Adrian H. Elcock - Publications

Affiliations: 
University of Iowa, Iowa City, IA 
Area:
Biochemistry

80 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
2023 Hacker WC, Elcock AH. spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes. Nucleic Acids Research. PMID 37602419 DOI: 10.1093/nar/gkad682  0.314
2023 Tworek JW, Elcock AH. Orientationally Averaged Version of the Rotne-Prager-Yamakawa Tensor Provides a Fast but Still Accurate Treatment of Hydrodynamic Interactions in Brownian Dynamics Simulations of Biological Macromolecules. Journal of Chemical Theory and Computation. 19: 5099-5111. PMID 37409946 DOI: 10.1021/acs.jctc.3c00476  0.402
2023 McDonnell RT, Elcock AH. AutoRNC: an automated modeling program for building atomic models of ribosome-nascent chain complexes. Biorxiv : the Preprint Server For Biology. PMID 37398297 DOI: 10.1101/2023.06.14.544999  0.336
2023 Henderson AN, McDonnell RT, Elcock AH. Modeling the 3D structure and conformational dynamics of very large RNAs using coarse-grained molecular simulations. Biorxiv : the Preprint Server For Biology. PMID 37333149 DOI: 10.1101/2023.06.06.543892  0.348
2023 Tworek JW, Elcock AH. An Orientationally Averaged Version of the Rotne-Prager-Yamakawa Tensor Provides A Fast But Still Accurate Treatment Of Hydrodynamic Interactions In Brownian Dynamics Simulations Of Biological Macromolecules. Biorxiv : the Preprint Server For Biology. PMID 37162930 DOI: 10.1101/2023.04.21.537865  0.402
2023 Hacker WC, Elcock AH. : A single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes. Biorxiv : the Preprint Server For Biology. PMID 37131791 DOI: 10.1101/2023.04.21.537861  0.314
2020 Elcock AH. Challenges to the Creation of Dynamic Structural Models of Intracellular Systems Biophysical Journal. 118: 352a-353a. DOI: 10.1016/J.Bpj.2019.11.2033  0.333
2019 Yang L, Sun X, Ye Y, Lu Y, Zuo J, Liu W, Elcock A, Zhu S. p38α Mitogen-Activated Protein Kinase Is a Druggable Target in Pancreatic Adenocarcinoma. Frontiers in Oncology. 9: 1294. PMID 31828036 DOI: 10.3389/Fonc.2019.01294  0.556
2018 Schrodt MV, Andrews CT, Elcock AH. Correction to Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 μs Explicit-Solvent Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 30427670 DOI: 10.1021/Acs.Jctc.8B00595  0.384
2018 Andrews CT, Campbell BA, Elcock AH. Correction to Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 30427668 DOI: 10.1021/acs.jctc.8b00596  0.308
2018 Natan E, Endoh T, Haim-Vilmovsky L, Flock T, Chalancon G, Hopper JTS, Kintses B, Horvath P, Daruka L, Fekete G, Pál C, Papp B, Oszi E, Magyar Z, Marsh JA, ... Elcock AH, et al. Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins. Nature Structural & Molecular Biology. PMID 29434345 DOI: 10.1038/S41594-018-0029-5  0.409
2018 Powers KT, Elcock AH, Washington MT. The C-terminal region of translesion synthesis DNA polymerase η is partially unstructured and has high conformational flexibility. Nucleic Acids Research. PMID 29385534 DOI: 10.1093/Nar/Gky031  0.329
2017 Lay WK, Miller MS, Elcock AH. Reparameterization of Solute-Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 28437100 DOI: 10.1021/Acs.Jctc.7B00194  0.435
2017 Miller MS, Lay WK, Li S, Hacker WC, An J, Ren J, Elcock AH. Reparameterization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 28296391 DOI: 10.1021/Acs.Jctc.6B01059  0.435
2017 Andrews CT, Campbell BA, Elcock AH. Direct comparison of amino acid and salt interactions with double-stranded and single-stranded DNA from explicit-solvent molecular dynamics simulations. Journal of Chemical Theory and Computation. PMID 28288277 DOI: 10.1021/Acs.Jctc.6B00883  0.415
