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Thomas A. Darden, Ph.D. - Publications

Affiliations: 
National Institute of Environmental Health Sciences (NIEHS), Durham, NC, United States 
Area:
Statistics, Molecular Dynamics

124 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
2018 Gokcan H, Kratz EG, Darden TA, Piquemal JP, Cisneros GA. QM/MM Simulations with the Gaussian Electrostatic Model, A Density-Based Polarizable Potential. The Journal of Physical Chemistry Letters. PMID 29775314 DOI: 10.1021/Acs.Jpclett.8B01412  1
2014 Chaudret R, Gresh N, Narth C, Lagardère L, Darden TA, Cisneros GA, Piquemal JP. S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations. The Journal of Physical Chemistry. A. 118: 7598-612. PMID 24878003 DOI: 10.1021/Jp5051657  1
2011 Elking DM, Perera L, Duke R, Darden T, Pedersen LG. A finite field method for calculating molecular polarizability tensors for arbitrary multipole rank. Journal of Computational Chemistry. 32: 3283-95. PMID 21915883 DOI: 10.1002/Jcc.21914  1
2010 Elking DM, Perera L, Duke R, Darden T, Pedersen LG. Atomic forces for geometry-dependent point multipole and gaussian multipole models. Journal of Computational Chemistry. 31: 2702-13. PMID 20839297 DOI: 10.1002/Jcc.21563  1
2010 Zurita A, Zhang Y, Pedersen L, Darden T, Birnbaumer L. Obligatory role in GTP hydrolysis for the amide carbonyl oxygen of the Mg(2+)-coordinating Thr of regulatory GTPases. Proceedings of the National Academy of Sciences of the United States of America. 107: 9596-601. PMID 20457940 DOI: 10.1073/Pnas.1004803107  1
2010 de la Lande A, Maddaluno J, Parisel O, Darden TA, Piquemal JP. Study of the docking of competitive inhibitors at a model of tyrosinase active site: insights from joint broken-symmetry/Spin-Flip DFT computations and ELF topological analysis. Interdisciplinary Sciences, Computational Life Sciences. 2: 3-11. PMID 20396590 DOI: 10.1007/S12539-010-0096-8  1
2010 Elking DM, Cisneros GA, Piquemal JP, Darden TA, Pedersen LG. Gaussian Multipole Model (GMM). Journal of Chemical Theory and Computation. 6: 190-202. PMID 20209077 DOI: 10.1021/Ct900348B  1
2009 Cerutti DS, Duke RE, Darden TA, Lybrand TP. Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility. Journal of Chemical Theory and Computation. 5: 2322. PMID 20174456 DOI: 10.1021/Ct9001015  1
2009 Moradi M, Babin V, Roland C, Darden TA, Sagui C. Conformations and free energy landscapes of polyproline peptides. Proceedings of the National Academy of Sciences of the United States of America. 106: 20746-51. PMID 19923435 DOI: 10.1073/Pnas.0906500106  1
2009 Hobbs CA, Deterding LJ, Perera L, Bobay BG, Thompson RJ, Darden TA, Cavanagh J, Tomer KB. Structural characterization of the conformational change in calbindin-D28k upon calcium binding using differential surface modification analyzed by mass spectrometry. Biochemistry. 48: 8603-14. PMID 19658395 DOI: 10.1021/Bi900350Q  1
2009 Cisneros GA, Perera L, Schaaper RM, Pedersen LC, London RE, Pedersen LG, Darden TA. Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues. Journal of the American Chemical Society. 131: 1550-6. PMID 19119875 DOI: 10.1021/Ja8082818  1
2009 Chaudref R, Ulmera S, Van Severena MC, Gresh N, Pansela O, Cisnerosd GA, Darden TA, Piquemal JP. Progress Towards Accurate Molecular Modeling of Metal Complexes Using Polarizable Force Fields Aip Conference Proceedings. 1102: 185-192. DOI: 10.1063/1.3108373  1
