| Year |
Citation |
Score |
| 2023 |
Viegas RG, Sanches MN, Chen AA, Paulovich FV, Garcia AE, Leite VBP. Characterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop. Journal of Chemical Information and Modeling. PMID 37606640 DOI: 10.1021/acs.jcim.3c00426 |
0.596 |
|
| 2022 |
Ngo VA, Garcia AE. Millisecond molecular dynamics simulations of KRas-dimer formation and interfaces. Biophysical Journal. PMID 35462078 DOI: 10.1016/j.bpj.2022.04.026 |
0.331 |
|
| 2022 |
Pulavarti SVSRK, Maguire JB, Yuen S, Harrison JS, Griffin J, Premkumar L, Esposito EA, Makhatadze GI, Garcia AE, Weiss TM, Snell EH, Kuhlman B, Szyperski T. From Protein Design to the Energy Landscape of a Cold Unfolding Protein. The Journal of Physical Chemistry. B. PMID 35128921 DOI: 10.1021/acs.jpcb.1c10750 |
0.354 |
|
| 2022 |
Janke JJ, Yu Y, Pomin VH, Zhao J, Wang C, Linhardt RJ, García AE. Characterization of Heparin's Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy. Journal of Chemical Theory and Computation. PMID 35108013 DOI: 10.1021/acs.jctc.1c00760 |
0.689 |
|
| 2020 |
Ngo VA, Sarkar S, Neale C, Garcia AE. How Anionic Lipids Affect Spatiotemporal Properties of KRAS4B on Model Membranes. The Journal of Physical Chemistry. B. PMID 32438809 DOI: 10.1021/Acs.Jpcb.0C02642 |
0.33 |
|
| 2020 |
Neale C, García AE. The Plasma Membrane as a Competitive Inhibitor and Positive Allosteric Modulator of KRas4B Signaling. Biophysical Journal. PMID 32027820 DOI: 10.1016/J.Bpj.2019.12.039 |
0.302 |
|
| 2020 |
Ngo VA, Sarka S, Neale C, Garcia AE. How Different Anionic Lipids Sort Dynamics of KRAS4B on Model Membranes, POPS versus PIP2 in Millisecond all Atom Molecular Dynamics Simulations Biophysical Journal. 118: 55a. DOI: 10.1016/J.Bpj.2019.11.479 |
0.356 |
|
| 2019 |
Stephen AG, Agarwal A, Garcia AE, Gnanakaran GS, Hettige J, Neale C, Travers T, Bhatia H, Bremer P, Carpenter T, Glosli J, Ingolfsson H, Karande P, Lightstone F, Oppelstrup T, et al. Abstract 3373: Identification of KRAS membrane bound states using an integrated computational and experimental approach Cancer Research. 79: 3373-3373. DOI: 10.1158/1538-7445.Am2019-3373 |
0.329 |
|
| 2018 |
Neale CA, Garcia AE. Methionine 170 Is an Environmentally Sensitive Membrane Anchor in the Disordered HVR of K-Ras4B. The Journal of Physical Chemistry. B. PMID 30351122 DOI: 10.1021/Acs.Jpcb.8B07919 |
0.327 |
|
| 2018 |
Miner JC, García AE. Concentration-dependent and configuration-dependent interactions of monovalent ions with an RNA tetraloop. The Journal of Chemical Physics. 148: 222837. PMID 29907048 DOI: 10.1063/1.5019939 |
0.344 |
|
| 2018 |
Ye L, Neale C, Sljoka A, Lyda B, Pichugin D, Tsuchimura N, Larda ST, Pomès R, García AE, Ernst OP, Sunahara RK, Prosser RS. Mechanistic insights into allosteric regulation of the A adenosine G protein-coupled receptor by physiological cations. Nature Communications. 9: 1372. PMID 29636462 DOI: 10.1038/S41467-018-03314-9 |
0.409 |
|
| 2017 |
Zwarycz AS, Fossat MJ, Akanyeti O, Lin Z, Rosenman DJ, Garcia AE, Royer CA, Mills KV, Wang C. V67L Mutation Fills Internal Cavity to Stabilize RecA Mtu Intein. Biochemistry. PMID 28488863 DOI: 10.1021/Acs.Biochem.6B01264 |
0.392 |
|
| 2017 |
Miner JC, Garcia AE. Equilibrium Denaturation and Preferential Interactions of an RNA Tetraloop With Urea. The Journal of Physical Chemistry. B. PMID 28181434 DOI: 10.1021/Acs.Jpcb.6B10767 |
0.345 |
|
| 2017 |
Kitazawa S, Fossat MJ, McCallum SA, Garcia AE, Royer CA. NMR and Computation Reveal a Pressure-Sensitive Folded Conformation of Trp-Cage. The Journal of Physical Chemistry. B. PMID 28107009 DOI: 10.1021/Acs.Jpcb.6B11810 |
0.488 |
|
| 2017 |
Fossat MJ, Kitazawa S, McCallum S, Garcia A, Royer C. A Novel Trp Cage Conformer Revealed by Combining High Pressure NMR and MD Simulations Biophysical Journal. 112: 61a. DOI: 10.1016/J.Bpj.2016.11.366 |
0.412 |
|
| 2017 |
Neale C, Pomès R, Sterne-Marr R, García A. Protein Folding upon Binding Revealed by Molecular Dynamics Simulation Biophysical Journal. 112: 54a. DOI: 10.1016/J.Bpj.2016.11.329 |
0.43 |
|
| 2017 |
Miner JC, Garcia AE. Preferential Interactions of Charged and Neutral Cosolutes with a Model RNA Hairpin Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.1988 |
0.328 |
|
| 2016 |
Fossat MJ, Dao TP, Jenkins K, Dellarole M, Yang Y, McCallum SA, Garcia AE, Barrick D, Roumestand C, Royer CA. High-Resolution Mapping of a Repeat Protein Folding Free Energy Landscape. Biophysical Journal. 111: 2368-2376. PMID 27926838 DOI: 10.1016/J.Bpj.2016.08.027 |