2017 Walsh IM, Li S, Elcock AH, Clark PL. Integrated In Vivo and In Silico Studies of Cotranslational Protein Folding as a Function of Translation Rate Biophysical Journal. 112: 40a. DOI: 10.1016/J.Bpj.2016.11.256  0.489
2016 Clark PL, Elcock AH. Molecular chaperones: providing a safe place to weather a midlife protein-folding crisis. Nature Structural & Molecular Biology. 23: 621-623. PMID 27384188 DOI: 10.1038/Nsmb.3255  0.414
2016 Chen R, Subramanyam S, Elcock AH, Spies M, Wold MS. Dynamic binding of replication protein a is required for DNA repair. Nucleic Acids Research. PMID 27131385 DOI: 10.1093/Nar/Gkw339  0.327
2016 Miller MS, Lay WK, Elcock AH. Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization. The Journal of Physical Chemistry. B. PMID 27052117 DOI: 10.1021/Acs.Jpcb.6B01902  0.423
2016 Lay WK, Miller MS, Elcock AH. Optimizing Solute-Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements. Journal of Chemical Theory and Computation. PMID 26967542 DOI: 10.1021/Acs.Jctc.5B01136  0.34
2015 Schrodt MV, Andrews CT, Elcock AH. Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 μs Explicit-Solvent Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 26580891 DOI: 10.1021/Acs.Jctc.5B00899  0.463
2015 Li S, Andrews CT, Frembgen-Kesner T, Miller MS, Siemonsma SL, Collingsworth TD, Rockafellow IT, Ngo NA, Campbell BA, Brown RF, Guo C, Schrodt M, Liu YT, Elcock AH. Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field. Journal of Chemical Theory and Computation. 11: 1315-1329. PMID 26579777 DOI: 10.1021/Ct5010966  0.416
2015 Frembgen-Kesner T, Andrews CT, Li S, Ngo NA, Shubert SA, Jain A, Olayiwola OJ, Weishaar MR, Elcock AH. Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides. Journal of Chemical Theory and Computation. 11: 2341-54. PMID 26574429 DOI: 10.1021/Acs.Jctc.5B00038  0.515
2015 Brown RF, Andrews CT, Elcock AH. Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment. Journal of Chemical Theory and Computation. 11: 2315-28. PMID 26574427 DOI: 10.1021/Ct501170H  0.362
2015 Cressiot B, Braselmann E, Oukhaled A, Elcock AH, Pelta J, Clark PL. Dynamics and Energy Contributions for Transport of Unfolded Pertactin through a Protein Nanopore. Acs Nano. 9: 9050-61. PMID 26302243 DOI: 10.1021/Acsnano.5B03053  0.448
2015 Li S, Elcock AH. Residue-Specific Force Field (RSFF2) Improves the Modeling of Conformational Behavior of Peptides and Proteins. The Journal of Physical Chemistry Letters. 6: 2127-33. PMID 26266514 DOI: 10.1021/Acs.Jpclett.5B00654  0.41
2015 Frembgen-Kesner T, Andrews CT, Li S, Ngo NA, Shubert SA, Jain A, Olayiwola OJ, Weishaar MR, Elcock AH. Parametrization of backbone flexibility in a Coarse-grained Force Field for Proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-Residue reptides Journal of Chemical Theory and Computation. 11: 2341-2354. DOI: 10.1021/acs.jctc.5b00038  0.379
2014 Andrews CT, Elcock AH. Erratum to Molecular Dynamics Simulations of Highly Crowded Amino Acid Solutions: Comparisons of Eight Different Force Field Combinations with Experiment and with Each Other. Journal of Chemical Theory and Computation. 10: 1834. PMID 26580390 DOI: 10.1021/ct500151a  0.307
2014 Andrews CT, Elcock AH. COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids. Journal of Chemical Theory and Computation. 10: 5178-5194. PMID 25400526 DOI: 10.1021/Ct5006328  0.531
2014 Theillet FX, Binolfi A, Frembgen-Kesner T, Hingorani K, Sarkar M, Kyne C, Li C, Crowley PB, Gierasch L, Pielak GJ, Elcock AH, Gershenson A, Selenko P. Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs). Chemical Reviews. 114: 6661-714. PMID 24901537 DOI: 10.1021/Cr400695P  0.346
2013 Andrews CT, Elcock AH. Molecular dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other. Journal of Chemical Theory and Computation. 9. PMID 24409104 DOI: 10.1021/Ct400371H  0.509