2008 Cisneros GA, Tholander SN, Parisel O, Darden TA, Elking D, Perera L, Piquemal JP. Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hybrid Quantum Mechanical/Molecular Mechanical Embedding. International Journal of Quantum Chemistry. 108: 1905-1912. PMID 19606279 DOI: 10.1002/Qua.21675  1
2008 Li W, Huang Y, Reid R, Steiner J, Malpica-Llanos T, Darden TA, Shankar SK, Mahadevan A, Satishchandra P, Nath A. NMDA receptor activation by HIV-Tat protein is clade dependent. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 28: 12190-8. PMID 19020013 DOI: 10.1523/Jneurosci.3019-08.2008  1
2008 Wei SJ, Williams JG, Dang H, Darden TA, Betz BL, Humble MM, Chang FM, Trempus CS, Johnson K, Cannon RE, Tennant RW. Identification of a specific motif of the DSS1 protein required for proteasome interaction and p53 protein degradation. Journal of Molecular Biology. 383: 693-712. PMID 18775730 DOI: 10.1016/J.Jmb.2008.08.044  1
2008 Jiao D, Golubkov PA, Darden TA, Ren P. Calculation of protein-ligand binding free energy by using a polarizable potential. Proceedings of the National Academy of Sciences of the United States of America. 105: 6290-5. PMID 18427113 DOI: 10.1073/Pnas.0711686105  1
2008 Li W, Huang Y, Reid R, Steiner J, Malpica-Llanos T, Darden TA, Shankar SK, Mahadevan A, Satishchandra P, Nath A. NMDA receptor activation by HIV-Tat protein is clade dependent (Journal of Neuroscience (2008) (12190-12198)) Journal of Neuroscience. 28.  1
2007 Gresh N, Cisneros GA, Darden TA, Piquemal JP. Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. Journal of Chemical Theory and Computation. 3: 1960-1986. PMID 18978934 DOI: 10.1021/Ct700134R  1
2007 Cisneros GA, Elking D, Piquemal JP, Darden TA. Numerical fitting of molecular properties to Hermite Gaussians. The Journal of Physical Chemistry. A. 111: 12049-56. PMID 17973464 DOI: 10.1021/Jp074817R  1
2007 Herce HD, Garcia AE, Darden T. The electrostatic surface term: (I) periodic systems. The Journal of Chemical Physics. 126: 124106. PMID 17411107 DOI: 10.1063/1.2714527  1
2006 Cutalo JM, Darden TA, Kunkel TA, Tomer KB. Mapping the dimer interface in the C-terminal domains of the yeast MLH1-PMS1 heterodimer. Biochemistry. 45: 15458-67. PMID 17176067 DOI: 10.1021/Bi061392A  1
2006 Babin V, Roland C, Darden TA, Sagui C. The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections. The Journal of Chemical Physics. 125: 204909. PMID 17144742 DOI: 10.1063/1.2393236  1
2006 Cisneros GA, Piquemal JP, Darden TA. Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods. The Journal of Chemical Physics. 125: 184101. PMID 17115732 DOI: 10.1063/1.2363374  1
2006 Jiao D, King C, Grossfield A, Darden TA, Ren P. Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential. The Journal of Physical Chemistry. B. 110: 18553-9. PMID 16970483 DOI: 10.1021/Jp062230R  1
2006 Piquemal JP, Perera L, Cisneros GA, Ren P, Pedersen LG, Darden TA. Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. The Journal of Chemical Physics. 125: 054511. PMID 16942230 DOI: 10.1063/1.2234774  1
2006 Cisneros GA, Piquemal JP, Darden TA. Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions. The Journal of Physical Chemistry. B. 110: 13682-4. PMID 16836309 DOI: 10.1021/Jp062768X  1
2006 Babin V, Baucom J, Darden TA, Sagui C. Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure. The Journal of Physical Chemistry. B. 110: 11571-81. PMID 16771434 DOI: 10.1021/Jp061421R  1