0.515 |
|
| 2016 |
Miner JC, Chen AA, García AE. Free-energy landscape of a hyperstable RNA tetraloop. Proceedings of the National Academy of Sciences of the United States of America. PMID 27233937 DOI: 10.1073/Pnas.1603154113 |
0.592 |
|
| 2016 |
Bellissent-Funel MC, Hassanali A, Havenith M, Henchman R, Pohl P, Sterpone F, van der Spoel D, Xu Y, Garcia AE. Water Determines the Structure and Dynamics of Proteins. Chemical Reviews. PMID 27186992 DOI: 10.1021/Acs.Chemrev.5B00664 |
0.456 |
|
| 2016 |
Neale C, Pomès R, García AE. Peptide Bond Isomerization in High-Temperature Simulations. Journal of Chemical Theory and Computation. 12: 1989-99. PMID 26866899 DOI: 10.1021/Acs.Jctc.5B01022 |
0.347 |
|
| 2016 |
Janke JJ, Zhang F, Linhardt RJ, Garcia AE. Heparin-Sclerostin Interactions from Surface Plasmon Resonance and Molecular Dynamics Simulations Biophysical Journal. 110: 544a. DOI: 10.1016/J.Bpj.2015.11.2912 |
0.417 |
|
| 2016 |
Fossat MJ, Garcia A, Barrick D, Roumestand C, Royer CA. Exploring Folding Cooperativity of a Repeat Protein Folding by 2D-NMR Detected Pressure Perturbation Biophysical Journal. 110: 391a. DOI: 10.1016/J.Bpj.2015.11.2115 |
0.459 |
|
| 2016 |
Neale C, Huang K, Garcia AE, Tristram-Nagle S. Penetration of HIV-1 Tat47-57 into PC/PE Bilayers Assessed by MD Simulation and X-Ray Scattering Biophysical Journal. 110: 204a. DOI: 10.1016/J.Bpj.2015.11.1137 |
0.336 |
|
| 2015 |
Krafnick RC, García AE. Efficient Schmidt number scaling in dissipative particle dynamics. The Journal of Chemical Physics. 143: 243106. PMID 26723591 DOI: 10.1063/1.4930921 |
0.332 |
|
| 2015 |
Rosenman DJ, Wang C, Garcia AE. Characterization of Aβ Monomers Through the Convergence of Ensemble Properties Among Simulations with Multiple Force Fields. The Journal of Physical Chemistry. B. PMID 26562747 DOI: 10.1021/Acs.Jpcb.5B09379 |
0.376 |
|
| 2015 |
Neale C, Herce HD, Pomès R, García AE. Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor? Biophysical Journal. 109: 1652-62. PMID 26488656 DOI: 10.1016/J.Bpj.2015.08.028 |
0.387 |
|
| 2015 |
Tripathi S, Garcìa AE, Makhatadze GI. Alterations of Nonconserved Residues Affect Protein Stability and Folding Dynamics through Charge-Charge Interactions. The Journal of Physical Chemistry. B. 119: 13103-12. PMID 26413861 DOI: 10.1021/Acs.Jpcb.5B08527 |
0.433 |
|
| 2015 |
English CA, García AE. Charged Termini on the Trp-Cage Roughen the Folding Energy Landscape. The Journal of Physical Chemistry. B. 119: 7874-81. PMID 26018669 DOI: 10.1021/Acs.Jpcb.5B02040 |
0.8 |
|
| 2015 |
Krafnick RC, García AE. Impact of hydrodynamics on effective interactions in suspensions of active and passive matter. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 91: 022308. PMID 25768506 DOI: 10.1103/Physreve.91.022308 |
0.307 |
|
| 2015 |
Garcia AE, Miner J, Chen AA. Reversible Folding of Hyperstable RNA Tetraloops Using Molecular Dynamics Simulations Biophysical Journal. 108: 370a. DOI: 10.1016/J.Bpj.2014.11.2029 |
0.655 |
|
| 2015 |
Miner JC, Chen AA, García AE. Molecular Simulations Studies of RNA Tetraloop Hyperstability: The Effect of Stem Length on Folding Dynamics Biophysical Journal. 108: 237a. DOI: 10.1016/J.Bpj.2014.11.1313 |
0.614 |
|
| 2015 |
Alarcon Ochoa JA, Garcia AE. Simulations of Cosolute Effects on Protein's Stability Biophysical Journal. 108: 218a. DOI: 10.1016/J.Bpj.2014.11.1204 |
0.503 |
|
| 2014 |
Huang K, García AE. Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering. Journal of Chemical Theory and Computation. 10: 4264-4272. PMID 25328493 DOI: 10.1021/Ct500305U |
0.409 |
|
| 2014 |
Huang K, García AE. Effects of truncating van der Waals interactions in lipid bilayer simulations. The Journal of Chemical Physics. 141: 105101. PMID 25217953 DOI: 10.1063/1.4893965 |
0.383 |
|
| 2014 |
Akabori K, Huang K, Treece BW, Jablin MS, Maranville B, Woll A, Nagle JF, Garcia AE, Tristram-Nagle S. HIV-1 Tat membrane interactions probed using X-ray and neutron scattering, CD spectroscopy and MD simulations. Biochimica Et Biophysica Acta. 1838: 3078-87. PMID 25148702 DOI: 10.1016/J.Bbamem.2014.08.014 |
0.333 |
|
| 2014 |
Jimenez-Cruz CA, Garcia AE. Equilibrium thermodynamics and folding kinetics of a short, fast-folding, beta-hairpin. Physical Chemistry Chemical Physics : Pccp. 16: 6422-9. PMID 24472872 DOI: 10.1039/C3Cp54336F |
0.48 |
|
| 2014 |
