| Year |
Citation |
Score |
| 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, ... ... Baker NA, 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 |
0.489 |
|
| 2016 |
Pabit SA, Katz AM, Tolokh IS, Drozdetski A, Baker N, Onufriev AV, Pollack L. Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations. The Journal of Chemical Physics. 144: 205102. PMID 27250330 DOI: 10.1063/1.4950814 |
0.324 |
|
| 2015 |
Harper B, Thomas D, Chikkagoudar S, Baker N, Tang K, Heredia-Langner A, Lins R, Harper S. Comparative hazard analysis and toxicological modeling of diverse nanomaterials using the embryonic zebrafish (EZ) metric of toxicity. Journal of Nanoparticle Research : An Interdisciplinary Forum For Nanoscale Science and Technology. 17: 250. PMID 26069453 DOI: 10.1007/S11051-015-3051-0 |
0.545 |
|
| 2014 |
Daily MD, Olsen BN, Schlesinger PH, Ory DS, Baker NA. Improved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers. Journal of Chemical Theory and Computation. 10: 2137-2150. PMID 24910542 DOI: 10.1021/Ct401028G |
0.786 |
|
| 2014 |
Bielska AA, Olsen BN, Gale SE, Mydock-McGrane L, Krishnan K, Baker NA, Schlesinger PH, Covey DF, Ory DS. Side-chain oxysterols modulate cholesterol accessibility through membrane remodeling. Biochemistry. 53: 3042-51. PMID 24758724 DOI: 10.1021/Bi5000096 |
0.784 |
|
| 2013 |
Olsen BN, Bielska AA, Lee T, Daily MD, Covey DF, Schlesinger PH, Baker NA, Ory DS. The structural basis of cholesterol accessibility in membranes. Biophysical Journal. 105: 1838-47. PMID 24138860 DOI: 10.1016/J.Bpj.2013.08.042 |
0.787 |
|
| 2013 |
Olsen BN, Bielska A, Daily M, Schlesinger P, Baker N, Ory D. The Structural Basis of Cholesterol Activation in Membranes Biophysical Journal. 104: 662a. DOI: 10.1016/J.Bpj.2012.11.3657 |
0.796 |
|
| 2013 |
Daily MD, Olsen BN, Schlesinger PH, Ory DS, Baker NA. Improved Coarse-Grained Modeling of Cholesterol Activation in Lipid Bilayers Biophysical Journal. 104: 590a-591a. DOI: 10.1016/J.Bpj.2012.11.3281 |
0.785 |
|
| 2012 |
Ren P, Chun J, Thomas DG, Schnieders MJ, Marucho M, Zhang J, Baker NA. Biomolecular electrostatics and solvation: a computational perspective. Quarterly Reviews of Biophysics. 45: 427-91. PMID 23217364 DOI: 10.1017/S003358351200011X |
0.305 |
|
| 2012 |
Konecny R, Baker NA, McCammon JA. iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver (APBS). Computational Science & Discovery. 5. PMID 22905037 DOI: 10.1088/1749-4699/5/1/015005 |
0.363 |
|
| 2012 |
Lee SJ, Schlesinger PH, Wickline SA, Lanza GM, Baker NA. Simulation of fusion-mediated nanoemulsion interactions with model lipid bilayers. Soft Matter. 8: 3024-3035. PMID 22712024 DOI: 10.1039/C2Sm25847A |
0.309 |
|
| 2012 |
Olsen BN, Schlesinger PH, Ory DS, Baker NA. Side-chain oxysterols: from cells to membranes to molecules. Biochimica Et Biophysica Acta. 1818: 330-6. PMID 21745458 DOI: 10.1016/J.Bbamem.2011.06.014 |
0.79 |
|
| 2011 |
Lee SJ, Schlesinger PH, Wickline SA, Lanza GM, Baker NA. Interaction of melittin peptides with perfluorocarbon nanoemulsion particles. The Journal of Physical Chemistry. B. 115: 15271-9. PMID 22050303 DOI: 10.1021/Jp209543C |
0.351 |
|
| 2011 |
Alexov E, Mehler EL, Baker N, Baptista AM, Huang Y, Milletti F, Nielsen JE, Farrell D, Carstensen T, Olsson MH, Shen JK, Warwicker J, Williams S, Word JM. Progress in the prediction of pKa values in proteins. Proteins. 79: 3260-75. PMID 22002859 DOI: 10.1002/Prot.23189 |
0.417 |
|
| 2011 |
Carstensen T, Farrell D, Huang Y, Baker NA, Nielsen JE. On the development of protein pKa calculation algorithms. Proteins. 79: 3287-98. PMID 21744393 DOI: 10.1002/Prot.23091 |
0.36 |
|
| 2011 |
Unni S, Huang Y, Hanson RM, Tobias M, Krishnan S, Li WW, Nielsen JE, Baker NA. Web servers and services for electrostatics calculations with APBS and PDB2PQR. Journal of Computational Chemistry. 32: 1488-91. PMID 21425296 DOI: 10.1002/Jcc.21720 |
