Teresa Head-Gordon, Ph.D. - Publications

Affiliations: 
Chemistry, Bioengineering, Chemical and Biomolecular Engineering University of California, Berkeley, Berkeley, CA 
Area:
Theoretical and computational chemistry, biophysics
Website:
http://thglab.berkeley.edu/

182 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Tan S, Leven I, An D, Lin L, Head-Gordon T. Stochastic Constrained Extended System Dynamics for Solving Charge Equilibration Models. Journal of Chemical Theory and Computation. PMID 32956587 DOI: 10.1021/acs.jctc.0c00514  1
2020 Gomes GW, Krzeminski M, Namini A, Martin EW, Mittag T, Head-Gordon T, Forman-Kay JD, Gradinaru CC. Conformational ensembles of an intrinsically disordered protein consistent with NMR, SAXS and single-molecule FRET. Journal of the American Chemical Society. PMID 32840111 DOI: 10.1021/jacs.0c02088  0.36
2020 Lincoff J, Haghighatlari M, Krzeminski M, Teixeira JMC, Gomes GW, Gradinaru CC, Forman-Kay JD, Head-Gordon T. Extended Experimental Inferential Structure Determination Method in Determining the Structural Ensembles of Disordered Protein States. Communications Chemistry. 3. PMID 32775701 DOI: 10.1038/s42004-020-0323-0  1
2020 Haghighatlari M, Li J, Heidar-Zadeh F, Liu Y, Guan X, Head-Gordon T. Learning to Make Chemical Predictions: the Interplay of Feature Representation, Data, and Machine Learning Methods. Chem. 6: 1527-1542. PMID 32695924 DOI: 10.1016/j.chempr.2020.05.014  0.52
2020 Novelli F, Ruiz Pestana L, Bennett KC, Sebastiani F, Adams EM, Stavrias N, Ockelmann T, Colchero A, Hoberg C, Schwaab G, Head-Gordon T, Havenith M. Strong Anisotropy in Liquid Water upon Librational Excitation Using Terahertz Laser Fields. The Journal of Physical Chemistry. B. PMID 32450043 DOI: 10.1021/acs.jpcb.0c02448  1
2019 Rossomme E, Lininger CN, Bell AT, Head-Gordon T, Head-Gordon M. Electronic structure calculations permit identification of the driving forces behind frequency shifts in transition metal monocarbonyls. Physical Chemistry Chemical Physics : Pccp. PMID 31833489 DOI: 10.1039/c9cp04643g  1
2019 Ruiz Pestana L, Hao H, Head-Gordon T. Diels-Alder Reactions in Water are Determined by Microsolvation. Nano Letters. PMID 31771330 DOI: 10.1021/acs.nanolett.9b04369  1
2019 Loipersberger M, Lee J, Mao Y, Das AK, Ikeda K, Thirman J, Head-Gordon T, Head-Gordon M. Energy Decomposition Analysis for Interactions of Radicals: Theory and Implementation at the MP2 Level with Application to Hydration of Halogenated Benzene Cations and Complexes between CO and Pyridine and Imidazole. The Journal of Physical Chemistry. A. PMID 31621324 DOI: 10.1021/acs.jpca.9b08586  1
2019 Leven I, Head-Gordon T. C-GeM: Coarse-Grained Electron Model for Predicting the Electrostatic Potential in Molecules. The Journal of Physical Chemistry Letters. 6820-6826. PMID 31613629 DOI: 10.1021/acs.jpclett.9b02771  1
2019 Leven I, Head-Gordon T. Inertial extended-Lagrangian scheme for solving charge equilibration models. Physical Chemistry Chemical Physics : Pccp. 21: 18652-18659. PMID 31460521 DOI: 10.1039/c9cp02979f  1
2019 Das AK, Urban L, Leven I, Loipersberger M, Aldossary A, Head-Gordon M, Head-Gordon T. Development of an Advanced Force Field for Water using Variational Energy Decomposition Analysis. Journal of Chemical Theory and Computation. PMID 31408601 DOI: 10.1021/acs.jctc.9b00478  1
2019 Qiu Y, Nerenberg PS, Head-Gordon T, Wang LP. Systematic Optimization of Water Models Using Liquid/Vapor Surface Tension Data. The Journal of Physical Chemistry. B. PMID 31314516 DOI: 10.1021/acs.jpcb.9b05455  1
2019 Liu S, Li J, Bennett K, Ganoe B, Stauch T, Head-Gordon M, Hexemer A, Ushizima D, Head-Gordon T. A Multi-Resolution 3D-DenseNet for Chemical Shift Prediction in NMR Crystallography. The Journal of Physical Chemistry Letters. PMID 31305081 DOI: 10.1021/acs.jpclett.9b01570  1
2019 Lincoff J, Sasmal S, Head-Gordon T. The combined force field-sampling problem in simulations of disordered amyloid-β peptides. The Journal of Chemical Physics. 150: 104108. PMID 30876367 DOI: 10.1063/1.5078615  1
2019 Albaugh A, Tuckerman ME, Head-Gordon T. Combining Iteration-Free Polarization with Large Time Step Stochastic-Isokinetic Integration. Journal of Chemical Theory and Computation. PMID 30830768 DOI: 10.1021/acs.jctc.9b00072  1
2019 Dziedzic J, Head-Gordon T, Head-Gordon M, Skylaris CK. Mutually polarizable QM/MM model with in situ optimized localized basis functions. The Journal of Chemical Physics. 150: 074103. PMID 30795653 DOI: 10.1063/1.5080384  1
2018 Krylov A, Windus TL, Barnes T, Marin-Rimoldi E, Nash JA, Pritchard B, Smith DGA, Altarawy D, Saxe P, Clementi C, Crawford TD, Harrison RJ, Jha S, Pande VS, Head-Gordon T. Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science. The Journal of Chemical Physics. 149: 180901. PMID 30441927 DOI: 10.1063/1.5052551  1