Akabori K, Treece BW, Jablin MS, Nagle JF, Maranville B, Huang K, Garcia AE, Tristram-Nagle S. Hiv-1 Tat Membrane Translocation Probed by Low- and Wide-Angle X-Ray Scattering, Neutron Scattering, CD Spectroscopy and MD Simulations Biophysical Journal. 106: 91a. DOI: 10.1016/J.Bpj.2013.11.574 |
0.31 |
|
| 2014 |
English CA, García AE. Effects of Neutral, Capped Ends Versus Charged Ends on the Folding of the Trp-cage Miniprotein Biophysical Journal. 106: 670a. DOI: 10.1016/J.Bpj.2013.11.3711 |
0.805 |
|
| 2014 |
Turgut D, Okan OB, Rammohan A, Garcia AE, Ozisik R. Simple Rules Imposed on a Primitive Cubic Lattice Robustly Generate Structures that Mimic Features of Real Proteins Biophysical Journal. 106: 655a. DOI: 10.1016/J.Bpj.2013.11.3624 |
0.416 |
|
| 2014 |
Miner JC, Chen AA, Garcia AE. De Novo Folding of RNA Hairpins by Temperature Replica Exchange Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.1642 |
0.576 |
|
| 2014 |
Rosenman DJ, Clemente N, Wang C, García AE. Systematic Characterization of Wild Type and Familial Alzheimer's Disease Mutant Aβ Monomers Through the Convergence of Ensembles Simulated with Different Force Fields Biophysical Journal. 106: 269a. DOI: 10.1016/J.Bpj.2013.11.1578 |
0.405 |
|
| 2013 |
Jimenez-Cruz CA, Garcia AE. Reconstructing the Most Probable Folding Transition Path from Replica Exchange Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 9: 3750-5. PMID 26584126 DOI: 10.1021/Ct400170X |
0.417 |
|
| 2013 |
Roche J, Dellarole M, Caro JA, Norberto DR, Garcia AE, Garcia-Moreno B, Roumestand C, Royer CA. Effect of internal cavities on folding rates and routes revealed by real-time pressure-jump NMR spectroscopy. Journal of the American Chemical Society. 135: 14610-8. PMID 23987660 DOI: 10.1021/Ja406682E |
0.437 |
|
| 2013 |
Connors CR, Rosenman DJ, Lopes DH, Mittal S, Bitan G, Sorci M, Belfort G, Garcia A, Wang C. Tranilast binds to aβ monomers and promotes aβ fibrillation. Biochemistry. 52: 3995-4002. PMID 23679559 DOI: 10.1021/Bi400426T |
0.364 |
|
| 2013 |
Garcia AE. Please, get in my way so that I can be more efficient! Biophysical Journal. 104: 1842-3. PMID 23663825 DOI: 10.1016/J.Bpj.2013.03.042 |
0.355 |
|
| 2013 |
Stephenson W, Asare-Okai PN, Chen AA, Keller S, Santiago R, Tenenbaum SA, Garcia AE, Fabris D, Li PT. The essential role of stacking adenines in a two-base-pair RNA kissing complex. Journal of the American Chemical Society. 135: 5602-11. PMID 23517345 DOI: 10.1021/Ja310820H |
0.595 |
|
| 2013 |
Sathyamoorthy B, Singarapu KK, Garcia AE, Szyperski T. Protein conformational space populated in solution probed with aromatic residual dipolar (13) C-(1) H couplings. Chembiochem : a European Journal of Chemical Biology. 14: 684-8. PMID 23494854 DOI: 10.1002/Cbic.201300016 |
0.392 |
|
| 2013 |
Tripathi S, Makhatadze GI, Garcia AE. Backtracking due to residual structure in the unfolded state changes the folding of the third fibronectin type III domain from tenascin-C. The Journal of Physical Chemistry. B. 117: 800-10. PMID 23268597 DOI: 10.1021/Jp310046K |
0.453 |
|
| 2013 |
Roche J, Caro JA, Dellarole M, Guca E, Royer CA, GarcÃa-Moreno BE, Garcia AE, Roumestand C. Structural, energetic, and dynamic responses of the native state ensemble of staphylococcal nuclease to cavity-creating mutations. Proteins. 81: 1069-80. PMID 23239146 DOI: 10.1002/Prot.24231 |
0.439 |
|
| 2013 |
Li PT, Stephenson W, Nii Asare-Okai P, Chen AA, Tenenbaum S, Garcia AE, Fabris D. The Essential Adenosine Stacking in a Two-Base-Pair Minimal Kissing Complex Biophysical Journal. 104: 411a. DOI: 10.1080/07391102.2013.786474 |
0.57 |
|
| 2013 |
Stephenson W, Asare-Okai PN, Chen AA, Tenenbaum S, Garcia AE, Fabris D, Li PT. 41 The essential adenosine stacking in a two-base-pair minimal kissing complex Journal of Biomolecular Structure and Dynamics. 31: 25-25. DOI: 10.1080/07391102.2013.786474 |
0.434 |
|
| 2013 |
Jimenez-Cruz CA, Garcia AE. Reconstruction of the Most Probable Folding Transition Path from All-Atom Replica Exchange Simulations, using the Dynamic String Method Biophysical Journal. 104: 504a. DOI: 10.1016/J.Bpj.2012.11.2784 |
0.429 |
|
| 2013 |
English CA, Garcia AE. Simulations of the Thermodynamics and Structural Properties of the TC10b Trp-Cage Protein Biophysical Journal. 104: 398a. DOI: 10.1016/J.Bpj.2012.11.2222 |
0.799 |
|
| 2013 |
