Nathan Baker - Publications

Biology & Biomedical Sciences (Molecular Cell Biology) Washington University, Saint Louis, St. Louis, MO 
General Biophysics

77 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
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  0.68
2016 Lei H, Baker NA, Wu L, Schenter GK, Mundy CJ, Tartakovsky AM. Smoothed dissipative particle dynamics model for mesoscopic multiphase flows in the presence of thermal fluctuations. Physical Review. E. 94: 023304. PMID 27627409 DOI: 10.1103/PhysRevE.94.023304  0.56
2016 Drozdetski AV, Tolokh IS, Pollack L, Baker N, Onufriev AV. Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA. Physical Review Letters. 117: 028101. PMID 27447528 DOI: 10.1103/Physrevlett.117.028101  0.56
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  0.56
2016 Purvine E, Monson K, Jurrus E, Star KT, Baker NA. Energy Minimization of Discrete Protein Titration State Models Using Graph Theory. The Journal of Physical Chemistry. B. PMID 27089174 DOI: 10.1021/acs.jpcb.6b02059  0.56
2016 Sushko ML, Thomas DG, Pabit SA, Pollack L, Onufriev AV, Baker NA. The Role of Correlation and Solvation in Ion Interactions with B-DNA. Biophysical Journal. 110: 315-26. PMID 26789755 DOI: 10.1016/J.Bpj.2015.12.011  0.56
2016 Jurrus E, Hodas N, Baker N, Marrinan T, Hoover MD. Adaptive visual sort and summary of micrographic images of nanoparticles for forensic analysis 2016 Ieee Symposium On Technologies For Homeland Security, Hst 2016. DOI: 10.1109/THS.2016.7568959  0.56
2016 Tolokh IS, Drozdetski AV, Pollack L, Baker NA, Onufriev AV. Multi-shell model of ion-induced nucleic acid condensation Journal of Chemical Physics. 144. DOI: 10.1063/1.4945382  0.56
2015 Lei H, Yang X, Zheng B, Lin G, Baker NA. CONSTRUCTING SURROGATE MODELS OF COMPLEX SYSTEMS WITH ENHANCED SPARSITY: QUANTIFYING THE INFLUENCE OF CONFORMATIONAL UNCERTAINTY IN BIOMOLECULAR SOLVATION. Multiscale Modeling & Simulation : a Siam Interdisciplinary Journal. 13: 1327-1353. PMID 26766929 DOI: 10.1137/140981587  0.56
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  0.56
2014 Thomas DG, Chikkagoudar S, Heredia-Langer A, Tardiff MF, Xu Z, Hourcade DE, Pham CT, Lanza GM, Weinberger KQ, Baker NA. Physicochemical signatures of nanoparticle-dependent complement activation. Computational Science & Discovery. 7: 015003. PMID 25254068 DOI: 10.1088/1749-4699/7/1/015003  0.56
2014 Tolokh IS, Pabit SA, Katz AM, Chen Y, Drozdetski A, Baker N, Pollack L, Onufriev AV. Why double-stranded RNA resists condensation. Nucleic Acids Research. 42: 10823-31. PMID 25123663 DOI: 10.1093/Nar/Gku756  0.56
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  0.56
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  0.56
2014 Pham CT, Thomas DG, Beiser J, Mitchell LM, Huang JL, Senpan A, Hu G, Gordon M, Baker NA, Pan D, Lanza GM, Hourcade DE. Application of a hemolysis assay for analysis of complement activation by perfluorocarbon nanoparticles. Nanomedicine : Nanotechnology, Biology, and Medicine. 10: 651-60. PMID 24211337 DOI: 10.1016/j.nano.2013.10.012  0.56
2014 Gosink LJ, Hogan EA, Pulsipher TC, Baker NA. Bayesian model aggregation for ensemble-based estimates of protein pKa values. Proteins. 82: 354-63. PMID 23946048 DOI: 10.1002/prot.24390  0.56
2013 Harper SL, Hutchison JE, Baker N, Ostraat M, Tinkle S, Steevens J, Hoover MD, Adamick J, Rajan K, Gaheen S, Cohen Y, Nel A, Cachau RE, Tuominen M. Nanoinformatics workshop report: Current resources, community needs, and the proposal of a collaborative framework for data sharing and information integration. Computational Science & Discovery. 6: 14008. PMID 24454543 DOI: 10.1088/1749-4699/6/1/014008  0.56
2013 Daily MD, Chun J, Heredia-Langner A, Wei G, Baker NA. Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies. The Journal of Chemical Physics. 139: 204108. PMID 24289345 DOI: 10.1063/1.4832900  0.56
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  0.56