2018 Das AK, Demerdash ON, Head-Gordon T. Improvements to the AMOEBA Force Field by Introducing Anisotropic Atomic Polarizability of the Water Molecule. Journal of Chemical Theory and Computation. PMID 30428257 DOI: 10.1021/acs.jctc.8b00978  1
2018 Ruiz Pestana L, Marsalek O, Markland TE, Head-Gordon T. The Quest for Accurate Liquid Water Properties from First Principles. The Journal of Physical Chemistry Letters. 5009-5016. PMID 30118601 DOI: 10.1021/acs.jpclett.8b02400  1
2018 Schaettle K, Ruiz Pestana L, Head-Gordon T, Lammers LN. A structural coarse-grained model for clays using simple iterative Boltzmann inversion. The Journal of Chemical Physics. 148: 222809. PMID 29907051 DOI: 10.1063/1.5011817  1
2018 Pestana LR, Minnetian N, Lammers LN, Head-Gordon T. Dynamical inversion of the energy landscape promotes non-equilibrium self-assembly of binary mixtures. Chemical Science. 9: 1640-1646. PMID 29675210 DOI: 10.1039/c7sc03524a  1
2018 Nerenberg PS, Head-Gordon T. New developments in force fields for biomolecular simulations. Current Opinion in Structural Biology. 49: 129-138. PMID 29477047 DOI: 10.1016/j.sbi.2018.02.002  1
2018 Albaugh A, Head-Gordon T, Niklasson AMN. Higher-order Extended Lagrangian Born-Oppenheimer Molecular Dynamics for Classical Polarizable Models. Journal of Chemical Theory and Computation. PMID 29316388 DOI: 10.1021/acs.jctc.7b01041  1
2017 Ruiz Pestana L, Mardirossian N, Head-Gordon M, Head-Gordon T. molecular dynamics simulations of liquid water using high quality meta-GGA functionals. Chemical Science. 8: 3554-3565. PMID 30155200 DOI: 10.1039/c6sc04711d  1
2017 Ruiz Pestana L, Felberg LE, Head-Gordon T. Coexistence of Multilayered Phases of Nanoconfined Water: the Importance of Flexible Confining Surfaces. Acs Nano. PMID 29236478 DOI: 10.1021/acsnano.7b06805  1
2017 Demerdash O, Mao Y, Liu T, Head-Gordon M, Head-Gordon T. Assessing many-body contributions to intermolecular interactions of the AMOEBA force field using energy decomposition analysis of electronic structure calculations. The Journal of Chemical Physics. 147: 161721. PMID 29096520 DOI: 10.1063/1.4999905  1
2017 Albaugh A, Head-Gordon T. A New Method for Treating Drude Polarization in Classical Molecular Simulation. Journal of Chemical Theory and Computation. PMID 28965397 DOI: 10.1021/acs.jctc.7b00838  1
2017 Belsare S, Pattni V, Heyden M, Head-Gordon T. Solvent Entropy Contributions to Catalytic Activity in Designed and Optimized Kemp Eliminases. The Journal of Physical Chemistry. B. PMID 28899094 DOI: 10.1021/acs.jpcb.7b07526  1
2017 Sasmal S, Lincoff J, Head-Gordon T. Effect of a Paramagnetic Spin Label on the Intrinsically Disordered Peptide Ensemble of Amyloid-β. Biophysical Journal. 113: 1002-1011. PMID 28877484 DOI: 10.1016/j.bpj.2017.06.067  1
2017 Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, ... ... Head-Gordon T, et al. Improvements to the APBS biomolecular solvation software suite. Protein Science : a Publication of the Protein Society. PMID 28836357 DOI: 10.1002/pro.3280  1
2017 Mao Y, Shao Y, Dziedzic J, Skylaris CK, Head-Gordon T, Head-Gordon M. Performance of the AMOEBA water model in the vicinity of QM solutes: A diagnosis using energy decomposition analysis. Journal of Chemical Theory and Computation. PMID 28430427 DOI: 10.1021/acs.jctc.7b00089  1
2017 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. The Journal of Chemical Physics. 146: 124115. PMID 28388116 DOI: 10.1063/1.4978684  1
2017 Bhowmick A, Sharma SC, Head-Gordon T. The Importance of the Scaffold for de Novo Enzymes: a Case Study with Kemp Eliminase. Journal of the American Chemical Society. PMID 28383910 DOI: 10.1021/jacs.6b12265  1
2017 Albaugh A, Niklasson AM, Head-Gordon T. Accurate Classical Polarization Solution with No Self-Consistent Field Iterations. The Journal of Physical Chemistry Letters. PMID 28350167 DOI: 10.1021/acs.jpclett.7b00450  1
2017 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. The Journal of Physical Chemistry. B. PMID 28306259 DOI: 10.1021/acs.jpcb.7b02320  1
2017 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. The Journal of Physical Chemistry. B. PMID 28290691 DOI: 10.1021/acs.jpcb.7b00865  1
2017 Esser A, Belsare S, Marx D, Head-Gordon T. Mode specific THz spectra of solvated amino acids using the AMOEBA polarizable force field. Physical Chemistry Chemical Physics : Pccp. PMID 28165073 DOI: 10.1039/c6cp07388c  1
2016 Ruiz Pestana L, Kolluri K, Head-Gordon T, Lammers LN. Direct Exchange Mechanism for Interlayer Ions in Non-Swelling Clays. Environmental Science & Technology. PMID 27997121 DOI: 10.1021/acs.est.6b04747  1
2016 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. The Journal of Physical Chemistry Letters. 35-40. PMID 27936759 DOI: 10.1021/acs.jpclett.6b02527  1
