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    Head-Gordon, Teresa Lyn

    TitleBiochemist Faculty
    SchoolLawrence Berkeley National Lab
    DepartmentChemical Sciences
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/666-2744
    vCardDownload vCard

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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Vitale V, Dziedzic J, Albaugh A, Niklasson AM, Head-Gordon T, Skylaris CK. Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory. J Chem Phys. 2017 Mar 28; 146(12):124115. PMID: 28388116.
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      2. Wang LP, McKiernan KA, Gomes J, Beauchamp KA, Head-Gordon T, Rice JE, Swope WC, Martínez TJ, Pande VS. Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15. J Phys Chem B. 2017 Mar 17. PMID: 28306259.
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      3. Carr AC, Felberg LE, Piunova VA, Rice JE, Head-Gordon T, Swope WC. The Effect of Hydrophobic Core Topology and Composition on the Structure and Kinetics of Star Polymers, a Molecular Dynamics Study. J Phys Chem B. 2017 Mar 14. PMID: 28290691.
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      4. Esser A, Belsare S, Marx D, Head-Gordon T. Mode specific THz spectra of solvated amino acids using the AMOEBA polarizable force field. Phys Chem Chem Phys. 2017 Feb 06. PMID: 28165073.
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      5. Ruiz Pestana L, Kolluri K, Head-Gordon T, Lammers LN. Direct Exchange Mechanism for Interlayer Ions in Non-Swelling Clays. Environ Sci Technol. 2016 Dec 20. PMID: 27997121.
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      6. Mardirossian N, Ruiz Pestana L, Womack JC, Skylaris CK, Head-Gordon T, Head-Gordon M. Use of the rVV10 Nonlocal Correlation Functional in the B97M-V Density Functional: Defining B97M-rV and Related Functionals. J Phys Chem Lett. 2016 Dec 12; 35-40. PMID: 27936759.
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      7. Lincoff J, Sasmal S, Head-Gordon T. Comparing generalized ensemble methods for sampling of systems with many degrees of freedom. J Chem Phys. 2016 Nov 7; 145(17):174107. PMID: 27825215.
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      8. Felberg LE, Brookes DH, Yap EH, Jurrus E, Baker NA, Head-Gordon T. PB-AM: An open-source, fully analytical linear poisson-boltzmann solver. J Comput Chem. 2016 Nov 2. PMID: 27804145.
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      9. Sasmal S, Schwierz N, Head-Gordon T. Mechanism of Nucleation and Growth of Aß40-Fibrils from All-Atom and Coarse-Grained Simulations. J Phys Chem B. 2016 Nov 2. PMID: 27806205.
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      10. Mao Y, Demerdash O, Head-Gordon M, Head-Gordon T. Assessing water-water and water-ion dimer interactions in the AMOEBA force field using energy decomposition analysis of electronic structure calculations. J Chem Theory Comput. 2016 Oct 6. PMID: 27709939.
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      11. Dziedzic J, Mao Y, Shao Y, Ponder J, Head-Gordon T, Head-Gordon M, Skylaris CK. TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field. J Chem Phys. 2016 Sep 28; 145(12):124106. PMID: 27782640.
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      12. Albaugh A, Boateng HA, Bradshaw RT, Demerdash ON, Dziedzic J, Mao Y, Margul DT, Swails J, Zeng Q, Case DA, Eastman P, Wang LP, Essex JW, Head-Gordon M, Pande VS, Ponder JW, Shao Y, Skylaris CK, Todorov IT, Tuckerman ME, Head-Gordon T. Advanced Potential Energy Surfaces for Molecular Simulation. J Phys Chem B. 2016 Sep 22; 120(37):9811-32. PMID: 27513316.
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      13. Mao Y, Horn PR, Mardirossian N, Head-Gordon T, Skylaris CK, Head-Gordon M. Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation. J Chem Phys. 2016 Jul 28; 145(4):044109. PMID: 27475350.
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      14. Demerdash O, Head-Gordon T. Convergence of the Many-Body Expansion for Energy and Forces for Classical Polarizable Models in the Condensed Phase. J Chem Theory Comput. 2016 Aug 9; 12(8):3884-93. PMID: 27405002.