Dellarole M, Roche J, Caro JA, Rouget J, Garcia AE, Garcia-Moreno B, Roumestand C, Royer CA. Assessing the Contribution of Cavity Density to Protein Partial Molar Expansivity by High-Pressure NMR Biophysical Journal. 104: 397a. DOI: 10.1016/J.Bpj.2012.11.2213 |
0.398 |
|
| 2013 |
Huang K, Garcia AE. Methodological Issues in Free Energy Calculation of Lipid Flip-Flop in Bilayers Biophysical Journal. 104: 31a. DOI: 10.1016/J.Bpj.2012.11.211 |
0.379 |
|
| 2013 |
Canchi DR, Jayasimha P, Rao DC, Makhatadze GI, Garcia AE. Molecular Mechanism for the Preferential Exclusion of Osmolytes from Protein Surfaces Biophysical Journal. 104: 189a. DOI: 10.1016/J.Bpj.2012.11.1065 |
0.799 |
|
| 2012 |
Roche J, Dellarole M, Caro JA, Guca E, Norberto DR, Yang Y, Garcia AE, Roumestand C, GarcÃa-Moreno B, Royer CA. Remodeling of the folding free energy landscape of staphylococcal nuclease by cavity-creating mutations. Biochemistry. 51: 9535-46. PMID 23116341 DOI: 10.1021/Bi301071Z |
0.426 |
|
| 2012 |
Canchi DR, Jayasimha P, Rau DC, Makhatadze GI, Garcia AE. Molecular mechanism for the preferential exclusion of TMAO from protein surfaces. The Journal of Physical Chemistry. B. 116: 12095-104. PMID 22970901 DOI: 10.1021/Jp304298C |
0.803 |
|
| 2012 |
Noel JK, Schug A, Verma A, Wenzel W, Garcia AE, Onuchic JN. Mirror images as naturally competing conformations in protein folding. The Journal of Physical Chemistry. B. 116: 6880-8. PMID 22497217 DOI: 10.1021/Jp212623D |
0.472 |
|
| 2012 |
Roche J, Caro JA, Norberto DR, Barthe P, Roumestand C, Schlessman JL, Garcia AE, GarcÃa-Moreno BE, Royer CA. Cavities determine the pressure unfolding of proteins. Proceedings of the National Academy of Sciences of the United States of America. 109: 6945-50. PMID 22496593 DOI: 10.1073/Pnas.1200915109 |
0.458 |
|
| 2012 |
Jimenez-Cruz CA, Garcia AE. Multiscale Conformational Dynamics of Trp-Cage by Markov State Models Biophysical Journal. 102: 170a. DOI: 10.1016/J.Bpj.2011.11.924 |
0.476 |
|
| 2012 |
Chen AA, García AE. Mechanism of Enhanced Mechanical Stability of Retroviral Kissing-Loops Elucidated by Non-Equilibrium Molecular Dynamics Simulations Biophysical Journal. 102: 644a-645a. DOI: 10.1016/J.Bpj.2011.11.3508 |
0.632 |
|
| 2012 |
Rosenman DJ, Connors C, Chen W, Wang C, García AE. Characterization of the Structural Ensembles of Aβ Monomers using a Combined MD/NMR Approach Biophysical Journal. 102: 631a-632a. DOI: 10.1016/J.Bpj.2011.11.3439 |
0.45 |
|
| 2012 |
English CA, Garcia AE. Computational Study of the Thermodynamics and Stability of Two Trp-Cage Miniprotein Sequences Biophysical Journal. 102: 458a. DOI: 10.1016/J.Bpj.2011.11.2512 |
0.806 |
|
| 2012 |
Huang K, Garcia AE. Free Energy Calculations of the Transferring of a Cyclic Arginine 9 Peptide across a Lipid Bilayer Suggest a Water-Pore Assisted Mechanism Biophysical Journal. 102: 399a. DOI: 10.1016/J.Bpj.2011.11.2180 |
0.315 |
|
| 2012 |
Roche J, Caro JA, Norberto D, Barthe P, Roumestand C, Schlessman JL, Garcia AE, Garcia-Moreno E. B, Royer CA. Cavities in the Hydrophobic Core Govern Pressure Unfolding of Proteins Biophysical Journal. 102: 218a. DOI: 10.1016/J.Bpj.2011.11.1194 |
0.438 |
|
| 2011 |
Tian J, Garcia AE. Simulation studies of protein folding/unfolding equilibrium under polar and nonpolar confinement. Journal of the American Chemical Society. 133: 15157-64. PMID 21854029 DOI: 10.1021/Ja2054572 |
0.682 |
|
| 2011 |
Jimenez-Cruz CA, Makhatadze GI, Garcia AE. Protonation/deprotonation effects on the stability of the Trp-cage miniprotein. Physical Chemistry Chemical Physics : Pccp. 13: 17056-63. PMID 21773639 DOI: 10.1039/C1Cp21193E |
0.503 |
|
| 2011 |
Vaitheeswaran S, Garcia AE. Protein stability at a carbon nanotube interface. The Journal of Chemical Physics. 134: 125101. PMID 21456701 DOI: 10.1016/J.Bpj.2010.12.2380 |
0.465 |
|
| 2011 |
Rouget JB, Aksel T, Roche J, Saldana JL, Garcia AE, Barrick D, Royer CA. Size and sequence and the volume change of protein folding. Journal of the American Chemical Society. 133: 6020-7. PMID 21446709 DOI: 10.1021/Ja200228W |
0.467 |
|
| 2011 |
Sgourakis NG, Merced-Serrano M, Boutsidis C, Drineas P, Du Z, Wang C, Garcia AE. Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms. Journal of Molecular Biology. 405: 570-83. PMID 21056574 DOI: 10.1016/J.Jmb.2010.10.015 |
0.694 |
|
| 2011 |
Chen AA, Garcia AE. Atomistic Simulations of the Force-Induced Dissociation of Retroviral RNA Kissing-Loops Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.3065 |
0.602 |
|
| 2011 |