2016 Lincoff J, Sasmal S, Head-Gordon T. Comparing generalized ensemble methods for sampling of systems with many degrees of freedom. The Journal of Chemical Physics. 145: 174107. PMID 27825215 DOI: 10.1063/1.4965439  1
2016 Sasmal S, Schwierz N, Head-Gordon T. Mechanism of Nucleation and Growth of Aβ40-Fibrils from All-Atom and Coarse-Grained Simulations. The Journal of Physical Chemistry. B. PMID 27806205 DOI: 10.1021/acs.jpcb.6b09655  1
2016 Felberg LE, Brookes DH, Yap EH, Jurrus E, Baker NA, Head-Gordon T. PB-AM: An open-source, fully analytical linear poisson-boltzmann solver. Journal of Computational Chemistry. PMID 27804145 DOI: 10.1002/jcc.24528  1
2016 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. The Journal of Chemical Physics. 145: 124106. PMID 27782640 DOI: 10.1063/1.4962909  1
2016 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. Journal of Chemical Theory and Computation. PMID 27709939 DOI: 10.1021/acs.jctc.6b00764  1
2016 Albaugh A, Boateng HA, Bradshaw RT, Demerdash ON, Dziedzic J, Mao Y, Margul DT, Swails JM, Zeng Q, Case DA, Eastman PK, Essex JW, Head-Gordon M, Pande VS, Ponder JW, ... ... Head-Gordon T, et al. Advanced Potential Energy Surfaces for Molecular Simulation. The Journal of Physical Chemistry. B. PMID 27513316 DOI: 10.1021/acs.jpcb.6b06414  1
2016 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. The Journal of Chemical Physics. 145: 044109. PMID 27475350 DOI: 10.1063/1.4959125  1
2016 Demerdash ON, Head-Gordon T. Convergence of the Many-Body Expansion for Energy and Forces for Classical Polarizable Models in the Condensed Phase. Journal of Chemical Theory and Computation. PMID 27405002 DOI: 10.1021/acs.jctc.6b00335  1
2016 Bhowmick A, Brookes DH, Yost S, 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. Journal of the American Chemical Society. PMID 27387657 DOI: 10.1021/jacs.6b06543  1
2016 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. Physical Chemistry Chemical Physics : Pccp. PMID 27374812 DOI: 10.1039/c6cp03622h  1
2016 Brookes DH, Head-Gordon T. Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins. Journal of the American Chemical Society. PMID 26967199 DOI: 10.1021/jacs.6b00351  1
2016 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 Journal of Chemical Physics. 145. DOI: 10.1063/1.4962909  1
2015 Albaugh A, Demerdash O, Head-Gordon T. An efficient and stable hybrid extended Lagrangian/self-consistent field scheme for solving classical mutual induction. The Journal of Chemical Physics. 143: 174104. PMID 26547155 DOI: 10.1063/1.4933375  1
2015 Brookes DH, Head-Gordon T. Family of Oxygen-Oxygen Radial Distribution Functions for Water. The Journal of Physical Chemistry Letters. 6: 2938-43. PMID 26267185 DOI: 10.1021/acs.jpclett.5b01066  1
2015 Sharma SC, Armand T, Aurelia Ball K, Chen A, Pelton JG, Wemmer DE, Head-Gordon T. A Facile method for expression and purification of (15)N isotope-labeled human Alzheimer's β-amyloid peptides from E. coli for NMR-based structural analysis. Protein Expression and Purification. PMID 26231074 DOI: 10.1016/j.pep.2015.07.012  1
2015 Laury ML, Wang LP, Pande VS, Head-Gordon T, Ponder JW. Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model. The Journal of Physical Chemistry. B. 119: 9423-37. PMID 25683601 DOI: 10.1021/jp510896n  1
2015 Bhowmick A, Head-Gordon T. A monte carlo method for generating side chain structural ensembles. Structure (London, England : 1993). 23: 44-55. PMID 25482539 DOI: 10.1016/j.str.2014.10.011  1
2015 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. The Journal of Physical Chemistry. B. 119: 944-57. PMID 25254622 DOI: 10.1021/jp506203k  1
2015 Yedvabny E, Nerenberg PS, So C, Head-Gordon T. Disordered structural ensembles of vasopressin and oxytocin and their mutants. The Journal of Physical Chemistry. B. 119: 896-905. PMID 25231121 DOI: 10.1021/jp505902m  1
2015 Yedvabny E, Nerenberg PS, So C, Head-Gordon T. Disordered structural ensembles of vasopressin and oxytocin and their mutants Journal of Physical Chemistry B. 119: 896-905. DOI: 10.1021/jp505902m  1
2015 Bhowmick A, Head-Gordon T. A Monte Carlo method for generating side chain structural ensembles Structure. 23: 44-55. DOI: 10.1016/j.str.2014.10.011  1
2014 Ball KA, Wemmer DE, Head-Gordon T. Comparison of structure determination methods for intrinsically disordered amyloid-β peptides. The Journal of Physical Chemistry. B. 118: 6405-16. PMID 24410358 DOI: 10.1021/jp410275y  1
2014 Demerdash O, Yap EH, Head-Gordon T. Advanced potential energy surfaces for condensed phase simulation Annual Review of Physical Chemistry. 65: 149-174. PMID 24328448 DOI: 10.1146/annurev-physchem-040412-110040  1