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      15. Bhowmick A, Brookes DH, Yost SR, Dyson HJ, Forman-Kay JD, Gunter D, Head-Gordon M, Hura GL, Pande VS, Wemmer DE, Wright PE, Head-Gordon T. Finding Our Way in the Dark Proteome. J Am Chem Soc. 2016 Aug 10; 138(31):9730-42. PMID: 27387657.
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      16. Bhowmick A, Sharma SC, Honma H, Head-Gordon T. The role of side chain entropy and mutual information for improving the de novo design of Kemp eliminases KE07 and KE70. Phys Chem Chem Phys. 2016 Jul 28; 18(28):19386-96. PMID: 27374812.
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      17. Brookes DH, Head-Gordon T. Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins. J Am Chem Soc. 2016 Apr 6; 138(13):4530-8. PMID: 26967199.
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      18. Albaugh A, Demerdash O, Head-Gordon T. An efficient and stable hybrid extended Lagrangian/self-consistent field scheme for solving classical mutual induction. J Chem Phys. 2015 Nov 7; 143(17):174104. PMID: 26547155.
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      19. Sharma SC, Armand T, Ball KA, Chen A, Pelton JG, Wemmer DE, Head-Gordon T. A facile method for expression and purification of (15)N isotope-labeled human Alzheimer's ß-amyloid peptides from E. coli for NMR-based structural analysis. Protein Expr Purif. 2015 Dec; 116:82-9. PMID: 26231074.
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      20. Brookes DH, Head-Gordon T. Family of Oxygen-Oxygen Radial Distribution Functions for Water. J Phys Chem Lett. 2015 Aug 6; 6(15):2938-43. PMID: 26267185.
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      21. Head-Gordon T. 158 Statistical fluctuations, dynamics, and de novo enzyme catalysis. J Biomol Struct Dyn. 2015 May; 33 Suppl 1:101-2. PMID: 26103367.
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      22. Bhowmick A, Head-Gordon T. A monte carlo method for generating side chain structural ensembles. Structure. 2015 Jan 6; 23(1):44-55. PMID: 25482539.
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      23. Yedvabny E, Nerenberg PS, So C, Head-Gordon T. Disordered structural ensembles of vasopressin and oxytocin and their mutants. J Phys Chem B. 2015 Jan 22; 119(3):896-905. PMID: 25231121.
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      24. Felberg LE, Brookes DH, Head-Gordon T, Rice JE, Swope WC. Role of hydrophilicity and length of diblock arms for determining star polymer physical properties. J Phys Chem B. 2015 Jan 22; 119(3):944-57. PMID: 25254622.
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      25. Head-Gordon T, Rice J. Tribute to william C. Swope. J Phys Chem B. 2014 Jun 19; 118(24):6357-9. PMID: 24945854.
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      26. Ball KA, Wemmer DE, Head-Gordon T. Comparison of Structure Determination Methods for Intrinsically Disordered Amyloid-ß Peptides. J Phys Chem B. 2014 Jun 19; 118(24):6405-16. PMID: 24410358.
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      27. Demerdash O, Yap EH, Head-Gordon T. Advanced potential energy surfaces for condensed phase simulation. Annu Rev Phys Chem. 2014 Apr; 65:149-74. PMID: 24328448.
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      28. Vazin T, Ball KA, Lu H, Park H, Ataeijannati Y, Head-Gordon T, Poo MM, Schaffer DV. Efficient derivation of cortical glutamatergic neurons from human pluripotent stem cells: A model system to study neurotoxicity in Alzheimer's disease. Neurobiol Dis. 2014 Feb; 62:62-72. PMID: 24055772.
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      29. Liguori N, Nerenberg PS, Head-Gordon T. Embedding Aß42 in heterogeneous membranes depends on cholesterol asymmetries. Biophys J. 2013 Aug 20; 105(4):899-910. PMID: 23972842.