2013 Baker NA, Klemm JD, Harper SL, Gaheen S, Heiskanen M, Rocca-Serra P, Sansone SA. Standardizing data. Nature Nanotechnology. 8: 73-4. PMID 23380926 DOI: 10.1038/nnano.2013.12  0.56
2013 Thomas DG, Gaheen S, Harper SL, Fritts M, Klaessig F, Hahn-Dantona E, Paik D, Pan S, Stafford GA, Freund ET, Klemm JD, Baker NA. ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format. Bmc Biotechnology. 13: 2. PMID 23311978 DOI: 10.1186/1472-6750-13-2  0.56
2013 Thomas DG, Chun J, Chen Z, Wei G, Baker NA. Parameterization of a geometric flow implicit solvation model. Journal of Computational Chemistry. 34: 687-95. PMID 23212974 DOI: 10.1002/Jcc.23181  0.56
2013 Baker NA, Barr JL, Bonheyo GT, Joslyn CA, Krishnaswami K, Oxley ME, Quadrel R, Sego LH, Tardiff MF, Wynne AS. Research towards a systematic signature discovery process Ieee Isi 2013 - 2013 Ieee International Conference On Intelligence and Security Informatics: Big Data, Emergent Threats, and Decision-Making in Security Informatics. 301-308. DOI: 10.1109/ISI.2013.6578848  0.56
2012 Thomas DG, Chikkagoudar S, Chappell AR, Baker NA. Annotating the structure and components of a nanoparticle formulation using computable string expressions. Proceedings. Ieee International Conference On Bioinformatics and Biomedicine. 2012: 889-894. PMID 24533226 DOI: 10.1109/BIBMW.2012.6470259  0.56
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  0.56
2012 Chen Z, Zhao S, Chun J, Thomas DG, Baker NA, Bates PW, Wei GW. Variational approach for nonpolar solvation analysis. The Journal of Chemical Physics. 137: 084101. PMID 22938212 DOI: 10.1063/1.4745084  0.56
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  0.68
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  0.56
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  0.56
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  0.56
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  0.56
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  0.56
2011 Thomas DG, Klaessig F, Harper SL, Fritts M, Hoover MD, Gaheen S, Stokes TH, Reznik-Zellen R, Freund ET, Klemm JD, Paik DS, Baker NA. Informatics and standards for nanomedicine technology. Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology. 3: 511-32. PMID 21721140 DOI: 10.1002/wnan.152  0.56
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  0.56
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  0.56
2011 Chen Z, Baker NA, Wei GW. Differential geometry based solvation model II: Lagrangian formulation. Journal of Mathematical Biology. 63: 1139-200. PMID 21279359 DOI: 10.1007/S00285-011-0402-Z  0.56
2011 Thomas DG, Pappu RV, Baker NA. NanoParticle Ontology for cancer nanotechnology research. Journal of Biomedical Informatics. 44: 59-74. PMID 20211274 DOI: 10.1016/J.Jbi.2010.03.001  0.56
2010 Callenberg KM, Choudhary OP, de Forest GL, Gohara DW, Baker NA, Grabe M. APBSmem: a graphical interface for electrostatic calculations at the membrane. Plos One. 5. PMID 20949122 DOI: 10.1371/Journal.Pone.0012722  0.56
2010 Chen Z, Baker NA, Wei GW. Differential geometry based solvation model I: Eulerian formulation. Journal of Computational Physics. 229: 8231-8258. PMID 20938489 DOI: 10.1016/  0.56
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  0.56
2009 Chen AA, Marucho M, Baker NA, Pappu RV. Simulations of RNA interactions with monovalent ions. Methods in Enzymology. 469: 411-32. PMID 20946801 DOI: 10.1016/S0076-6879(09)69020-0  0.56
2009 Thomas DG, Pappu RV, Baker NA. Ontologies for cancer nanotechnology research. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 4158-61. PMID 19964619 DOI: 10.1109/IEMBS.2009.5333941  0.56
2009 Silva JR, Pan H, Wu D, Nekouzadeh A, Decker KF, Cui J, Baker NA, Sept D, Rudy Y. A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential. Proceedings of the National Academy of Sciences of the United States of America. 106: 11102-6. PMID 19549851 DOI: 10.1073/Pnas.0904505106  0.56