2014 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. Neurobiology of Disease. 62: 62-72. PMID 24055772 DOI: 10.1016/j.nbd.2013.09.005  1
2014 Vazin T, Ball KA, Lu H, Park H, Ataeijannati Y, Head-Gordon T, Poo Mm, Schaffer DV. Corrigendum to "Efficient derivation of cortical glutamatergic neurons from human pluripotent stem cells: A model system to study neurotoxicity in Alzheimer's disease" [Neurobiol. Dis. 62 (2014) 62-72] Neurobiology of Disease. 65: 1. DOI: 10.1016/j.nbd.2013.12.012  1
2013 Yap EH, Head-Gordon T. Calculating the Bimolecular Rate of Protein-Protein Association with Interacting Crowders. Journal of Chemical Theory and Computation. 9: 2481-9. PMID 26583736 DOI: 10.1021/ct400048q  1
2013 Liguori N, Nerenberg PS, Head-Gordon T. Embedding Aβ42 in heterogeneous membranes depends on cholesterol asymmetries Biophysical Journal. 105: 899-910. PMID 23972842 DOI: 10.1016/j.bpj.2013.06.046  1
2013 Ball KA, Phillips AH, Wemmer DE, Head-Gordon T. Differences in β-strand populations of monomeric Aβ40 and Aβ42. Biophysical Journal. 104: 2714-24. PMID 23790380 DOI: 10.1016/j.bpj.2013.04.056  1
2013 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. The Journal of Physical Chemistry. B. 117: 9956-72. PMID 23750713 DOI: 10.1021/jp403802c  1
2013 Yap EH, Head-Gordon T. Calculating the bimolecular rate of protein-protein association with interacting crowders Journal of Chemical Theory and Computation. 9: 2481-2489. DOI: 10.1021/ct400048q  1
2012 Head-Gordon T, Lynden-Bell RM, Dowdle JR, Rossky PJ. Predicting cavity formation free energy: how far is the Gaussian approximation valid? Physical Chemistry Chemical Physics : Pccp. PMID 22495173 DOI: 10.1039/c2cp00046f  1
2012 Nerenberg PS, Jo B, So C, Tripathy A, Head-Gordon T. Optimizing solute-water van der Waals interactions to reproduce solvation free energies. The Journal of Physical Chemistry. B. 116: 4524-34. PMID 22443635 DOI: 10.1021/jp2118373  1
2012 Wales DJ, Head-Gordon T. Evolution of the potential energy landscape with static pulling force for two model proteins. The Journal of Physical Chemistry. B. 116: 8394-411. PMID 22432920 DOI: 10.1021/jp211806z  1
2012 Nerenberg PS, Jo B, So C, Tripathy A, Head-Gordon T. Optimizing solute-water van der waals interactions to reproduce solvation free energies Journal of Physical Chemistry B. 116: 4524-4534. DOI: 10.1021/jp2118373  1
2012 Wales DJ, Head-Gordon T. Evolution of the potential energy landscape with static pulling force for two model proteins Journal of Physical Chemistry B. 116: 8394-8411. DOI: 10.1021/jp211806z  1
2012 Ball KA, Phillips AH, Fawzi NL, Wemmer DE, Head-Gordon T. Amyloid-Beta Heterogeneous Conformational Ensembles: Differences Between the 40- and 42-Residue Peptides and Implications for Dimer Polyamorphism Biophysical Journal. 102: 631a. DOI: 10.1016/j.bpj.2011.11.3437  1
2011 Nerenberg PS, Head-Gordon T. Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides. Journal of Chemical Theory and Computation. 7: 1220-1230. PMID 26606367 DOI: 10.1021/ct2000183  1
2011 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. The Journal of Physical Chemistry. A. 115: 11438-54. PMID 21888323 DOI: 10.1021/jp206064n  1
2011 Peng C, Head-Gordon T. The dynamical mechanism of auto-inhibition of AMP-activated protein kinase Plos Computational Biology. 7. PMID 21814500 DOI: 10.1371/journal.pcbi.1002082  1
2011 Ball KA, Phillips AH, Nerenberg PS, Fawzi NL, Wemmer DE, Head-Gordon T. Homogeneous and heterogeneous tertiary structure ensembles of amyloid-β peptides. Biochemistry. 50: 7612-28. PMID 21797254 DOI: 10.1021/bi200732x  1
2011 Lambrecht DS, Clark GN, Head-Gordon T, Head-Gordon M. Simulated photoelectron spectra of the cyanide-water anion via quasiclassical molecular dynamics. The Journal of Physical Chemistry. A. 115: 5928-35. PMID 21405045 DOI: 10.1021/jp110334w  1
2011 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. Physical Chemistry Chemical Physics : Pccp. 13: 2748-57. PMID 21152590 DOI: 10.1039/c0cp01701a  1
2011 Lin MS, Head-Gordon T. Reliable protein structure refinement using a physical energy function Journal of Computational Chemistry. 32: 709-717. PMID 20925085 DOI: 10.1002/jcc.21664  1
2011 Fawzi NL, Phillips AH, Ruscio JZ, Doucleff M, Wemmer DE, Head-Gordon T. Structure and dynamics of the Aβ 21-30 peptide from the interplay of NMR experiments and molecular simulations (Journal of the American Chemical Society (2008) 130 (6145-6158) DOI: 10.1021/ja710366c) Journal of the American Chemical Society. 133: 11816. DOI: 10.1021/ja204315n  1
2011 Nerenberg PS, Head-Gordon T. Optimizing protein-solvent force fields to reproduce intrinsic conformational preferences of model peptides Journal of Chemical Theory and Computation. 7: 1220-1230. DOI: 10.1021/ct2000183  1