2013 Stark AC, Andrews CT, Elcock AH. Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field. Journal of Chemical Theory and Computation. 9. PMID 24223529 DOI: 10.1021/Ct400008P  0.543
2013 Thomas AS, Mao S, Elcock AH. Flexibility of the bacterial chaperone trigger factor in microsecond-timescale molecular dynamics simulations. Biophysical Journal. 105: 732-44. PMID 23931321 DOI: 10.1016/J.Bpj.2013.06.028  0.529
2013 Frembgen-Kesner T, Elcock AH. Computer Simulations of the Bacterial Cytoplasm. Biophysical Reviews. 5: 109-119. PMID 23914257 DOI: 10.1007/S12551-013-0110-6  0.571
2013 Elcock AH. A molecule-centered method for accelerating the calculation of hydrodynamic interactions in Brownian dynamics simulations containing many flexible biomolecules. Journal of Chemical Theory and Computation. 9: 3224-3239. PMID 23914146 DOI: 10.1021/Ct400240W  0.516
2013 Zhu S, Travis SM, Elcock AH. Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: a combined computational and experimental study. Journal of Chemical Theory and Computation. 9: 3151-3164. PMID 23914145 DOI: 10.1021/Ct400104X  0.616
2013 Zhu S, Travis SM, Elcock AH. Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: A combined computational and experimental study Journal of Chemical Theory and Computation. 9: 3151-3164. DOI: 10.1021/ct400104x  0.487
2013 Elcock AH, Frembgen Kesner T. Structure and Dynamics of Ire1 Assembly in the Endoplasmic Reticulum Studied by Molecular Simulation Biophysical Journal. 104: 578a. DOI: 10.1016/J.Bpj.2012.11.3208  0.46
2012 Reinert ZE, Musselman ED, Elcock AH, Horne WS. A PEG-based oligomer as a backbone replacement for surface-exposed loops in a protein tertiary structure. Chembiochem : a European Journal of Chemical Biology. 13: 1107-11. PMID 22539233 DOI: 10.1002/Cbic.201200200  0.443
2011 Thomas AS, Elcock AH. Molecular Dynamics Simulations Predict a Favorable and Unique Mode of Interaction between Lithium (Li(+)) Ions and Hydrophobic Molecules in Aqueous Solution. Journal of Chemical Theory and Computation. 7: 818-24. PMID 26606333 DOI: 10.1021/Ct100521V  0.425
2011 Thomas AS, Elcock AH. Direct Measurement of the Kinetics and Thermodynamics of Association of Hydrophobic Molecules from Molecular Dynamics Simulations. The Journal of Physical Chemistry Letters. 2: 19-24. PMID 26295208 DOI: 10.1021/Jz1014899  0.515
2011 Elcock AH. Challenges in Large-Scale Molecular Simulations of Intracellular Environments Biophysical Journal. 100: 6a. DOI: 10.1016/J.Bpj.2010.12.242  0.502
2010 Frembgen-Kesner T, Elcock AH. Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association. Biophysical Journal. 99: L75-7. PMID 21044566 DOI: 10.1016/J.Bpj.2010.09.006  0.513
2010 McGuffee SR, Elcock AH. Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. Plos Computational Biology. 6: e1000694. PMID 20221255 DOI: 10.1371/Journal.Pcbi.1000694  0.687
2010 Elcock AH. Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Current Opinion in Structural Biology. 20: 196-206. PMID 20167475 DOI: 10.1016/J.Sbi.2010.01.008  0.507
2010 Zhu S, Elcock AH. A complete thermodynamic characterization of electrostatic and hydrophobic associations in the temperature range 0 to 100 °c from explicit-solvent molecular dynamics simulations Journal of Chemical Theory and Computation. 6: 1293-1306. DOI: 10.1021/Ct1000704  0.646
2010 Elcock A. Molecular Modeling of the Bacterial Cytoplasm Biophysical Journal. 98: 4a. DOI: 10.1016/J.Bpj.2009.12.026  0.495
2009 Frembgen-Kesner T, Elcock AH. Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins. Journal of Chemical Theory and Computation. 5: 242-56. PMID 26610102 DOI: 10.1021/Ct800499P  0.526