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      30. Wang LP, Head-Gordon T, Ponder JW, Ren P, Chodera JD, Eastman PK, Martinez TJ, Pande VS. Systematic improvement of a classical molecular model of water. J Phys Chem B. 2013 Aug 29; 117(34):9956-72. PMID: 23750713.
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      31. Ball KA, Phillips AH, Wemmer DE, Head-Gordon T. Differences in ß-strand populations of monomeric Aß40 and Aß42. Biophys J. 2013 Jun 18; 104(12):2714-24. PMID: 23790380.
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      32. Yap EH, Head-Gordon T. Calculating the Bimolecular Rate of Protein-Protein Association with Interacting Crowders. J Chem Theory Comput. 2013 May 14; 9(5):2481-9. PMID: 26583736.
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      33. Wales DJ, Head-Gordon T. Evolution of the potential energy landscape with static pulling force for two model proteins. J Phys Chem B. 2012 Jul 26; 116(29):8394-411. PMID: 22432920.
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      34. Head-Gordon T, Lynden-Bell RM, Dowdle JR, Rossky PJ. Predicting cavity formation free energy: how far is the Gaussian approximation valid? Phys Chem Chem Phys. 2012 May 21; 14(19):6996-7004. PMID: 22495173.
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      35. Nerenberg PS, Jo B, So C, Tripathy A, Head-Gordon T. Optimizing solute-water van der Waals interactions to reproduce solvation free energies. J Phys Chem B. 2012 Apr 19; 116(15):4524-34. PMID: 22443635.
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      36. Lambrecht DS, Clark GN, Head-Gordon T, Head-Gordon M. Exploring the rich energy landscape of sulfate-water clusters SO4(2-) (H2O)(n=3-7): an electronic structure approach. J Phys Chem A. 2011 Oct 20; 115(41):11438-54. PMID: 21888323.
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      37. Ball KA, Phillips AH, Nerenberg PS, Fawzi NL, Wemmer DE, Head-Gordon T. Homogeneous and heterogeneous tertiary structure ensembles of amyloid-ß peptides. Biochemistry. 2011 Sep 6; 50(35):7612-28. PMID: 21797254.
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      38. Peng C, Head-Gordon T. The dynamical mechanism of auto-inhibition of AMP-activated protein kinase. PLoS Comput Biol. 2011 Jul; 7(7):e1002082. PMID: 21814500.
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      39. Lambrecht DS, Clark GN, Head-Gordon T, Head-Gordon M. Simulated photoelectron spectra of the cyanide-water anion via quasiclassical molecular dynamics. J Phys Chem A. 2011 Jun 16; 115(23):5928-35. PMID: 21405045.
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      40. Nerenberg PS, Head-Gordon T. Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides. J Chem Theory Comput. 2011 Apr 12; 7(4):1220-30. PMID: 26606367.
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      41. Lynden-Bell RM, Giovambattista N, Debenedetti PG, Head-Gordon T, Rossky PJ. Hydrogen bond strength and network structure effects on hydration of non-polar molecules. Phys Chem Chem Phys. 2011 Feb 21; 13(7):2748-57. PMID: 21152590.
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      42. Lin MS, Head-Gordon T. Reliable protein structure refinement using a physical energy function. J Comput Chem. 2011 Mar; 32(4):709-17. PMID: 20925085.
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      43. Kohn JE, Afonine PV, Ruscio JZ, Adams PD, Head-Gordon T. Evidence of functional protein dynamics from X-ray crystallographic ensembles. PLoS Comput Biol. 2010; 6(8). PMID: 20865158.
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      44. Clark GN, Hura GL, Teixeira J, Soper AK, Head-Gordon T. Small-angle scattering and the structure of ambient liquid water. Proc Natl Acad Sci U S A. 2010 Aug 10; 107(32):14003-7. PMID: 20647388.
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      45. Sodt AJ, Head-Gordon T. Driving forces for transmembrane alpha-helix oligomerization. Biophys J. 2010 Jul 7; 99(1):227-37. PMID: 20655851.
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      46. Yap EH, Head-Gordon T. A New and Efficient Poisson-Boltzmann Solver for Interaction of Multiple Proteins. J Chem Theory Comput. 2010 Jun 17; 6(7):2214-2224. PMID: 20711494.