2010 Kohn JE, Afonine PV, Ruscio JZ, Adams PD, Head-Gordon T. Evidence of functional protein dynamics from X-ray crystallographic ensembles Plos Computational Biology. 6. PMID 20865158 DOI: 10.1371/journal.pcbi.1000911  1
2010 Yap EH, Head-Gordon T. A New and Efficient Poisson-Boltzmann Solver for Interaction of Multiple Proteins. Journal of Chemical Theory and Computation. 6: 2214-2224. PMID 20711494  1
2010 Sodt AJ, Head-Gordon T. Driving forces for transmembrane α-helix oligomerization Biophysical Journal. 99: 227-237. PMID 20655851 DOI: 10.1016/j.bpj.2010.03.071  1
2010 Clark GNI, Hura GL, Teixeira J, Soper AK, Head-Gordon T. Small-angle scattering and the structure of ambient liquid water Proceedings of the National Academy of Sciences of the United States of America. 107: 14003-14007. PMID 20647388 DOI: 10.1073/pnas.1006599107  1
2010 Sodt AJ, Head-Gordon T. An implicit solvent coarse-grained lipid model with correct stress profile. The Journal of Chemical Physics. 132: 205103. PMID 20515115 DOI: 10.1063/1.3408285  1
2010 Peng C, Zhang L, Head-Gordon T. Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions. Biophysical Journal. 98: 2356-2364. PMID 20483345 DOI: 10.1016/j.bpj.2010.01.044  1
2010 Soper AK, Teixeira J, Head-Gordon T. Is ambient water inhomogeneous on the nanometer-length scale? Proceedings of the National Academy of Sciences of the United States of America. 107: E44; author reply E4. PMID 20220097 DOI: 10.1073/pnas.0912158107  1
2010 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. The Journal of Physical Chemistry. B. 114: 2549-64. PMID 20136072 DOI: 10.1021/jp910674d  1
2010 Johnson ME, Malardier-Jugroot C, Head-Gordon T. Effects of co-solvents on peptide hydration water structure and dynamics. Physical Chemistry Chemical Physics : Pccp. 12: 393-405. PMID 20023817 DOI: 10.1039/b915888j  1
2010 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. Physical Chemistry Chemical Physics : Pccp. 12: 382-92. PMID 20023816 DOI: 10.1039/b915346b  1
2010 Ruscio JZ, Fawzi NL, Head-Gordon T. How hot? Systematic convergence of the replica exchange method using multiple reservoirs. Journal of Computational Chemistry. 31: 620-7. PMID 19554556 DOI: 10.1002/jcc.21355  1
2010 Clark GNI, Cappa CD, Smith JD, Saykally RJ, Head-Gordon T. The structure of ambient water Molecular Physics. 108: 1415-1433. DOI: 10.1080/00268971003762134  1
2010 Soper AK, Teixeira J, Head-Gordon T. Is ambient water inhomogeneous on the nanometer-length scale? Proceedings of the National Academy of Sciences of the United States of America. 107: E44. DOI: 10.1073/pnas.0912158107  1
2010 Sodt AJ, Head-Gordon T. An implicit solvent coarse-grained lipid model with correct stress profile Journal of Chemical Physics. 132. DOI: 10.1063/1.3408285  1
2010 Yap EH, Head-Gordon T. New and efficient poisson-Boltzmann solver for interaction of multiple proteins Journal of Chemical Theory and Computation. 6: 2214-2224. DOI: 10.1021/ct100145f  1
2009 Ruscio JZ, Kohn JE, Ball KA, Head-Gordon T. The influence of protein dynamics on the success of computational enzyme design. Journal of the American Chemical Society. 131: 14111-5. PMID 19788332 DOI: 10.1021/ja905396s  1
2009 Johnson ME, Head-Gordon T. Assessing thermodynamic-dynamic relationships for waterlike liquids. The Journal of Chemical Physics. 130: 214510. PMID 19508079 DOI: 10.1063/1.3140608  1
2009 Johnson ME, Malardier-Jugroot C, Murarka RK, Head-Gordon T. Hydration water dynamics near biological interfaces. The Journal of Physical Chemistry. B. 113: 4082-92. PMID 19425247 DOI: 10.1021/jp806183v  0.96
2008 Lin MS, Head-Gordon T. Improved Energy Selection of Nativelike Protein Loops from Loop Decoys. Journal of Chemical Theory and Computation. 4: 515-21. PMID 26620791 DOI: 10.1021/ct700292u  1
2008 Malardier-Jugroot C, Johnson ME, Murarka RK, Head-Gordon T. Aqueous peptides as experimental models for hydration water dynamics near protein surfaces. Physical Chemistry Chemical Physics : Pccp. 10: 4903-8. PMID 18688534 DOI: 10.1039/b806995f  1
2008 Fawzi NL, Yap EH, Okabe Y, Kohlstedt KL, Brown SP, Head-Gordon T. Contrasting disease and nondisease protein aggregation by molecular simulation. Accounts of Chemical Research. 41: 1037-47. PMID 18646868 DOI: 10.1021/ar800062k  1
2008 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. Journal of the American Chemical Society. 130: 6145-58. PMID 18412346 DOI: 10.1021/ja710366c  1
2008 Head-Gordon T, Lynden-Bell RM. Hydrophobic solvation of Gay-Berne particles in modified water models. The Journal of Chemical Physics. 128: 104506. PMID 18345905 DOI: 10.1063/1.2837289  1
2008 Murarka RK, Head-Gordon T. Dielectric relaxation of aqueous solutions of hydrophilic versus amphiphilic peptides. The Journal of Physical Chemistry. B. 112: 179-86. PMID 18069810 DOI: 10.1021/jp073440m  1