Jimenez-Cruz CA, Garcia A. Studying the Stabilizing Effects of the W-WTG Capping Motif for Short Beta Hairpins by Replica Exchange Molecular Dynamics Biophysical Journal. 100: 401a. DOI: 10.1016/J.Bpj.2010.12.2381 |
0.434 |
|
| 2011 |
Hutchison AL, Garcia AE. Molecular Simulations of the Configurational Entropy of the Trp-Cage Miniprotein Biophysical Journal. 100: 400a. DOI: 10.1016/J.Bpj.2010.12.2377 |
0.5 |
|
| 2011 |
Caro JA, Roche J, Rouget J, Schlessman J, García AE, Royer CA, García-Moreno B. Role of Internal Cavities as Determinants of Pressure Unfolding of Proteins Biophysical Journal. 100: 398a. DOI: 10.1016/J.Bpj.2010.12.2363 |
0.426 |
|
| 2011 |
Canchi DR, Garcia AE. Equilibrium Studies of Protein Denaturation by Urea - Examining Backbone and Sidechain Contributions Biophysical Journal. 100: 211a. DOI: 10.1016/J.Bpj.2010.12.1365 |
0.812 |
|
| 2011 |
Huang K, Garcia AE. The Equilibrium of Cholesterol DPPC Lipid Bilayers in Atomistic Molecular Dynamic Simulations Biophysical Journal. 100: 150a. DOI: 10.1016/J.Bpj.2010.12.1030 |
0.391 |
|
| 2010 |
Patel MM, Sgourakis NG, Garcia AE, Makhatadze GI. Experimental test of the thermodynamic model of protein cooperativity using temperature-induced unfolding of a Ubq-UIM fusion protein. Biochemistry. 49: 8455-67. PMID 20836541 DOI: 10.1021/Bi101163U |
0.687 |
|
| 2010 |
Zhuang W, Sgourakis NG, Li Z, Garcia AE, Mukamel S. Discriminating early stage A{beta}42 monomer structures using chirality-induced 2DIR spectroscopy in a simulation study. Proceedings of the National Academy of Sciences of the United States of America. 107: 15687-92. PMID 20798063 DOI: 10.1073/Pnas.1002131107 |
0.662 |
|
| 2010 |
Day R, Paschek D, Garcia AE. Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein. Proteins. 78: 1889-99. PMID 20408169 DOI: 10.1002/Prot.22702 |
0.449 |
|
| 2010 |
Sgourakis NG, Garcia AE. The membrane complex between transducin and dark-state rhodopsin exhibits large-amplitude interface dynamics on the sub-microsecond timescale: insights from all-atom MD simulations. Journal of Molecular Biology. 398: 161-73. PMID 20184892 DOI: 10.1016/J.Jmb.2010.02.032 |
0.719 |
|
| 2010 |
Sgourakis NG, Patel MM, Garcia AE, Makhatadze GI, McCallum SA. Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain. Journal of Molecular Biology. 396: 1128-44. PMID 20053359 DOI: 10.1016/J.Jmb.2009.12.052 |
0.689 |
|
| 2010 |
Garcia AE. The Translocation Mechanism of Arginine Rich Cell Penetrating Peptides Biophysical Journal. 98: 609a. DOI: 10.1016/J.Bpj.2009.12.3320 |
0.342 |
|
| 2009 |
Herce HD, Garcia AE, Litt J, Kane RS, Martin P, Enrique N, Rebolledo A, Milesi V. Arginine-rich peptides destabilize the plasma membrane, consistent with a pore formation translocation mechanism of cell-penetrating peptides. Biophysical Journal. 97: 1917-25. PMID 19804722 DOI: 10.1016/J.Bpj.2009.05.066 |
0.311 |
|
| 2009 |
Tian J, Garcia AE. An alpha-helical peptide in AOT micelles prefers to be localized at the water/headgroup interface. Biophysical Journal. 96: L57-9. PMID 19450460 DOI: 10.1016/J.Bpj.2009.03.014 |
0.613 |
|
| 2009 |
Canchi DR, Garcia AE. Equilibrium Thermodynamics of Urea Denaturation of Trp-cage Miniprotein Biophysical Journal. 96: 587a. DOI: 10.1016/J.Bpj.2008.12.3073 |
0.801 |
|
| 2009 |
Guo D, Garcia AE. Molecular Simulations of the Folding Kinetics of an RNA Tetraloop Biophysical Journal. 96: 5-5. DOI: 10.1016/J.Bpj.2008.12.3003 |
0.446 |
|
| 2009 |
Tian J, Garcia AE. Self Assembly Of AOT Reverse Micelles With/without Peptides Biophysical Journal. 96: 428a. DOI: 10.1016/J.Bpj.2008.12.2194 |
0.598 |
|
| 2009 |
Sgourakis NG, Garcia AE. Modeling and Simulation Of A Protein Tertiary Complex: Study of the Interaction Interface and Conformational Dynamics of Dark State Rhodopsin in complex with Transducin Biophysical Journal. 96: 368a-369a. DOI: 10.1016/J.Bpj.2008.12.1985 |
0.723 |
|
| 2009 |
Garcia AE, Herce H, Paschek D. ChemInform Abstract: Simulations of Temperature and Pressure Unfolding of Peptides and Proteins with Replica Exchange Molecular Dynamics Cheminform. 40. DOI: 10.1002/CHIN.200908276 |
0.323 |
|
| 2008 |
Sgourakis NG, Day R, McCallum SA, Garcia AE. Pressure effects on the ensemble dynamics of ubiquitin inspected with molecular dynamics simulations and isotropic reorientational eigenmode dynamics. Biophysical Journal. 95: 3943-55. PMID 18621814 DOI: 10.1529/Biophysj.108.133702 |
0.693 |
|
| 2008 |