2006 Cho J, Choi K, Darden T, Reynolds PR, Petitte JN, Shears SB. Avian multiple inositol polyphosphate phosphatase is an active phytase that can be engineered to help ameliorate the planet's "phosphate crisis" Journal of Biotechnology. 126: 248-259. PMID 16759730 DOI: 10.1016/J.Jbiotec.2006.04.028  1
2006 Gentile S, Darden T, Erxleben C, Romeo C, Russo A, Martin N, Rossie S, Armstrong DL. Rac GTPase signaling through the PP5 protein phosphatase. Proceedings of the National Academy of Sciences of the United States of America. 103: 5202-6. PMID 16549782 DOI: 10.1073/Pnas.0600080103  1
2006 Piquemal JP, Cisneros GA, Reinhardt P, Gresh N, Darden TA. Towards a force field based on density fitting. The Journal of Chemical Physics. 124: 104101. PMID 16542062 DOI: 10.1063/1.2173256  1
2006 Lee JG, Asciutto E, Babin V, Sagui C, Darden T, Roland C. Deprotonation of solvated formic acid: Car-Parrinello and metadynamics simulations. The Journal of Physical Chemistry. B. 110: 2325-31. PMID 16471820 DOI: 10.1021/Jp055809I  1
2006 Hamburgh ME, Curr KA, Monaghan M, Rao VR, Tripathi S, Preston BD, Sarafianos S, Arnold E, Darden T, Prasad VR. Structural determinants of slippage-mediated mutations by human immunodeficiency virus type 1 reverse transcriptase. The Journal of Biological Chemistry. 281: 7421-8. PMID 16423828 DOI: 10.1074/Jbc.M511380200  1
2006 López-Lemus J, Romero-Bastida M, Darden TA, Alejandre J. Liquid-vapour equilibrium of n -alkanes using interface simulations Molecular Physics. 104: 2413-2421. DOI: 10.1080/00268970600691274  1
2006 Lee JG, Asciutto E, Babin V, Sagui C, Darden T, Roland C. Deprotonation of solvated formic acid: Car-parrinello and metadynamics simulations Journal of Physical Chemistry B. 110: 2325-2331. DOI: 10.1021/jp055809i  1
2006 Babin V, Baucom J, Darden TA, Sagui C. Molecular dynamics simulations of polarizable DNA in crystal environment International Journal of Quantum Chemistry. 106: 3260-3269. DOI: 10.1002/Qua.21152  1
2006 Sagui C, Roland C, Pedersen LG, Darden TA. New Distributed Multipole Metdhods for Accurate Electrostatics in Large-Scale Biomolecular Simulations Lecture Notes in Computational Science and Engineering. 49: 297-312.  1
2005 Le Gouill C, Darden T, Madziva MT, Birnbaumer M. A role for K268 in V2R folding Febs Letters. 579: 4985-4990. PMID 16115624 DOI: 10.1016/J.Febslet.2005.08.003  1
2005 Cisneros GA, Piquemal JP, Darden TA. Intermolecular electrostatic energies using density fitting. The Journal of Chemical Physics. 123: 044109. PMID 16095348 DOI: 10.1063/1.1947192  1
2005 Herce DH, Perera L, Darden TA, Sagui C. Surface solvation for an ion in a water cluster. The Journal of Chemical Physics. 122: 024513. PMID 15638604 DOI: 10.1063/1.1829635  1
2005 Colina CM, Duke RE, Venkateswarlu D, Perera L, Darden T, Pedersen LG. Atomic molecular dynamical modeling of a large protein complex: Stf-fviia Aiche Annual Meeting, Conference Proceedings. 10513.  1
2004 Baucom J, Transue T, Fuentes-Cabrera M, Krahn JM, Darden TA, Sagui C. Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer in crystal environment: comparison of atomic point-charge, extra-point, and polarizable force fields. The Journal of Chemical Physics. 121: 6998-7008. PMID 15473761 DOI: 10.1063/1.1788631  1
2004 Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G. Making optimal use of empirical energy functions: force-field parameterization in crystal space. Proteins. 57: 678-83. PMID 15390263 DOI: 10.1002/Prot.20251  1
2004 Sagui C, Pomorski P, Darden TA, Roland C. Ab initio calculation of electrostatic multipoles with Wannier functions for large-scale biomolecular simulations. The Journal of Chemical Physics. 120: 4530-44. PMID 15268621 DOI: 10.1063/1.1644800  1