2008 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. Biophysical Journal. 94: 2007-16. PMID 18032553 DOI: 10.1529/biophysj.107.121467  1
2008 Yap EH, Fawzi NL, Head-Gordon T. A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding. Proteins. 70: 626-38. PMID 17879350 DOI: 10.1002/prot.21515  1
2008 Murarka RK, Head-Gordon T. Dielectric relaxation of aqueous solutions of hydrophilic versus amphiphilic peptides Journal of Physical Chemistry B. 112: 179-186. DOI: 10.1021/jp073440m  1
2008 Lin MS, Head-Gordon T. Improved energy selection of nativelike protein loops from loop decoys Journal of Chemical Theory and Computation. 4: 515-521. DOI: 10.1021/ct700292u  1
2007 Murarka RK, Head-Gordon T. Single particle and collective hydration dynamics for hydrophobic and hydrophilic peptides. The Journal of Chemical Physics. 126: 215101. PMID 17567218 DOI: 10.1063/1.2737050  1
2007 Lin MS, Fawzi NL, Head-Gordon T. Hydrophobic potential of mean force as a solvation function for protein structure prediction. Structure (London, England : 1993). 15: 727-40. PMID 17562319 DOI: 10.1016/j.str.2007.05.004  1
2007 Johnson ME, Head-Gordon T, Louis AA. Representability problems for coarse-grained water potentials. The Journal of Chemical Physics. 126: 144509. PMID 17444725 DOI: 10.1063/1.2715953  1
2007 Malardier-Jugroot C, Head-Gordon T. Separable cooperative and localized translational motions of water confined by a chemically heterogeneous environment Physical Chemistry Chemical Physics. 9: 1962-1971. PMID 17431524 DOI: 10.1039/b616997j  1
2007 Head-Gordon T, Rick SW. Consequences of chain networks on thermodynamic, dielectric and structural properties for liquid water. Physical Chemistry Chemical Physics : Pccp. 9: 83-91. PMID 17164889 DOI: 10.1039/b614742a  1
2007 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. Journal of Molecular Biology. 365: 535-50. PMID 17070840 DOI: 10.1016/j.jmb.2006.10.011  1
2007 Murarka RK, Head-Gordon T. Single particle and collective hydration dynamics for hydrophobic and hydrophilic peptides Journal of Chemical Physics. 126. DOI: 10.1063/1.2737050  1
2007 Head-Gordon T, Rick SW. Consequences of chain networks on thermodynamic, dielectric and structural properties for liquid water Physical Chemistry Chemical Physics. 9: 83-91. DOI: 10.1039/b614742a  1
2006 Lotan I, Head-Gordon T. An Analytical Electrostatic Model for Salt Screened Interactions between Multiple Proteins. Journal of Chemical Theory and Computation. 2: 541-55. PMID 26626662 DOI: 10.1021/ct050263p  1
2006 Head-Gordon T, Johnson ME. Tetrahedral structure or chains for liquid water. Proceedings of the National Academy of Sciences of the United States of America. 103: 7973-7. PMID 16698934 DOI: 10.1073/pnas.0510593103  1
2006 Lynden-Bell RM, Head-Gordon T. Solvation in modified water models: Towards understanding hydrophobic effects Molecular Physics. 104: 3593-3605. DOI: 10.1080/00268970601022727  1
2006 Lotan I, Head-Gordon T. An analytical electrostatic model for salt screened interactions between multiple proteins Journal of Chemical Theory and Computation. 2: 541-555. DOI: 10.1021/ct050263p  1
2005 Russo D, Murarka RK, Copley JRD, Head-Gordon T. Molecular view of water dynamics near model peptides Journal of Physical Chemistry B. 109: 12966-12975. PMID 16852609 DOI: 10.1021/jp051137k  1
2005 Marianayagam NJ, Fawzi NL, Head-Gordon T. Protein folding by distributed computing and the denatured state ensemble. Proceedings of the National Academy of Sciences of the United States of America. 102: 16684-9. PMID 16267133 DOI: 10.1073/pnas.0506388102  1
2005 Fawzi NL, Chubukov V, Clark LA, Brown S, Head-Gordon T. Influence of denatured and intermediate states of folding on protein aggregation. Protein Science : a Publication of the Protein Society. 14: 993-1003. PMID 15772307 DOI: 10.1110/ps.041177505  1
2004 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. The Journal of Chemical Physics. 120: 9665-78. PMID 15267980 DOI: 10.1063/1.1683075  1
2004 Brown S, Head-Gordon T. Intermediates and the folding of proteins L and G Protein Science. 13: 958-970. PMID 15044729 DOI: 10.1110/ps.03316004  1
2004 Russo D, Hura G, Head-Gordon T. Hydration Dynamics Near a Model Protein Surface Biophysical Journal. 86: 1852-1862. PMID 14990511 DOI: 10.1016/S0006-3495(04)74252-6  1
2004 Russo D, Murarka RK, Hura G, Verschell E, Copley JRD, Head-Gordon T. Evidence for anomalous hydration dynamics near a model hydrophobic peptide Journal of Physical Chemistry B. 108: 19885-19893. DOI: 10.1021/jp046847p  1
2004 Eskow E, Bader B, Byrd R, Crivelli S, Head-Gordon T, Lamberti V, Schnabel R. An optimization approach to the problem of protein structure prediction Mathematical Programming. 101: 497-514. DOI: 10.1007/s10107-003-0493-4  1