Gnanakaran S, Scott B, McCleskey TM, Garcia AE. Perturbation of local solvent structure by a small dication: a theoretical study on structural, vibrational, and reactive properties of beryllium ion in water. The Journal of Physical Chemistry. B. 112: 2958-63. PMID 18281967 DOI: 10.1021/Jp076001W |
0.39 |
|
| 2008 |
Garcia AE, Paschek D. Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin. Journal of the American Chemical Society. 130: 815-7. PMID 18154332 DOI: 10.1021/ja074191i |
0.335 |
|
| 2008 |
Garcia AE. Molecular dynamics simulations of protein folding. Methods in Molecular Biology (Clifton, N.J.). 413: 315-30. PMID 18075171 DOI: 10.1007/978-1-59745-574-9_12 |
0.506 |
|
| 2008 |
Mitra L, Rouget J, Garcia-Moreno B, Royer CA, Winter R, Oleinikova A, Winter R, Holzmann J, Ludwig R, Geiger A, Paschek D, Riemenschneider J, Rüppert A, Pühse M, Perez-Goicochea A, et al. Cover Picture: Towards a Quantitative Understanding of Protein Hydration and Volumetric Properties / Intrinsic Volumetric Properties of Trialanine Isomers in Aqueous Solution / Temperature and Concentration Effects on the Solvophobic Solvation of Methane Chemphyschem. 9: 2633-2633. DOI: 10.1002/Cphc.200890072 |
0.344 |
|
| 2007 |
Herce HD, Garcia AE. Cell penetrating peptides: how do they do it? Journal of Biological Physics. 33: 345-56. PMID 19669523 DOI: 10.1007/S10867-008-9074-3 |
0.365 |
|
| 2007 |
Herce HD, Garcia AE. Molecular dynamics simulations suggest a mechanism for translocation of the HIV-1 TAT peptide across lipid membranes. Proceedings of the National Academy of Sciences of the United States of America. 104: 20805-10. PMID 18093956 DOI: 10.1073/Pnas.0706574105 |
0.365 |
|
| 2007 |
Sgourakis NG, Yan Y, McCallum SA, Wang C, Garcia AE. The Alzheimer's peptides Abeta40 and 42 adopt distinct conformations in water: a combined MD / NMR study. Journal of Molecular Biology. 368: 1448-57. PMID 17397862 DOI: 10.1016/J.Jmb.2007.02.093 |
0.628 |
|
| 2006 |
Herce HD, Garcia AE. Correction of apparent finite size effects in the area per lipid of lipid membranes simulations. The Journal of Chemical Physics. 125: 224711. PMID 17176158 DOI: 10.1063/1.2378893 |
0.362 |
|
| 2006 |
Garcia AE, Herce H, Paschek D. Chapter 5 Simulations of Temperature and Pressure Unfolding of Peptides and Proteins with Replica Exchange Molecular Dynamics Annual Reports in Computational Chemistry. 2: 83-95. DOI: 10.1016/S1574-1400(06)02005-6 |
0.482 |
|
| 2005 |
Garcia AE, Onuchic JN. Folding a protein in the computer: reality or hope? Structure (London, England : 1993). 13: 497-8. PMID 15837185 DOI: 10.1016/J.Str.2005.03.005 |
0.38 |
|
| 2005 |
Nymeyer H, Woolf TB, Garcia AE. Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer. Proteins. 59: 783-90. PMID 15828005 DOI: 10.1002/Prot.20460 |
0.416 |
|
| 2005 |
Paschek D, Gnanakaran S, Garcia AE. Simulations of the pressure and temperature unfolding of an alpha-helical peptide. Proceedings of the National Academy of Sciences of the United States of America. 102: 6765-70. PMID 15800045 DOI: 10.1073/Pnas.0408527102 |
0.41 |
|
| 2005 |
Damjanović A, García-Moreno E. B, Lattman EE, García AE. Molecular dynamics study of hydration of the protein interior Computer Physics Communications. 169: 126-129. DOI: 10.1016/J.Cpc.2005.03.030 |
0.464 |
|
| 2004 |
Petrone PM, Garcia AE. MHC-peptide binding is assisted by bound water molecules. Journal of Molecular Biology. 338: 419-35. PMID 15066441 DOI: 10.1016/J.Jmb.2004.02.039 |
0.349 |
|
| 2004 |
Nymeyer H, Gnanakaran S, García AE. Atomic simulations of protein folding, using the replica exchange algorithm. Methods in Enzymology. 383: 119-49. PMID 15063649 DOI: 10.1016/S0076-6879(04)83006-4 |
0.437 |
|
| 2004 |
Garcia AE. Characterization of non-alpha helical conformations in Ala peptides Polymer. 45: 669-676. DOI: 10.1016/J.Polymer.2003.10.070 |
0.347 |
|
| 2003 |
Gnanakaran S, Garcia AE. Folding of a highly conserved diverging turn motif from the SH3 domain. Biophysical Journal. 84: 1548-62. PMID 12609860 DOI: 10.1016/S0006-3495(03)74966-2 |
0.425 |
|
| 2003 |
Gnanakaran S, Garcia AE. Validation of an All-Atom Protein Force Field: From Dipeptides to Larger Peptides The Journal of Physical Chemistry B. 107: 12555-12557. DOI: 10.1021/Jp0359079 |
0.356 |
|
| 2002 |
Ghosh T, García AE, Garde S. Enthalpy and entropy contributions to the pressure dependence of hydrophobic interactions Journal of Chemical Physics. 116: 2480-2486. DOI: 10.1063/1.1431582 |
0.388 |
|
| 2001 |