2004 Sagui C, Pedersen LG, Darden TA. Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations. The Journal of Chemical Physics. 120: 73-87. PMID 15267263 DOI: 10.1063/1.1630791  1
2004 Perera L, Darden TA, Duke RE, Venkateswarlu D, Pedersen LG. Early unfolding response of a stable protein domain to environmental changes Journal of Physical Chemistry A. 108: 9834-9840. DOI: 10.1021/Jp048385L  1
2003 Venkateswarlu D, Duke RE, Perera L, Darden TA, Pedersen LG. An all-atom solution-equilibrated model for human extrinsic blood coagulation complex (sTF-VIIa-Xa): a protein-protein docking and molecular dynamics refinement study. Journal of Thrombosis and Haemostasis : Jth. 1: 2577-88. PMID 14750502 DOI: 10.1111/J.1538-7836.2003.00421.X  0.76
2003 Fisher TS, Darden T, Prasad VR. Mutations proximal to the minor groove-binding track of human immunodeficiency virus type 1 reverse transcriptase differentially affect utilization of RNA versus DNA as template. Journal of Virology. 77: 5837-45. PMID 12719577 DOI: 10.1128/Jvi.77.10.5837-5845.2003  1
2003 DeRose EF, Darden T, Harvey S, Gabel S, Perrino FW, Schaaper RM, London RE. Elucidation of the epsilon-theta subunit interface of Escherichia coli DNA polymerase III by NMR spectroscopy. Biochemistry. 42: 3635-44. PMID 12667053 DOI: 10.1021/Bi0205451  1
2003 Negishi M, Dong J, Darden TA, Pedersen LG, Pedersen LC. Glucosaminylglycan biosynthesis: what we can learn from the X-ray crystal structures of glycosyltransferases GlcAT1 and EXTL2. Biochemical and Biophysical Research Communications. 303: 393-8. PMID 12659829 DOI: 10.1016/S0006-291X(03)00356-5  1
2003 Erxleben C, Gomez-Alegria C, Darden T, Mori Y, Birnbaumer L, Armstrong DL. Modulation of cardiac Ca(V)1.2 channels by dihydropyridine and phosphatase inhibitor requires Ser-1142 in the domain III pore loop. Proceedings of the National Academy of Sciences of the United States of America. 100: 2929-34. PMID 12601159 DOI: 10.1073/Pnas.2628046100  1
2003 Gorokhov A, Negishi M, Johnson EF, Pedersen LC, Perera L, Darden TA, Pedersen LG. Explicit water near the catalytic I helix Thr in the predicted solution structure of CYP2A4. Biophysical Journal. 84: 57-68. PMID 12524265 DOI: 10.1016/S0006-3495(03)74832-2  1
2003 Fisher TS, Darden T, Prasad VR. Substitutions at Phe61 in the beta3-beta4 hairpin of HIV-1 reverse transcriptase reveal a role for the Fingers subdomain in strand displacement DNA synthesis. Journal of Molecular Biology. 325: 443-59. PMID 12498795 DOI: 10.1016/S0022-2836(02)01225-1  1
2003 Herce DH, Darden T, Sagui C. Calculation of ionic charging free energies in simulation systems with atomic charges, dipoles, and quadrupoles Journal of Chemical Physics. 119: 7621-7632. DOI: 10.1063/1.1609191  1
2003 Kholmurodov KT, Altaisky MV, Puzynin IV, Darden T, Filatov FP. Methods of molecular dynamics for simulation of physical and biological processes Physics of Particles and Nuclei. 34: 244-263.  1
2002 Venkateswarlu D, Krishnaswamy S, Darden TA, Pedersen LG. Three-dimensional solution structure of Tropidechis carinatus venom extract trocarin: a structural homologue of Xa and prothrombin activator. Journal of Molecular Modeling. 8: 302-13. PMID 12483230 DOI: 10.1007/S00894-002-0099-4  1
2002 Inga A, Storici F, Darden TA, Resnick MA. Differential transactivation by the p53 transcription factor is highly dependent on p53 level and promoter target sequence. Molecular and Cellular Biology. 22: 8612-25. PMID 12446780 DOI: 10.1128/Mcb.22.24.8612-8625.2002  1
