Science 14, 993-1003 [link]

D. Russo, R. K. Murarka, G. Hura, E. R. Verschell, J. R.D. Copley, & T. Head-Gordon (2004).  Evidence for anomalous hydration dynamics near a model hydrophobic peptide. J. Phys. Chem. B. 108, 19885-19893 [link]

E. Eskow, B. Bader, R. Byrd, S. Crivelli, T. Head-Gordon, V. Lamberti and R. Schnabel (2004).  An optimization approach to the problem of protein structure prediction. Mathematical Programming 101, 497-514 [pdf]

H. W. Horn, W. C. Swope, J. W. Pitera, J. D. Madura, T. J. Dick, Greg Hura, T. Head-Gordon (2004). Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. J. Chem. Phys. 120, 9665-9678. [link]

S. Brown & T. Head-Gordon (2004). Intermediates in the folding of proteins L and G. Protein Sci. 13, 958-970. [link]

D. Russo, G. Hura, & T. Head-Gordon (2004). Hydration dynamics near a model protein surface. Biophys. J. 86, 1852-1862  [link]

S. Crivelli & T. Head-Gordon (2004). A new load balancing strategy for the solution of dynamical large tree search problems using a hierarchical approach. IBM R&D Journal 48, 153-160. [link]

S. Brown, N. Fawzi, & T. Head-Gordon (2003). Coarse-grained sequences for protein folding and design. Proc. Natl. Acad. Sci 100, 10712-10717 [pdf]

T. Head-Gordon & S. Brown (2003). Minimalist models for protein folding and design. Curr. Opin. Struct. Biol. 13, 160-167. [pdf]

G. Hura, D. Russo, R.M. Glaeser, M. Krack, M. Parrinello, and T. Head-Gordon (2003). Water structure as a function of temperature from x-ray scattering experiments and ab initio molecular dynamics. Phys. Chem. Chem. Phys. 5, 1981-1991. [link]

S. Brown & T. Head-Gordon (2003). Cool-walking: a new markov chain monte carlo sampling method. J. Comp. Chem. PAK Symposium 24, 68-76.  [pdf]

T. Head-Gordon and G. Hura (2002). Water Structure from scattering experiments and simulation. Chemical Reviews 102, 2651-2670. [link]

J. M. Sorenson & T. Head-Gordon (2002). Protein engineering study of Protein L by Simulation. J. Comp. Biol. 9, 35-54. [pdf]

T. Head-Gordon, G. Hura, J. Sorenson,, R.M. Glaeser (2002). Pure water structure and hydration forces for protein folding, in V. V. Brazhkin. S. V. Buldyrev, V. N. Ryzhov, and H. E. Stanley, eds., New Kinds of Phase Transitions: Transformations in Disordered Substances Kluwer, Dordrecht, V. 8, 403-415.

J. M. Sorenson & T. Head-Gordon (2002). Toward minimalist models of larger proteins: a ubiquitin-like protein. Proteins: Structure, Function, Genetics 46, 368-379. [link]

S. Crivelli, E. Eskow, B. Bader, V. Lamberti, R. Byrd, R. Schnabel & T. Head-Gordon (2002). A physical approach to protein structure prediction. Biophys. J. 82, 36-49. [link]

T. Head-Gordon and J. Wooley (2001). Computational challenges in structural and functional genomics. IBM Systems Journal: Deep Computing in the Life Sciences 40, 265-296. [pdf]

C. P. Hsu, G. R. Fleming, M. Head-Gordon, and T. Head-Gordon (2001). Excitation energy transfer in condensed media. J. Chem. Phys. 114, 3065-3072 [pdf]

J. M. Sorenson & T. Head-Gordon (2000). Matching simulation and experiment: a new simplified model for simulating protein folding. J. Comp. Bio. 7, 469-481.[pdf]

G. Hura, J. Sorenson, R.M. Glaeser & T. Head-Gordon (2000). A high-quality x-ray scattering experiment on liquid water at ambient conditions. J. Chem. Phys. 113, 9140-9148.[link]