Hummer G, García AE, Garde S. Helix nucleation kinetics from molecular simulations in explicit solvent Proteins: Structure, Function and Genetics. 42: 77-84. PMID 11093262 DOI: 10.1002/1097-0134(20010101)42:1<77::Aid-Prot80>3.0.Co;2-# |
0.463 |
|
| 2000 |
Hummer G, García AE, Garde S. Conformational diffusion and helix formation kinetics Physical Review Letters. 85: 2637-2640. PMID 10978126 DOI: 10.1103/Physrevlett.85.2637 |
0.447 |
|
| 2000 |
Onuchic JN, Nymeyer H, García AE, Chahine J, Socci ND. The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. Advances in Protein Chemistry. 53: 87-152. PMID 10751944 DOI: 10.1016/S0065-3233(00)53003-4 |
0.452 |
|
| 2000 |
García AE, Hummer G. Water penetration and escape in proteins. Proteins. 38: 261-72. PMID 10713987 DOI: 10.1002/(Sici)1097-0134(20000215)38:3<261::Aid-Prot3>3.0.Co;2-Q |
0.324 |
|
| 2000 |
García AE, Hillson N, Onuchic JN. Solvent Effects on Protein Folding/Unfolding Progress of Theoretical Physics Supplement. 138: 282-291. DOI: 10.1143/PTPS.138.282 |
0.326 |
|
| 2000 |
García AE, Hillson N, Onuchic JN. Solvent effects on protein folding/unfolding Progress of Theoretical Physics Supplement. 282-291. DOI: 10.1143/Ptps.138.282 |
0.435 |
|
| 1999 |
Hillson N, Onuchic JN, Garcia AE. Pressure-induced protein-folding/unfolding kinetics Proceedings of the National Academy of Sciences of the United States of America. 96: 14848-14853. PMID 10611301 DOI: 10.1073/Pnas.96.26.14848 |
0.365 |
|
| 1999 |
García AE, Hummer G. Conformational dynamics of cytochrome c: correlation to hydrogen exchange. Proteins. 36: 175-91. PMID 10398365 DOI: 10.1002/(Sici)1097-0134(19990801)36:2<175::Aid-Prot4>3.0.Co;2-R |
0.39 |
|
| 1998 |
Nymeyer H, García AE, Onuchic JN. Folding funnels and frustration in off-lattice minimalist protein landscapes. Proceedings of the National Academy of Sciences of the United States of America. 95: 5921-8. PMID 9600893 DOI: 10.1073/Pnas.95.11.5921 |
0.436 |
|
| 1998 |
Mariappan SV, Silks LA, Chen X, Springer PA, Wu R, Moyzis RK, Bradbury EM, Garcia AE, Gupta G. Solution structures of the Huntington's disease DNA triplets, (CAG)n. Journal of Biomolecular Structure & Dynamics. 15: 723-44. PMID 9514249 DOI: 10.1080/07391102.1998.10508988 |
0.31 |
|
| 1998 |
Hummer G, Garde S, García AE, Paulaitis ME, Pratt LR. The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins. Proceedings of the National Academy of Sciences of the United States of America. 95: 1552-5. PMID 9465053 DOI: 10.1073/Pnas.95.4.1552 |
0.426 |
|
| 1998 |
Hummer G, Garde S, García AE, Paulaitis ME, Pratt LR. Hydrophobic Effects on a Molecular Scale The Journal of Physical Chemistry B. 102: 10469-10482. DOI: 10.1021/Jp982873+ |
0.411 |
|
| 1998 |
Hummer G, Pratt LR, García AE. Molecular theories and simulation of ions and polar molecules in water Journal of Physical Chemistry A. 102: 7885-7895. DOI: 10.1021/Jp982195R |
0.356 |
|
| 1997 |
García AE, Hummer G, Soumpasis DM. Hydration of an alpha-helical peptide: comparison of theory and molecular dynamics simulation. Proteins. 27: 471-80. PMID 9141128 DOI: 10.1002/(Sici)1097-0134(199704)27:4<471::Aid-Prot1>3.0.Co;2-E |
0.391 |
|
| 1997 |
Oprea TI, Hummer G, Garcia AE. Identification of a functional water channel in cytochrome P450 enzymes. Proceedings of the National Academy of Sciences of the United States of America. 94: 2133-8. PMID 9122160 DOI: 10.1073/Pnas.94.6.2133 |
0.346 |
|
| 1997 |
Garcia AE, Hummer G, Soumpasis DM. Theoretical description of biomolecular hydration. Application to A-DNA. Basic Life Sciences. 64: 299-308. PMID 9031515 DOI: 10.1007/978-1-4615-5847-7_26 |
0.338 |
|
| 1997 |
Schoenborn BP, Garcia A, Knott R. Hydration in protein crystallography. Progress in Biophysics and Molecular Biology. 64: 105-19. PMID 8987380 DOI: 10.1016/0079-6107(95)00012-7 |
0.399 |
|
| 1997 |
Hummer G, Pratt LR, García AE, Berne BJ, Rick SW. Electrostatic potentials and free energies of solvation of polar and charged molecules Journal of Physical Chemistry B. 101: 3017-3020. DOI: 10.1021/Jp964037A |
0.369 |
|
| 1997 |
Hummer G, Pratt LR, García AE. Multistate Gaussian model for electrostatic solvation free energies Journal of the American Chemical Society. 119: 8523-8527. DOI: 10.1021/Ja971148U |
0.35 |
|
| 1997 |
García AE, Blumenfeld R, Hummer G, Krumhansl JA. Multi-basin dynamics of a protein in a crystal environment Physica D: Nonlinear Phenomena. 107: 225-239. DOI: 10.1016/S0167-2789(97)00090-0 |
0.408 |
|
| 1997 |