2002 Pedersen LC, Darden TA, Negishi M. Crystal structure of beta 1,3-glucuronyltransferase I in complex with active donor substrate UDP-GlcUA. The Journal of Biological Chemistry. 277: 21869-73. PMID 11950836 DOI: 10.1074/Jbc.M112343200  1
2002 Perera L, Darden TA, Pedersen LG. Predicted solution structure of zymogen human coagulation FVII. Journal of Computational Chemistry. 23: 35-47. PMID 11913388 DOI: 10.1002/Jcc.1155  1
2002 Venkateswarlu D, Perera L, Darden T, Pedersen LG. Structure and dynamics of zymogen human blood coagulation factor X. Biophysical Journal. 82: 1190-206. PMID 11867437 DOI: 10.1016/S0006-3495(02)75476-3  1
2002 DeRose EF, Li D, Darden T, Harvey S, Perrino FW, Schaaper RM, London RE. Model for the catalytic domain of the proofreading epsilon subunit of Escherichia coli DNA polymerase III based on NMR structural data. Biochemistry. 41: 94-110. PMID 11772007 DOI: 10.1021/Bi0114170  1
2001 Li L, Darden TA, Weinberg CR, Levine AJ, Pedersen LG. Gene assessment and sample classification for gene expression data using a genetic algorithm/k-nearest neighbor method. Combinatorial Chemistry & High Throughput Screening. 4: 727-39. PMID 11894805 DOI: 10.2174/1386207013330733  1
2001 Li L, Weinberg CR, Darden TA, Pedersen LG. Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method. Bioinformatics (Oxford, England). 17: 1131-42. PMID 11751221 DOI: 10.1093/Bioinformatics/17.12.1131  1
2001 Caffrey JJ, Darden T, Wenk MR, Shears SB. Expanding coincident signaling by PTEN through its inositol 1,3,4,5,6-pentakisphosphate 3-phosphatase activity Febs Letters. 499: 6-10. PMID 11418101 DOI: 10.1016/S0014-5793(01)02500-5  1
2001 Perera L, Darden TA, Pedersen LG. Modeling human zymogen factor IX. Thrombosis and Haemostasis. 85: 596-603. PMID 11341491 DOI: 10.1055/S-0037-1615639  1
2001 Inga A, Monti P, Fronza G, Darden T, Resnick MA. p53 mutants exhibiting enhanced transcriptional activation and altered promoter selectivity are revealed using a sensitive, yeast-based functional assay Oncogene. 20: 501-513. PMID 11313981 DOI: 10.1038/Sj.Onc.1204116  1
2001 Stenger JE, Lobachev KS, Gordenin D, Darden TA, Jurka J, Resnick MA. Biased distribution of inverted and direct Alus in the human genome: implications for insertion, exclusion, and genome stability. Genome Research. 11: 12-27. PMID 11156612 DOI: 10.1101/Gr.158801  1
2001 Pedersen LC, Darden TA, Kakuta Y, Negishi M. Crystal Structure-Based Analysis of Human Glucuronyltransferase 1 Trends in Glycoscience and Glycotechnology. 13: 121-129. DOI: 10.4052/Tigg.13.121  1
2001 Sagui C, Darden T. Efficient treatment of fixed and induced dipolar interactions Materials Research Society Symposium - Proceedings. 653: Z7.22.1-Z7.22.6. DOI: 10.1557/Proc-653-Z7.22  1
2001 Sagui C, Darden T. Multigrid methods for classical molecular dynamics simulations of biomolecules Journal of Chemical Physics. 114: 6578-6591. DOI: 10.1063/1.1352646  1
2001 Li L, Pedersen LG, Darden TA, Weinberg CR. Class prediction and discovery based on gene expression data Proceedings of the Atlantic Symposium On Computational Biology and Genome Information Systems and Technolgoy, Cbgist 2001. 245-249.  1
2000 Perera L, Foley C, Darden TA, Stafford D, Mather T, Esmon CT, Pedersen LG. Modeling zymogen protein C. Biophysical Journal. 79: 2925-43. PMID 11106601 DOI: 10.1016/S0006-3495(00)76530-1  1