0.318 |
|
| 2011 |
Olsen BN, Schlesinger PH, Ory DS, Baker NA. 25-Hydroxycholesterol increases the availability of cholesterol in phospholipid membranes. Biophysical Journal. 100: 948-56. PMID 21320439 DOI: 10.1016/J.Bpj.2010.12.3728 |
0.787 |
|
| 2010 |
Lee SJ, Olsen B, Schlesinger PH, Baker NA. Characterization of perfluorooctylbromide-based nanoemulsion particles using atomistic molecular dynamics simulations. The Journal of Physical Chemistry. B. 114: 10086-96. PMID 20684632 DOI: 10.1021/Jp103228C |
0.738 |
|
| 2010 |
Lee S, Olsen BN, Schlesinger PH, Baker NA. Multi-Scale Modeling of the “Contact-Facilitated” Delivery Mechanism of Perfluorocarbon-Based Nanoemulsions Biophysical Journal. 98: 672a. DOI: 10.1016/J.Bpj.2009.12.3691 |
0.767 |
|
| 2010 |
Olsen BN, Schlesinger P, Baker NA. Perturbation of Membrane Structure by Oxysterols Biophysical Journal. 98: 491a. DOI: 10.1016/J.Bpj.2009.12.2674 |
0.79 |
|
| 2009 |
Olsen BN, Schlesinger PH, Baker NA. Perturbations of membrane structure by cholesterol and cholesterol derivatives are determined by sterol orientation. Journal of the American Chemical Society. 131: 4854-65. PMID 19334779 DOI: 10.1021/Ja8095224 |
0.79 |
|
| 2008 |
Lee SJ, Song Y, Baker NA. Molecular dynamics simulations of asymmetric NaCl and KCl solutions separated by phosphatidylcholine bilayers: potential drops and structural changes induced by strong Na+-lipid interactions and finite size effects. Biophysical Journal. 94: 3565-76. PMID 18222999 DOI: 10.1529/Biophysj.107.116335 |
0.375 |
|
| 2008 |
Dong F, Olsen B, Baker NA. Computational methods for biomolecular electrostatics. Methods in Cell Biology. 84: 843-70. PMID 17964951 DOI: 10.1016/S0091-679X(07)84026-X |
0.718 |
|
| 2007 |
Swanson JM, Wagoner JA, Baker NA, McCammon JA. Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies: Lessons Learned with Atom-Centered Dielectric Functions. Journal of Chemical Theory and Computation. 3: 170-83. PMID 26627162 DOI: 10.1021/ct600216k |
0.585 |
|
| 2007 |
Cerutti DS, Baker NA, McCammon JA. Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent models? The Journal of Chemical Physics. 127: 155101. PMID 17949217 DOI: 10.1063/1.2771171 |
0.674 |
|
| 2007 |
Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Research. 35: W522-5. PMID 17488841 DOI: 10.1093/Nar/Gkm276 |
0.402 |
|
| 2007 |
Cheng Y, Suen JK, Zhang D, Bond SD, Zhang Y, Song Y, Baker NA, Bajaj CL, Holst MJ, McCammon JA. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophysical Journal. 92: 3397-406. PMID 17307827 DOI: 10.1529/Biophysj.106.102533 |
0.566 |
|
| 2006 |
Zhang X, Bajaj CL, Kwon B, Dolinsky TJ, Nielsen JE, Baker NA. Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity. Multiscale Modeling & Simulation : a Siam Interdisciplinary Journal. 5: 1196-1213. PMID 18841247 DOI: 10.1137/050647670 |
0.377 |
|
| 2006 |
Konecny R, Trylska J, Tama F, Zhang D, Baker NA, Brooks CL, McCammon JA. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers. 82: 106-20. PMID 16278831 DOI: 10.1002/Bip.20409 |
0.342 |
|
| 2005 |
Song Y, Guallar V, Baker NA. Molecular dynamics simulations of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholine bilayer. Biochemistry. 44: 13425-38. PMID 16216066 DOI: 10.1021/Bi0506829 |
0.387 |
|
| 2005 |
Zhang D, Suen J, Zhang Y, Song Y, Radic Z, Taylor P, Holst MJ, Bajaj C, Baker NA, McCammon JA. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophysical Journal. 88: 1659-65. PMID 15626705 DOI: 10.1529/Biophysj.104.053850 |
0.377 |
|
| 2004 |
Zhang D, Konecny R, Baker NA, McCammon JA. Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach. Biopolymers. 75: 325-37. PMID 15386271 DOI: 10.1002/Bip.20120 |
0.351 |
|
| 2004 |
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Research. 32: W665-7. PMID 15215472 DOI: 10.1093/Nar/Gkh381 |