2007 Thomas AS, Elcock AH. Molecular dynamics simulations of hydrophobic associations in aqueous salt solutions indicate a connection between water hydrogen bonding and the Hofmeister effect. Journal of the American Chemical Society. 129: 14887-98. PMID 17994735 DOI: 10.1021/Ja073097Z  0.515
2006 Rockey WM, Elcock AH. Structure selection for protein kinase docking and virtual screening: homology models or crystal structures? Current Protein & Peptide Science. 7: 437-57. PMID 17073695 DOI: 10.2174/138920306778559368  0.312
2006 McGuffee SR, Elcock AH. Atomically detailed simulations of concentrated protein solutions: the effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems. Journal of the American Chemical Society. 128: 12098-110. PMID 16967959 DOI: 10.1021/Ja0614058  0.697
2006 Elcock AH. Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome. Plos Computational Biology. 2: e98. PMID 16789821 DOI: 10.1371/Journal.Pcbi.0020098  0.519
2006 Thomas AS, Elcock AH. Direct observation of salt effects on molecular interactions through explicit-solvent molecular dynamics simulations: differential effects on electrostatic and hydrophobic interactions and comparisons to Poisson-Boltzmann theory. Journal of the American Chemical Society. 128: 7796-806. PMID 16771493 DOI: 10.1021/Ja058637B  0.5
2006 Frembgen-Kesner T, Elcock AH. Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase. Journal of Molecular Biology. 359: 202-14. PMID 16616932 DOI: 10.1016/J.Jmb.2006.03.021  0.387
2005 Rockey WM, Elcock AH. Rapid computational identification of the targets of protein kinase inhibitors. Journal of Medicinal Chemistry. 48: 4138-52. PMID 15943486 DOI: 10.1021/Jm049461B  0.361
2004 Elcock AH. Molecular simulations of diffusion and association in multimacromolecular systems. Methods in Enzymology. 383: 166-98. PMID 15063651 DOI: 10.1016/S0076-6879(04)83008-8  0.548
2004 Thomas AS, Elcock AH. Molecular simulations suggest protein salt bridges are uniquely suited to life at high temperatures. Journal of the American Chemical Society. 126: 2208-14. PMID 14971956 DOI: 10.1021/Ja039159C  0.488
2003 Yang H, Elcock AH. Association lifetimes of hydrophobic amino acid pairs measured directly from molecular dynamics simulations. Journal of the American Chemical Society. 125: 13968-9. PMID 14611227 DOI: 10.1021/Ja037010V  0.457
2003 Morikis D, Elcock AH, Jennings PA, McCammon JA. The pH dependence of stability of the activation helix and the catalytic site of GART. Biophysical Chemistry. 105: 279-91. PMID 14499900 DOI: 10.1016/S0301-4622(03)00079-6  0.327
2003 Elcock AH. Atomic-level observation of macromolecular crowding effects: escape of a protein from the GroEL cage. Proceedings of the National Academy of Sciences of the United States of America. 100: 2340-4. PMID 12601146 DOI: 10.1073/Pnas.0535055100  0.512
2002 Rockey WM, Elcock AH. Progress toward virtual screening for drug side effects. Proteins. 48: 664-71. PMID 12211034 DOI: 10.1002/Prot.10186  0.335
2002 Elcock AH. Atomistic simulations of competition between substrates binding to an enzyme. Biophysical Journal. 82: 2326-32. PMID 11964223 DOI: 10.1016/S0006-3495(02)75578-1  0.421
2002 Elcock AH. Modeling supramolecular assemblages. Current Opinion in Structural Biology. 12: 154-60. PMID 11959491 DOI: 10.1016/S0959-440X(02)00303-2  0.457
2001 Morikis D, Elcock AH, Jennings PA, McCammon JA. Proton transfer dynamics of GART: the pH-dependent catalytic mechanism examined by electrostatic calculations. Protein Science : a Publication of the Protein Society. 10: 2379-92. PMID 11604543 DOI: 10.1110/Ps.17301  0.372