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      47. Sodt AJ, Head-Gordon T. An implicit solvent coarse-grained lipid model with correct stress profile. J Chem Phys. 2010 May 28; 132(20):205103. PMID: 20515115.
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      48. Peng C, Zhang L, Head-Gordon T. Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions. Biophys J. 2010 May 19; 98(10):2356-64. PMID: 20483345.
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      49. Soper AK, Teixeira J, Head-Gordon T. Is ambient water inhomogeneous on the nanometer-length scale? Proc Natl Acad Sci U S A. 2010 Mar 23; 107(12):E44; author reply E45. PMID: 20220097.
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      50. Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GN, Johnson ME, Head-Gordon T. Current status of the AMOEBA polarizable force field. J Phys Chem B. 2010 Mar 4; 114(8):2549-64. PMID: 20136072.
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      51. Ruscio JZ, Fawzi NL, Head-Gordon T. How hot? Systematic convergence of the replica exchange method using multiple reservoirs. J Comput Chem. 2010 Feb; 31(3):620-7. PMID: 19554556.
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      52. Malardier-Jugroot C, Bowron DT, Soper AK, Johnson ME, Head-Gordon T. Structure and water dynamics of aqueous peptide solutions in the presence of co-solvents. Phys Chem Chem Phys. 2010 Jan 14; 12(2):382-92. PMID: 20023816.
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      53. Johnson ME, Malardier-Jugroot C, Head-Gordon T. Effects of co-solvents on peptide hydration water structure and dynamics. Phys Chem Chem Phys. 2010 Jan 14; 12(2):393-405. PMID: 20023817.
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      54. Ruscio JZ, Kohn JE, Ball KA, Head-Gordon T. The influence of protein dynamics on the success of computational enzyme design. J Am Chem Soc. 2009 Oct 7; 131(39):14111-5. PMID: 19788332.
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      55. Johnson ME, Head-Gordon T. Assessing thermodynamic-dynamic relationships for waterlike liquids. J Chem Phys. 2009 Jun 7; 130(21):214510. PMID: 19508079.
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      56. Johnson ME, Malardier-Jugroot C, Murarka RK, Head-Gordon T. Hydration water dynamics near biological interfaces. J Phys Chem B. 2009 Apr 2; 113(13):4082-92. PMID: 19425247.
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      57. Fawzi NL, Yap EH, Okabe Y, Kohlstedt KL, Brown SP, Head-Gordon T. Contrasting disease and nondisease protein aggregation by molecular simulation. Acc Chem Res. 2008 Aug; 41(8):1037-47. PMID: 18646868.
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      58. Malardier-Jugroot C, Johnson ME, Murarka RK, Head-Gordon T. Aqueous peptides as experimental models for hydration water dynamics near protein surfaces. Phys Chem Chem Phys. 2008 Aug 28; 10(32):4903-8. PMID: 18688534.
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      59. Fawzi NL, Phillips AH, Ruscio JZ, Doucleff M, Wemmer DE, Head-Gordon T. Structure and dynamics of the Abeta(21-30) peptide from the interplay of NMR experiments and molecular simulations. J Am Chem Soc. 2008 May 14; 130(19):6145-58. PMID: 18412346.
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      60. Head-Gordon T, Lynden-Bell RM. Hydrophobic solvation of Gay-Berne particles in modified water models. J Chem Phys. 2008 Mar 14; 128(10):104506. PMID: 18345905.
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      61. Lin MS, Head-Gordon T. Improved Energy Selection of Nativelike Protein Loops from Loop Decoys. J Chem Theory Comput. 2008 Mar; 4(3):515-21. PMID: 26620791.
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      62. Yap EH, Fawzi NL, Head-Gordon T. A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding. Proteins. 2008 Feb 15; 70(3):626-38. PMID: 17879350.
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      63. Murarka RK, Head-Gordon T. Dielectric relaxation of aqueous solutions of hydrophilic versus amphiphilic peptides. J Phys Chem B. 2008 Jan 10; 112(1):179-86. PMID: 18069810.