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  0.56
2008 Dong F, Wagoner JA, Baker NA. Assessing the performance of implicit solvation models at a nucleic acid surface. Physical Chemistry Chemical Physics : Pccp. 10: 4889-902. PMID 18688533 DOI: 10.1039/b807384h  0.56
2008 Bradley MJ, Chivers PT, Baker NA. Molecular dynamics simulation of the Escherichia coli NikR protein: equilibrium conformational fluctuations reveal interdomain allosteric communication pathways. Journal of Molecular Biology. 378: 1155-73. PMID 18433769 DOI: 10.1016/j.jmb.2008.03.010  0.56
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  0.56
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  0.56
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  0.56
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  0.68
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  0.56
2007 Schnieders MJ, Baker NA, Ren P, Ponder JW. Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. The Journal of Chemical Physics. 126: 124114. PMID 17411115 DOI: 10.1063/1.2714528  0.56
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  0.68
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  0.56
2006 Wong CJ, Rice RL, Baker NA, Ju T, Lohman TM. Probing 3'-ssDNA loop formation in E. coli RecBCD/RecBC-DNA complexes using non-natural DNA: a model for "Chi" recognition complexes. Journal of Molecular Biology. 362: 26-43. PMID 16901504 DOI: 10.1016/j.jmb.2006.07.016  0.56
2006 Wagoner JA, Baker NA. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proceedings of the National Academy of Sciences of the United States of America. 103: 8331-6. PMID 16709675 DOI: 10.1073/pnas.0600118103  0.56
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  0.56
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  0.56
2005 Showalter SA, Baker NA, Tang C, Hall KB. Iron responsive element RNA flexibility described by NMR and isotropic reorientational eigenmode dynamics. Journal of Biomolecular Nmr. 32: 179-93. PMID 16132819 DOI: 10.1007/s10858-005-7948-2  0.56
2005 Baker NA. Improving implicit solvent simulations: a Poisson-centric view. Current Opinion in Structural Biology. 15: 137-43. PMID 15837170 DOI: 10.1016/  0.56
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  0.68
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  0.56
2004 Song Y, Zhang Y, Bajaj CL, Baker NA. Continuum diffusion reaction rate calculations of wild-type and mutant mouse acetylcholinesterase: adaptive finite element analysis. Biophysical Journal. 87: 1558-66. PMID 15345536 DOI: 10.1529/biophysj.104.041517  0.56
2004 Wagoner J, Baker NA. Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models. Journal of Computational Chemistry. 25: 1623-9. PMID 15264256 DOI: 10.1002/jcc.20089  0.56
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  0.68
2004 Baker NA. Poisson-Boltzmann methods for biomolecular electrostatics. Methods in Enzymology. 383: 94-118. PMID 15063648 DOI: 10.1016/S0076-6879(04)83005-2  0.56
2004 Dolinsky TJ, Burgers PMJ, Karplus K, Baker NA. SPrCY: Comparison of structural predictions in the Saccharomyces cerevisiae genome Bioinformatics. 20: 2312-2314. PMID 15059824 DOI: 10.1093/bioinformatics/bth223  0.56
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  0.68
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  0.56
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  0.56
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  0.56
2003 Baker NA, McCammon JA. Electrostatic interactions. Methods of Biochemical Analysis. 44: 427-40. PMID 12647398  0.56
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  0.68
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+  0.56
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  0.56
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  0.56
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  0.56
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