2001 Morikis D, Elcock AH, Jennings PA, McCammon JA. Native-state conformational dynamics of GART: a regulatory pH-dependent coil-helix transition examined by electrostatic calculations. Protein Science : a Publication of the Protein Society. 10: 2363-78. PMID 11604542 DOI: 10.1110/Ps.17201  0.347
2001 Elcock AH. Prediction of functionally important residues based solely on the computed energetics of protein structure Journal of Molecular Biology. 312: 885-896. PMID 11575940 DOI: 10.1006/Jmbi.2001.5009  0.427
2001 Elcock AH, McCammon JA. Identification of protein oligomerization states by analysis of interface conservation Proceedings of the National Academy of Sciences of the United States of America. 98: 2990-2994. PMID 11248019 DOI: 10.1073/Pnas.061411798  0.392
2001 Elcock AH, McCammon JA. Calculation of weak protein-protein interactions: The pH dependence of the second virial coefficient Biophysical Journal. 80: 613-625. PMID 11159430 DOI: 10.1016/S0006-3495(01)76042-0  0.493
2001 Elcock AH, Sept D, McCammon JA. Computer Simulation of Protein−Protein Interactions The Journal of Physical Chemistry B. 105: 1504-1518. DOI: 10.1021/Jp003602D  0.455
2001 Elcock AH, Sept D, McCammon JA. Computer simulation of protein-protein interactions Journal of Physical Chemistry B. 105: 1504-1508.  0.408
1999 Sept D, Elcock AH, McCammon JA. Computer simulations of actin polymerization can explain the barbed-pointed end asymmetry Journal of Molecular Biology. 294: 1181-1189. PMID 10600376 DOI: 10.1006/Jmbi.1999.3332  0.454
1999 Elcock AH. Realistic modeling of the denatured states of proteins allows accurate calculations of the pH dependence of protein stability Journal of Molecular Biology. 294: 1051-1062. PMID 10588906 DOI: 10.1006/Jmbi.1999.3305  0.435
1999 Elcock AH, Gabdoulline RR, Wade RC, McCammon JA. Computer simulation of protein-protein association kinetics: Acetylcholinesterase-fasciculin Journal of Molecular Biology. 291: 149-162. PMID 10438612 DOI: 10.1006/Jmbi.1999.2919  0.529
1998 Tara S, Elcock AH, Kirchhoff PD, Briggs JM, Radic Z, Taylor P, McCammon JA. Rapid binding of a cationic active site inhibitor to wild type and mutant mouse acetylcholinesterase: Brownian dynamics simulation including diffusion in the active site gorge. Biopolymers. 46: 465-74. PMID 9838872 DOI: 10.1002/(Sici)1097-0282(199812)46:7<465::Aid-Bip4>3.0.Co;2-Y  0.331
1998 Elcock AH. The stability of salt bridges at high temperatures: Implications for hyperthermophilic proteins Journal of Molecular Biology. 284: 489-502. PMID 9813132 DOI: 10.1006/Jmbi.1998.2159  0.38
1998 Elcock AH, McCammon JA. Electrostatic contributions to the stability of halophilic proteins Journal of Molecular Biology. 280: 731-748. PMID 9677300 DOI: 10.1006/Jmbi.1998.1904  0.448
1997 Fogolari F, Elcock AH, Esposito G, Viglino P, Briggs JM, McCammon JA. Electrostatic effects in homeodomain-DNA interactions. Journal of Molecular Biology. 267: 368-81. PMID 9096232 DOI: 10.1006/Jmbi.1996.0842  0.374
1996 Elcock AH, Potter MJ, Matthews DA, Knighton DR, McCammon JA. Electrostatic channeling in the bifunctional enzyme dihydrofolate reductase-thymidylate synthase Journal of Molecular Biology. 262: 370-374. PMID 8845002 DOI: 10.1006/Jmbi.1996.0520  0.325
1996 Elcock AH, Rodger A, Richards WG. Theoretical studies of the intercalation of 9-hydroxyellipticine in DNA Biopolymers. 39: 309-326. PMID 8756512 DOI: 10.1002/(Sici)1097-0282(199609)39:3<309::Aid-Bip4>3.0.Co;2-S  0.404
1996 Antosiewicz J, Briggs JM, Elcock AH, Gilson MK, McCammon JA. Computing ionization states of proteins with a detailed charge model Journal of Computational Chemistry. 17: 1633-1644. DOI: 10.1002/(Sici)1096-987X(19961115)17:14<1633::Aid-Jcc5>3.0.Co;2-M  0.42
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