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      64. Fawzi NL, Kohlstedt KL, Okabe Y, Head-Gordon T. Protofibril assemblies of the arctic, Dutch, and Flemish mutants of the Alzheimer's Abeta1-40 peptide. Biophys J. 2008 Mar 15; 94(6):2007-16. PMID: 18032553.
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      65. Murarka RK, Head-Gordon T. Single particle and collective hydration dynamics for hydrophobic and hydrophilic peptides. J Chem Phys. 2007 Jun 7; 126(21):215101. PMID: 17567218.
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      66. Lin MS, Fawzi NL, Head-Gordon T. Hydrophobic potential of mean force as a solvation function for protein structure prediction. Structure. 2007 Jun; 15(6):727-40. PMID: 17562319.
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      67. Johnson ME, Head-Gordon T, Louis AA. Representability problems for coarse-grained water potentials. J Chem Phys. 2007 Apr 14; 126(14):144509. PMID: 17444725.
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      68. Malardier-Jugroot C, Head-Gordon T. Separable cooperative and localized translational motions of water confined by a chemically heterogeneous environment. Phys Chem Chem Phys. 2007 Apr 28; 9(16):1962-71. PMID: 17431524.
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      69. Head-Gordon T, Rick SW. Consequences of chain networks on thermodynamic, dielectric and structural properties for liquid water. Phys Chem Chem Phys. 2007 Jan 7; 9(1):83-91. PMID: 17164889.
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      70. Fawzi NL, Okabe Y, Yap EH, Head-Gordon T. Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer's Abeta(1-40) peptide. J Mol Biol. 2007 Jan 12; 365(2):535-50. PMID: 17070840.
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      71. Head-Gordon T, Johnson ME. Tetrahedral structure or chains for liquid water. Proc Natl Acad Sci U S A. 2006 May 23; 103(21):7973-7. PMID: 16698934.
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      72. Lotan I, Head-Gordon T. An Analytical Electrostatic Model for Salt Screened Interactions between Multiple Proteins. J Chem Theory Comput. 2006 May; 2(3):541-55. PMID: 26626662.
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      73. Marianayagam NJ, Fawzi NL, Head-Gordon T. Protein folding by distributed computing and the denatured state ensemble. Proc Natl Acad Sci U S A. 2005 Nov 15; 102(46):16684-9. PMID: 16267133.
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      74. Russo D, Murarka RK, Copley JR, Head-Gordon T. Molecular view of water dynamics near model peptides. J Phys Chem B. 2005 Jul 7; 109(26):12966-75. PMID: 16852609.
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      75. Fawzi NL, Chubukov V, Clark LA, Brown S, Head-Gordon T. Influence of denatured and intermediate states of folding on protein aggregation. Protein Sci. 2005 Apr; 14(4):993-1003. PMID: 15772307.
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      76. Horn HW, Swope WC, Pitera JW, Madura JD, Dick TJ, Hura GL, Head-Gordon T. Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. J Chem Phys. 2004 May 22; 120(20):9665-78. PMID: 15267980.
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      77. Brown S, Head-Gordon T. Intermediates and the folding of proteins L and G. Protein Sci. 2004 Apr; 13(4):958-70. PMID: 15044729.
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      78. Russo D, Hura G, Head-Gordon T. Hydration dynamics near a model protein surface. Biophys J. 2004 Mar; 86(3):1852-62. PMID: 14990511.
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      79. Brown S, Fawzi NJ, Head-Gordon T. Coarse-grained sequences for protein folding and design. Proc Natl Acad Sci U S A. 2003 Sep 16; 100(19):10712-7. PMID: 12963815.
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      80. Head-Gordon T, Brown S. Minimalist models for protein folding and design. Curr Opin Struct Biol. 2003 Apr; 13(2):160-7. PMID: 12727508.
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      81. Brown S, Head-Gordon T. Cool walking: a new Markov chain Monte Carlo sampling method. J Comput Chem. 2003 Jan 15; 24(1):68-76. PMID: 12483676.