J. Sorenson, G. Hura, R.M. Glaeser & T. Head-Gordon (2000). What can x-ray scattering tell us about the radial distribution functions of water? J. Chem. Phys 113, 9149-9161. [link]

A. Azmi, R. H. Byrd, E. Eskow, R. Schnabel, S. Crivelli, T. M. Philip, T. Head-Gordon (2000). Predicting protein tertiary structure using a global optimization algorithm with smoothing. Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches, C. A. Floudas and P. M. Pardalos, editors (Kluwer Academic Publishers, Netherlands), 1-18.

S. Crivelli, T. M. Philip, R. Byrd, E. Eskow, R. Schnabel, R. C. Yu, T. Head-Gordon (2000). A global optimization strategy for predicting protein tertiary structure: α−helical proteins. Comp. & Chem 24, 489-497 [pdf]

S. Crivelli, T. Head-Gordon, R. H. Byrd, E. Eskow, R. Schnabel (1999). A hierarchical approach for parallelization of a global optimization method for protein structure prediction. Lecture Notes in Computer Science, Euro-Par '99, P. Amestoy, P. Berger, M. Dayde, I. Duff, V. Fraysse, L. Giraud, D. ruiz (eds.), pg. 578-585.[]

G. Hura, J. M. Sorenson, R. M. Glaeser & T. Head-Gordon (1999). Solution x-ray scattering as a probe of hydration-dependent structuring of aqueous solutions. Perspectives in Drug Discovery and Design 17, 97-118. [pdf]

J. M. Sorenson & T. Head-Gordon (1999). Redesigning the hydrophobic core of a model β-sheet protein: destabilizing traps through a threading approach. Proteins: Structure, Function, Genetics 37, 582-91.

C. P. Hsu, M. Head-Gordon & T. Head-Gordon (1999). Reaction field cavity optimization: A born-again Born model for ionic hydration. J. Chem. Phys. 111, 9700-9704. [link]

J. M. Sorenson, G. Hura, A, K, Soper, A. Pertsemlidis & T. Head-Gordon (1999). Determining the role of hydration forces in protein folding. Feature Article for J. Phys. Chem. B 103, 5413-5426. [link]

S. Chang, T. Head-Gordon, R. M. Glaeser & K. Downing (1999). Chemical bonding effects in the determination of protein structures by electron crystallography. Acta. Cryst. A55, 305-313. [pdf]

A. Pertsemlidis, A. K. Soper, J. M. Sorenson & T. Head-Gordon (1999). Evidence for microscopic, long-range hydration forces for a hydrophobic amino acid. Proc. Natl. Acad. Sci. 96, 481-486. [pdf]

J. M. Sorenson & T. Head-Gordon (1998). The importance of hydration for the kinetics and thermodynamics of protein folding: simplified lattice models. Fold & Design 3, 523-534.

T. Head-Gordon, J. M. Sorenson, A. Pertsemlidis & R. M. Glaeser (1997). Differences in hydration structure near hydrophobic and hydrophilic amino acid side chains. Biophys. J. 73, 2106-2115[link]

A. Pertsemlidis, A. M. Saxena, A. K. Soper, T. Head-Gordon & R. M. Glaeser (1996). Direct, structural evidence for modified solvent structure within the hydration shell of a hydrophobic amino acid. Proc. Natl. Acad. Sci. 93, 10769-10774. [pdf]

T. Head-Gordon (1995). A new solvent model for hydrophobic association in water. I. Thermodynamics. J. Am. Chem. Soc. 117, 501-507. [link]

R.C. Yu & T. Head-Gordon (1995). Neural network design applied to protein secondary structure prediction. Phys. Rev. E 51, 3619-3627. [link]

T. Head-Gordon (1995). Is water structure around hydrophobic groups clathrate-like? Proc. Natl. Acad. Sci. USA 92, 8308-8312. [pdf]

F.H. Stillinger & T. Head-Gordon (1995). Collective aspects of protein folding illustrated by a toy model. Phys. Rev. E 52, 2872-2877.  [link]

T. Head-Gordon (1994). Toward quantitative protein structure prediction, in The Protein folding problem and tertiary structure prediction. K. M. Merz Jr. & S. M. Le Grand, eds. (Boston, Birkhauser), ch. 15.