2000 Gorokhov A, Perera L, Darden TA, Negishi M, Pedersen LC, Pedersen LG. Heparan sulfate biosynthesis: a theoretical study of the initial sulfation step by N-deacetylase/N-sulfotransferase. Biophysical Journal. 79: 2909-17. PMID 11106599 DOI: 10.1016/S0006-3495(00)76528-3  1
2000 Pedersen LC, Tsuchida K, Kitagawa H, Sugahara K, Darden TA, Negishi M. Heparan/chondroitin sulfate biosynthesis. Structure and mechanism of human glucuronyltransferase I. The Journal of Biological Chemistry. 275: 34580-5. PMID 10946001 DOI: 10.1074/Jbc.M007399200  1
2000 Bevan DR, Li L, Pedersen LG, Darden TA. Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: influence of the crystal environment. Biophysical Journal. 78: 668-82. PMID 10653780 DOI: 10.1016/S0006-3495(00)76625-2  1
2000 Toukmaji A, Sagui C, Board J, Darden T. Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions Journal of Chemical Physics. 113: 10913-10927. DOI: 10.1063/1.1324708  1
2000 Donini O, Darden T, Kollman PA. QM-FE calculations of aliphatic hydrogen abstraction in citrate synthase and in solution: Reproduction of the effect of enzyme catalysis and demonstration that an enolate rather than an enol is formed Journal of the American Chemical Society. 122: 12270-12280. DOI: 10.1021/Ja001043I  1
2000 Li L, Pedersen LG, Beard WA, Bebenek K, Wilson SH, Kunkel TA, Darden TA. A Molecular Dynamics Model of HIV-1 Reverse Transcriptase Complexed with DNA: Comparison with Experimental Structures Journal of Molecular Modeling. 6: 575-586. DOI: 10.1007/S0089400060575  1
2000 Kholmurodov K, Smith W, Yasuoka K, Darden T, Ebisuzaki T. A Smooth-Particle Mesh Ewald Method for DL_POLY Molecular Dynamics Simulation Package on the Fujitsu VPP700 Journal of Computational Chemistry. 21: 1187-1191. DOI: 10.1002/1096-987X(200010)21:13<1187::Aid-Jcc7>3.0.Co;2-7  1
1999 Sagui C, Darden TA. Molecular dynamics simulations of biomolecules: long-range electrostatic effects. Annual Review of Biophysics and Biomolecular Structure. 28: 155-79. PMID 10410799 DOI: 10.1146/Annurev.Biophys.28.1.155  1
1999 Powell MD, Beard WA, Bebenek K, Howard KJ, Le Grice SF, Darden TA, Kunkel TA, Wilson SH, Levin JG. Residues in the alphaH and alphaI helices of the HIV-1 reverse transcriptase thumb subdomain required for the specificity of RNase H-catalyzed removal of the polypurine tract primer. The Journal of Biological Chemistry. 274: 19885-93. PMID 10391934 DOI: 10.1074/Jbc.274.28.19885  1
1999 Perera L, Darden TA, Pedersen LG. Probing the structural changes in the light chain of human coagulation factor VIIa due to tissue factor association. Biophysical Journal. 77: 99-113. PMID 10388743 DOI: 10.1016/S0006-3495(99)76875-X  1
1999 Darden T, Perera L, Li L, Lee P. New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations Structure. 7: R55-R60. PMID 10368306 DOI: 10.1016/S0969-2126(99)80033-1  1
1999 Li L, Darden TA, Bartolotti L, Kominos D, Pedersen LG. An atomic model for the pleated beta-sheet structure of Abeta amyloid protofilaments. Biophysical Journal. 76: 2871-8. PMID 10354415 DOI: 10.1016/S0006-3495(99)77442-4  1
1998 Perera L, Darden TA, Pedersen LG. Trans-cis isomerization of proline 22 in bovine prothrombin fragment 1: a surprising result of structural characterization. Biochemistry. 37: 10920-7. PMID 9692984 DOI: 10.1021/Bi980263U  1
1998 Darden T, Pearlman D, Pedersen LG. Ionic charging free energies: Spherical versus periodic boundary conditions Journal of Chemical Physics. 109: 10921-10935. DOI: 10.1063/1.477788  1