0.516 |
|
| 2004 |
Song Y, Zhang Y, Shen T, Bajaj CL, McCammon JA, Baker NA. Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophysical Journal. 86: 2017-29. PMID 15041644 DOI: 10.1016/S0006-3495(04)74263-0 |
0.372 |
|
| 2004 |
Vitalis A, Baker NA, McCammon JA. ISIM: A program for grand canonical Monte Carlo simulations of the ionic environment of biomolecules Molecular Simulation. 30: 45-61. DOI: 10.1080/08927020310001597862 |
0.386 |
|
| 2003 |
Sept D, Baker NA, McCammon JA. The physical basis of microtubule structure and stability. Protein Science : a Publication of the Protein Society. 12: 2257-61. PMID 14500883 DOI: 10.1110/Ps.03187503 |
0.381 |
|
| 2003 |
Tai K, Bond SD, MacMillan HR, Baker NA, Holst MJ, McCammon JA. Finite element simulations of acetylcholine diffusion in neuromuscular junctions. Biophysical Journal. 84: 2234-41. PMID 12668432 DOI: 10.1016/S0006-3495(03)75029-2 |
0.58 |
|
| 2003 |
Baker NA, McCammon JA. Electrostatic interactions. Methods of Biochemical Analysis. 44: 427-40. PMID 12647398 |
0.338 |
|
| 2002 |
Lin JH, Baker NA, McCammon JA. Bridging implicit and explicit solvent approaches for membrane electrostatics. Biophysical Journal. 83: 1374-9. PMID 12202363 DOI: 10.1016/S0006-3495(02)73908-8 |
0.464 |
|
| 2002 |
Ma C, Baker NA, Joseph S, McCammon JA. Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation. Journal of the American Chemical Society. 124: 1438-42. PMID 11841313 DOI: 10.1021/Ja016830+ |
0.362 |
|
| 2001 |
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: Application to microtubules and the ribosome Proceedings of the National Academy of Sciences of the United States of America. 98: 10037-10041. PMID 11517324 DOI: 10.1073/Pnas.181342398 |
0.384 |
|
| 2001 |
Baker NA, Sept D, Holst MJ, McCammon JA. The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers Ibm Journal of Research and Development. 45: 427-438. DOI: 10.1147/rd.453.0427 |
0.309 |
|
| 2000 |
Baker NA, Hünenberger PH, McCammon JA. Erratum: “Polarization around an ion in a dielectric continuum with truncated electrostatic interactions” [J. Chem. Phys. 110, 10679 (1999)] The Journal of Chemical Physics. 113: 2510-2511. DOI: 10.1063/1.482073 |
0.313 |
|
| 2000 |
Quinn DM, Feaster SR, Nair HK, Baker NA, Radi? Z, Taylor P. Delineation and decomposition of energies involved in quaternary ammonium binding in the active site of acetylcholinesterase Journal of the American Chemical Society. 122: 2975-2980. DOI: 10.1021/Ja9933588 |
0.488 |
|
| 1999 |
Baker NA, Helms V, McCammon JA. Dynamical properties of fasciculin-2 Proteins: Structure, Function and Genetics. 36: 447-453. PMID 10450086 DOI: 10.1002/(Sici)1097-0134(19990901)36:4<447::Aid-Prot8>3.0.Co;2-E |
0.39 |
|
| 1999 |
Malany S, Baker N, Verweyst M, Medhekar R, Quinn DM, Velan B, Kronman C, Shafferman A. Theoretical and experimental investigations of electrostatic effects on acetylcholinesterase catalysis and inhibition. Chemico-Biological Interactions. 119: 99-110. PMID 10421443 DOI: 10.1016/S0009-2797(99)00018-6 |
0.566 |
|
| 1999 |
Baker NA, Hünenberger PH, McCammon JA. Polarization around an ion in a dielectric continuum with truncated electrostatic interactions The Journal of Chemical Physics. 110: 10679-10692. DOI: 10.1063/1.479013 |
0.399 |
|
| 1999 |
Baker NA, McCammon JA. Non-Boltzmann Rate Distributions in Stochastically Gated Reactions The Journal of Physical Chemistry B. 103: 615-617. DOI: 10.1021/Jp984151O |
0.315 |
|
| 1996 |
Feaster SR, Lee K, Baker N, Hui DY, Quinn DM. Molecular recognition by cholesterol esterase of active site ligands: structure-reactivity effects for inhibition by aryl carbamates and subsequent carbamylenzyme turnover. Biochemistry. 35: 16723-34. PMID 8988009 DOI: 10.1021/Bi961677V |
0.593 |
|
| Show low-probability matches. |