2004 Crivelli S, Head-Gordon T. A new load-balancing strategy for the solution of dynamical large-tree-search problems using a hierarchical approach Ibm Journal of Research and Development. 48: 153-160.  1
2003 Brown S, Fawzi NJ, Head-Gordon T. Coarse-grained sequences for protein folding and design. Proceedings of the National Academy of Sciences of the United States of America. 100: 10712-7. PMID 12963815 DOI: 10.1073/pnas.1931882100  1
2003 Head-Gordon T, Brown S. Minimalist models for protein folding and design Current Opinion in Structural Biology. 13: 160-167. PMID 12727508 DOI: 10.1016/S0959-440X(03)00030-7  1
2003 Brown S, Head-Gordon T. Cool walking: a new Markov chain Monte Carlo sampling method. Journal of Computational Chemistry. 24: 68-76. PMID 12483676 DOI: 10.1002/jcc.10181  1
2003 Hura G, Russo D, Glaeser RM, Head-Gordon T, Krack M, Parrinello M. Water structure as a function of temperature from X-ray scattering experiments and ab initio molecular dynamics Physical Chemistry Chemical Physics. 5: 1981-1991. DOI: 10.1039/b301481a  1
2003 Brown S, Head-Gordon T. Cool walking: A new Markov chain Monte Carlo sampling method Journal of Computational Chemistry. 24: 68-76. DOI: 10.1002/jcc.10181  1
2002 Head-Gordon T, Hura G. Water structure from scattering experiments and simulation. Chemical Reviews. 102: 2651-70. PMID 12175263  1
2002 Sorenson JM, Head-Gordon T. Protein engineering study of protein L by simulation Journal of Computational Biology. 9: 35-54. PMID 11911794 DOI: 10.1089/10665270252833181  1
2002 Sorenson JM, Head-Gordon T. Toward minimalist models of larger proteins: A ubiquitin-like protein Proteins: Structure, Function and Genetics. 46: 368-379. PMID 11835512 DOI: 10.1002/prot.1174  1
2002 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 Crystallographica. Section a, Foundations of Crystallography. 58: 162-70. PMID 11832586 DOI: 10.1107/S0108767301020256  1
2002 Crivelli S, Eskow E, Bader B, Lamberti V, Byrd R, Schnabel R, Head-Gordon T. A physical approach to protein structure prediction Biophysical Journal. 82: 36-49. PMID 11751294  1
2002 Head-Gordon T, Hura G. Water structure from scattering experiments and simulation Chemical Reviews. 102: 2651-2670. DOI: 10.1021/cr0006831  1
2001 Hsu CP, Fleming GR, Head-Gordon M, Head-Gordon T. Excitation energy transfer in condensed media Journal of Chemical Physics. 114: 3065-3072. DOI: 10.1063/1.1338531  1
2001 Head-Gordon T, Wooley JC. Computational challenges in structural and functional genomics Ibm Systems Journal. 40: 265-296.  1
2000 Sorenson JM, Head-Gordon T. Matching simulation and experiment: A new simplified model for simulating protein folding Journal of Computational Biology. 7: 469-481. PMID 11108474 DOI: 10.1089/106652700750050899  1
2000 Crivelli S, Byrd R, Eskow E, Schnabe R, Yu R, Philip TM, Head-Gordon T. A global optimization strategy for predicting α-helical protein tertiary structure Computers and Chemistry. 24: 489-497. PMID 10816018  1
2000 Sorenson JM, Hura G, Glaeser RM, Head-Gordon T. What can X-ray scattering tell us about the radial distribution functions of water? Journal of Chemical Physics. 113: 9149-9161. DOI: 10.1063/1.1319615  1
2000 Hura G, Sorenson JM, Glaeser RM, Head-Gordon T. High-quality X-ray scattering experiment on liquid water at ambient conditions Journal of Chemical Physics. 113: 9140-9148. DOI: 10.1063/1.1319614  1
1999 Chang S, Head-Gordon T, Glaeser RM, Downing KH. Chemical bonding effects in the determination of protein structures by electron crystallography. Acta Crystallographica Section a: Foundations of Crystallography. 55: Pt 2 Pt 2/-. PMID 10927261  1
1999 Sorenson JM, Head-Gordon T. Redesigning the hydrophobic core of a model β-sheet protein: Destabilizing traps through a threading approach Proteins: Structure, Function and Genetics. 37: 582-591. PMID 10651274 DOI: 10.1002/(SICI)1097-0134(19991201)37:4<582::AID-PROT9>3.0.CO;2-M  1
1999 Pertsemlidis A, Soper AK, Sorenson JM, Head-Gordon T. Evidence for microscopic, long-range hydration forces for a hydrophobic amino acid Proceedings of the National Academy of Sciences of the United States of America. 96: 481-486. PMID 9892659 DOI: 10.1073/pnas.96.2.481  1
1999 Hura G, Sorenson JM, Glaeser RM, Head-Gordon T. Solution X-ray scattering as a probe of hydration-dependent structuring of aqueous solutions Perspectives in Drug Discovery and Design. 17: 97-118. DOI: 10.1023/A:1008778724866  1
1999 Crivelli S, Head-Gordon T, Byrd R, Eskow E, Schnabel R. A hierarchical approach for parallelization of a global optimization method for protein structure prediction Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1685: 578-585.  1
1999 Hsu CP, Head-Gordon M, Head-Gordon T. Reaction field cavity optimization: A born-again Born model for ionic hydration Journal of Chemical Physics. 111: 9700-9704.  1