Pratt LR, Tawa GJ, Hummer G, García AE, Corcelli SA. Boundary integral methods for the poisson equation of continuum dielectric solvation models International Journal of Quantum Chemistry. 64: 121-141. DOI: 10.1002/(Sici)1097-461X(1997)64:1<121::Aid-Qua12>3.0.Co;2-E |
0.306 |
|
| 1996 |
Hummer G, Garde S, García AE, Pohorille A, Pratt LR. An information theory model of hydrophobic interactions. Proceedings of the National Academy of Sciences of the United States of America. 93: 8951-5. PMID 11607700 DOI: 10.1073/Pnas.93.17.8951 |
0.342 |
|
| 1996 |
Garde S, Hummer G, García AE, Paulaitis ME, Pratt LR. Origin of Entropy Convergence in Hydrophobic Hydration and Protein Folding. Physical Review Letters. 77: 4966-4968. PMID 10062679 DOI: 10.1103/Physrevlett.77.4966 |
0.381 |
|
| 1996 |
Garde S, Hummer G, García AE, Pratt LR, Paulaitis ME. Hydrophobic hydration: Inhomogeneous water structure near nonpolar molecular solutes. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 53: R4310-R4313. PMID 9964911 DOI: 10.1103/Physreve.53.R4310 |
0.329 |
|
| 1996 |
Tung CS, Oprea TI, Hummer G, García AE. Three-dimensional model of a selective theophylline-binding RNA molecule Journal of Molecular Recognition. 9: 275-286. PMID 9131469 DOI: 10.1002/(Sici)1099-1352(199607)9:4<275::Aid-Jmr337>3.0.Co;2-8 |
0.313 |
|
| 1996 |
García AE, Harman JG. Simulations of CRP:(cAMP)2 in noncrystalline environments show a subunit transition from the open to the closed conformation Protein Science. 5: 62-71. PMID 8771197 DOI: 10.1002/Pro.5560050108 |
0.416 |
|
| 1996 |
Mariappan SVS, Garcia AE, Gupta G. Structure and Dynamics of the DNA Hairpins Formed by Tandemly Repeated CTG Triplets Associated With Myotonic Dystrophy Nucleic Acids Research. 24: 775-783. PMID 8604323 DOI: 10.1093/Nar/24.4.775 |
0.366 |
|
| 1996 |
Garde S, Hummer G, Paulaitis ME, Garcia AE. Hydration of Biological Macromolecules: From Small Solutes to Proteins and Nucleic Acids Mrs Proceedings. 463. DOI: 10.1557/Proc-463-21 |
0.366 |
|
| 1996 |
Hummer G, Pratt LR, Garcia AE. Free energy of ionic hydration Journal of Physical Chemistry. 100: 1206-1215. DOI: 10.1021/Jp951011V |
0.36 |
|
| 1995 |
Hummer G, García AE, Soumpasis DM. Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes. Biophysical Journal. 68: 1639-52. PMID 7542034 DOI: 10.1016/S0006-3495(95)80381-4 |
0.319 |
|
| 1995 |
Hummer G, Pratt LR, García AE. Hydration free energy of water Journal of Physical Chemistry. 99: 14188-14194. DOI: 10.1021/J100038A062 |
0.35 |
|
| 1994 |
Pratt LR, Hummer G, Garciá AE. Ion pair potentials-of-mean-force in water Biophysical Chemistry. 51: 147-165. DOI: 10.1016/0301-4622(94)00057-3 |
0.373 |
|
| 1993 |
Gupta G, García AE, Hiriyanna KT. Sampling of the conformations of the d(CGCTGCGGC) hairpin in solution by two-dimensional nuclear magnetic resonance and theoretical methods. Biochemistry. 32: 948-60. PMID 8422398 DOI: 10.1021/Bi00054A028 |
0.357 |
|
| 1993 |
Gupta G, Garcia AE, Guo Q, Lu M, Kallenbach NR. Structure of a parallel-stranded tetramer of the Oxytricha telomeric DNA sequence dT4G4. Biochemistry. 32: 7098-103. PMID 8393704 DOI: 10.1021/Bi00079A005 |
0.383 |
|
| 1993 |
García AE, Stiller L. Computation of the mean residence time of water in the hydration shells of biomolecules Journal of Computational Chemistry. 14: 1396-1406. DOI: 10.1002/Jcc.540141116 |
0.354 |
|
| 1992 |
García AE. Large-amplitude nonlinear motions in proteins Physical Review Letters. 68: 2696-2699. PMID 10045464 DOI: 10.1103/Physrevlett.68.2696 |
0.353 |
|
| 1990 |
Garcia AE, Gupta G, Sarma MH, Sarma RH. Stability and motion of a hairpin and the corresponding mismatched duplex: a theoretical exploration using molecular mechanics and normal mode analysis of 2D NMR results on d(GCCGCAGC). Journal of Biomolecular Structure & Dynamics. 6: 525-42. PMID 3271537 DOI: 10.1080/07391102.1988.10506505 |
0.393 |
|
| 1990 |
Garcia AE, Gupta G, Soumpasis DM, Tung CS. Energetics of the hairpin to mismatched duplex transition of d(Gccgcagc) on nacl solution Journal of Biomolecular Structure and Dynamics. 8: 173-186. PMID 2275792 DOI: 10.1080/07391102.1990.10507796 |
0.407 |
|
| 1989 |
García AE, Soumpasis DM. Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution. Proceedings of the National Academy of Sciences of the United States of America. 86: 3160-4. PMID 2717613 DOI: 10.1073/Pnas.86.9.3160 |
0.318 |
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