H.S. Shang & T. Head-Gordon (1994). Stabilization of helices in glycine  and alanine dipeptides in a reaction field model of solvent. J. Am. Chem. Soc. 116, 1528-1532. [pdf]

T. Head-Gordon (1994). An efficient solvent model for study of hydrophobic phenomena. Chem. Phys. Letts. 227, 215-220 [link]

M. Head-Gordon & T. Head-Gordon (1994). Analytic MP2 frequencies without fifth-order  storage. Theory and application to bifurcated hydrogen bonds in the water hexamer. Chem. Phys. Lett. 220, 122-128 [link]

F.H. Stillinger & T. Head-Gordon (1993). Perturbational view of inherent structures in water. Phys. Rev. E. 47, 2484-2490 [link]

T. Head-Gordon & F.H. Stillinger (1993). Toward optimal neural networks for protein structure prediction. Phys. Rev. E  48 1502-1515 [link]

F.H. Stillinger, T. Head-Gordon & C.L. Hirschfeld (1993). Toy model for protein folding. Phys. Rev. E 48, 1469-1477 [link]

T. Head-Gordon & F.H. Stillinger (1993). Predicting polypeptide and protein structures from amino acid sequence: antlion method applied to melittin. Biopolymers 33, 293-303.

T. Head-Gordon & F.H. Stillinger (1993). An orientational perturbation theory for pure liquid water. J. Chem. Phys. 98, 3313-3327.

T. Head-Gordon, F.H. Stillinger, M.H. Wright, & D.M. Gay (1992). Poly-L-alanine as a universal reference material for understanding protein energies and structures. Proc. Natl. Acad. Sci. USA 89, 11513-17. [pdf]

D.M. Gay, T. Head-Gordon, F. H. Stillinger & M.H. Wright (1992). An application of constrained optimization in protein folding: the poly-l-alanine hypothesis. Forefronts, Cornell Theory Center 8, 4-6.

T. Head-Gordon & F.H. Stillinger (1992). Enthalpy of knotted polypeptides. J. Phys. Chem. 96, 7796-7807.

T. Head-Gordon & C.L. Brooks (1991). Virtual rigid body dynamics. Biopolymers 31, 77-100.

T. Head-Gordon, M. Head-Gordon, M.J. Frisch, C.L. Brooks & J.A. Pople (1991). Theoretical study of blocked glycine and alanine dipeptide analogues. J. Am. Chem. Soc. 113, 5989-5997.

T. Head-Gordon, F.H. Stillinger & J. Arrecis (1991). A strategy for finding classes of minima on a hypersurface: implications for neural network approaches to the protein folding problem. Proc. Natl. Acad. Sci. U.S.A. 88, 11076-11080. [pdf]

T. Head-Gordon, M. Head-Gordon, M.J. Frisch, C.L. Brooks & J.A. Pople (1989). A theoretical study of alanine dipeptide and analogues. Int. J. Quant. Chem.: Quant. Biol. Symp. 16, 311-322.

T. Head-Gordon & C. L. Brooks (1988). Evaluation of simple model descriptions of the diffusional association rate for enzyme-ligand systems. J. Phys. Chem. 93, 490.

T. Head-Gordon & C.L. Brooks (1987). The role of electrostatics in the binding of small ligands to enzymes. J. Phys. Chem. 91, 3342-3349.

A.B. Anderson, T.L. Gordon & M.E. Kenney (1985). Electronic and redox properties of stacked-ring silicon pthalocyanines from molecular orbital theory. J. Am. Chem. Soc. 107, 192-195.