1999 Sorenson JM, Hura G, Soper AK, Pertsemlidis A, Head-Gordon T. Determining the role of hydration forces in protein folding Journal of Physical Chemistry B. 103: 5424-5426.  1
1998 Sorenson JM, Head-Gordon T. The importance of hydration for the kinetics and thermodynamics of protein folding: Simplified lattice models Folding and Design. 3: 523-534. PMID 9889163 DOI: 10.1016/S1359-0278(98)00068-6  1
1997 Head-Gordon T, Sorenson JM, Pertsemlidis A, Glaeser RM. Differences in hydration structure near hydrophobic and hydrophilic amino acids Biophysical Journal. 73: 2106-2115. PMID 9336206  1
1996 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 Proceedings of the National Academy of Sciences of the United States of America. 93: 10769-10774. PMID 8855255 DOI: 10.1073/pnas.93.20.10769  1
1995 Stillinger FH, Head-Gordon T. Collective aspects of protein folding illustrated by a toy model. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 52: 2872-2877. PMID 9963733  1
1995 Yu RC, Head-Gordon T. Neural-network design applied to protein-secondary-structure predictions. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 51: 3619-3627. PMID 9963044  1
1995 Stillinger FH, Head-Gordon T. Collective aspects of protein folding illustrated by a toy model Physical Review E. 52: 2872-2877. DOI: 10.1103/PhysRevE.52.2872  1
1995 Yu RC, Head-Gordon T. Neural-network design applied to protein-secondary-structure predictions Physical Review E. 51: 3619-3627. DOI: 10.1103/PhysRevE.51.3619  1
1995 Head-Gordon T. Is water structure around hydrophobic groups clathrate-like? Proceedings of the National Academy of Sciences of the United States of America. 92: 8308-8312. DOI: 10.1073/pnas.92.18.8308  1
1995 Head-Gordon T. A new solvent model for hydrophobic association in water. 1. Thermodynamics Journal of the American Chemical Society. 117: 501-507.  1
1994 Head-Gordon T. An efficient solvent model for study of hydrophobic phenomena Chemical Physics Letters. 227: 215-220. DOI: 10.1016/0009-2614(94)00811-6  1
1994 Head-Gordon M, Head-Gordon T. Analytic MP2 frequencies without fifth-order storage. Theory and application to bifurcated hydrogen bonds in the water hexamer Chemical Physics Letters. 220: 122-128. DOI: 10.1016/0009-2614(94)00116-2  1
1994 Shang HS, Head-Gordon T. Stabilization of helices in glycine and alanine dipeptides in a reaction field model of solvent Journal of the American Chemical Society. 116: 1528-1532.  1
1993 Head-Gordon T, Stillinger FH. Optimal neural networks for protein-structure prediction. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 48: 1502-1515. PMID 9960741  1
1993 Stillinger FH, Head-Gordon T, Hirshfeld CL. Toy model for protein folding. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 48: 1469-1477. PMID 9960736 DOI: 10.1103/PhysRevE.48.1469  1
1993 Stillinger FH, Head-Gordon T. Perturbational view of inherent structures in water. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 47: 2484-2490. PMID 9960280 DOI: 10.1103/PhysRevE.47.2484  1
1993 Head-Gordon T, Stillinger FH. Optimal neural networks for protein-structure prediction Physical Review E. 48: 1502-1515. DOI: 10.1103/PhysRevE.48.1502  1
1993 Head-Gordon T, Stillinger FH. An orientational perturbation theory for pure liquid water Journal of Chemical Physics. 98: 3313-3327.  1
1993 Head-Gordon T, Stillinger FH. Predicting polypeptide and protein structures from amino acid sequence: Antlion method applied to melittin Biopolymers. 33: 293-303.  1
1992 Head-Gordon T, Stillinger FH, Wright MH, Gay DM. Poly(L-alanine) as a universal reference material for understanding protein energies and structures. Proceedings of the National Academy of Sciences of the United States of America. 89: 11513-7. PMID 1454840  1
1992 Head-Gordon T, Stillinger FH. Enthalpy of knotted polypeptides Journal of Physical Chemistry. 96: 7792-7796.  1
1991 Head-Gordon T, Brooks CL. Virtual rigid body dynamics. Biopolymers. 31: 77-100. PMID 2025686 DOI: 10.1002/bip.360310108  1
1991 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. Proceedings of the National Academy of Sciences of the United States of America. 88: 11076-80. PMID 1763023  1
1991 Head-Gordon T, Head-Gordon M, Frisch MJ, Brooks CL, Pople JA. Theoretical study of blocked glycine and alanine peptide analogues Journal of the American Chemical Society. 113: 5989-5997.  1
1989 Head-Gordon T, Brooks CL. Evaluation of simple model descriptions of the diffusional association rate for enzyme-ligand systems Journal of Physical Chemistry. 93: 490-494.  1
1987 Head-Gordon T, Brooks CL. The role of electrostatics in the binding of small ligands to enzymes Journal of Physical Chemistry. 91: 3342-3349.  1
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