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      82. Head-Gordon T, Hura G. Water structure from scattering experiments and simulation. Chem Rev. 2002 Aug; 102(8):2651-70. PMID: 12175263.
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      83. Sorenson JM, Head-Gordon T. Toward minimalist models of larger proteins: a ubiquitin-like protein. Proteins. 2002 Mar 1; 46(4):368-79. PMID: 11835512.
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      84. Zhong S, Dadarlat VM, Glaeser RM, Head-Gordon T, Downing KH. Modeling chemical bonding effects for protein electron crystallography: the transferable fragmental electrostatic potential (TFESP) method. Acta Crystallogr A. 2002 Mar; 58(Pt 2):162-70. PMID: 11832586.
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      85. Crivelli S, Eskow E, Bader B, Lamberti V, Byrd R, Schnabel R, Head-Gordon T. A physical approach to protein structure prediction. Biophys J. 2002 Jan; 82(1 Pt 1):36-49. PMID: 11751294.
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      86. Sorenson JM, Head-Gordon T. Protein engineering study of protein L by simulation. J Comput Biol. 2002; 9(1):35-54. PMID: 11911794.
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      87. Crivelli S, Byrd R, Eskow E, Schnabe R, Yu R, Philip TM, Head-Gordon T. A global optimization strategy for predicting alpha-helical protein tertiary structure. Comput Chem. 2000 May; 24(3-4):489-97. PMID: 10816018.
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      88. Sorenson JM, Head-Gordon T. Matching simulation and experiment: a new simplified model for simulating protein folding. J Comput Biol. 2000; 7(3-4):469-81. PMID: 11108474.
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      89. Sorenson JM, Head-Gordon T. Redesigning the hydrophobic core of a model beta-sheet protein: destabilizing traps through a threading approach. Proteins. 1999 Dec 1; 37(4):582-91. PMID: 10651274.
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      90. Chang S, Head-Gordon T, Glaeser RM, Downing KH. Chemical bonding effects in the determination of protein structures by electron crystallography. Acta Crystallogr A. 1999 Mar 1; 55 ( Pt 2 Pt 2):305-13. PMID: 10927261.
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      91. Pertsemlidis A, Soper AK, Sorenson JM, Head-Gordon T. Evidence for microscopic, long-range hydration forces for a hydrophobic amino acid. Proc Natl Acad Sci U S A. 1999 Jan 19; 96(2):481-6. PMID: 9892659.
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      92. Sorenson JM, Head-Gordon T. The importance of hydration for the kinetics and thermodynamics of protein folding: simplified lattice models. Fold Des. 1998; 3(6):523-34. PMID: 9889163.
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      93. Head-Gordon T, Sorenson JM, Pertsemlidis A, Glaeser RM. Differences in hydration structure near hydrophobic and hydrophilic amino acids. Biophys J. 1997 Oct; 73(4):2106-15. PMID: 9336206.
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      94. Pertsemlidis A, Saxena AM, Soper AK, Head-Gordon T, Glaeser RM. Direct evidence for modified solvent structure within the hydration shell of a hydrophobic amino acid. Proc Natl Acad Sci U S A. 1996 Oct 1; 93(20):10769-74. PMID: 8855255.
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      95. Head-Gordon T. Is water structure around hydrophobic groups clathrate-like? Proc Natl Acad Sci U S A. 1995 Aug 29; 92(18):8308-12. PMID: 11607575.
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      96. Head-Gordon T, Stillinger FH, Wright MH, Gay DM. Poly(L-alanine) as a universal reference material for understanding protein energies and structures. Proc Natl Acad Sci U S A. 1992 Dec 1; 89(23):11513-7. PMID: 1454840.
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      97. Head-Gordon T, Stillinger FH, Arrecis J. A strategy for finding classes of minima on a hypersurface: implications for approaches to the protein folding problem. Proc Natl Acad Sci U S A. 1991 Dec 15; 88(24):11076-80. PMID: 1763023.
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      98. Head-Gordon T, Brooks CL. Virtual rigid body dynamics. Biopolymers. 1991 Jan; 31(1):77-100. PMID: 2025686.
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