1997 Perera L, Li L, Darden T, Monroe DM, Pedersen LG. Prediction of solution structures of the Ca2+-bound gamma-carboxyglutamic acid domains of protein S and homolog growth arrest specific protein 6: use of the particle mesh Ewald method. Biophysical Journal. 73: 1847-56. PMID 9336180 DOI: 10.1016/S0006-3495(97)78215-8  1
1997 Bebenek K, Beard WA, Darden TA, Li L, Prasad R, Luton BA, Gorenstein DG, Wilson SH, Kunkel TA. A minor groove binding track in reverse transcriptase. Nature Structural Biology. 4: 194-7. PMID 9164459 DOI: 10.1038/Nsb0397-194  1
1997 Uno T, Mitchell E, Aida K, Lambert MH, Darden TA, Pedersen LG, Negishi M. Reciprocal size-effect relationship of the key residues in determining regio- and stereospecificities of DHEA hydroxylase activity in P450 2a5. Biochemistry. 36: 3193-8. PMID 9115996 DOI: 10.1021/Bi962654J  1
1997 Li L, Darden TA, Freedman SJ, Furie BC, Furie B, Baleja JD, Smith H, Hiskey RG, Pedersen LG. Refinement of the NMR solution structure of the gamma-carboxyglutamic acid domain of coagulation factor IX using molecular dynamics simulation with initial Ca2+ positions determined by a genetic algorithm. Biochemistry. 36: 2132-8. PMID 9047312 DOI: 10.1021/Bi962250R  1
1997 Crowley MF, Darden TA, Cheatham TE, Deerfield DW. Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program Journal of Supercomputing. 11: 255-278. DOI: 10.1023/A:1007907925007  1
1997 Procacci P, Darden TA, Paci E, Marchi M. ORAC: A molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions Journal of Computational Chemistry. 18: 1848-1862.  1
1997 Darden TA, Toukmaji A, Pedersen LG. Long-range electrostatic effects in biomolecular simulations Journal De Chimie Physique Et De Physico-Chimie Biologique. 94: 1346-1364.  1
1996 Negishi M, Uno T, Honkakoski P, Sueyoshi T, Darden TA, Pedersen LP. The roles of individual amino acids in altering substrate specificity of the P450 2a4/2a5 enzymes. Biochimie. 78: 685-94. PMID 9010596 DOI: 10.1016/S0300-9084(97)82525-4  1
1996 Li L, Darden T, Hiskey R, Pedersen LG. Computational studies of human prothrombin fragment 1, the Gla domain of factor IX and several biological interesting mutants. Haemostasis. 26: 54-9. PMID 8904174 DOI: 10.1159/000217241  1
1996 Darden TA, Bartolotti L, Pedersen LG. Selected new developments in computational chemistry. Environmental Health Perspectives. 104: 69-74. PMID 8722111 DOI: 10.1289/Ehp.96104S169  1
1996 Negishi M, Iwasaki M, Juvonen RO, Sueyoshi T, Darden TA, Pedersen LG. Structural flexibility and functional versatility of cytochrome P450 and rapid evolution. Mutation Research. 350: 43-50. PMID 8657195 DOI: 10.1016/0027-5107(95)00089-5  1
1996 Bienstock RJ, Darden T, Wiseman R, Pedersen L, Barrett JC. Molecular modeling of the amino-terminal zinc ring domain of BRCA1 Cancer Research. 56: 2539-2545. PMID 8653694  1
1996 Negishi M, Uno T, Darden TA, Sueyoshi T, Pedersen LG. Structural flexibility and functional versatility of mammalian P450 enzymes. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 10: 683-9. PMID 8635685 DOI: 10.1096/Fasebj.10.7.8635685  1
1996 Lee H, Darden TA, Pedersen LG. An ab initio quantum mechanical model for the catalytic mechanism of HIV-1 protease Journal of the American Chemical Society. 118: 3946-3950. DOI: 10.1021/Ja9513188  1
1996 Lambert CG, Darden TA, Board JA. A multipole-based algorithm for efficient calculation of forces and potentials in macroscopic periodic assemblies of particles Journal of Computational Physics. 126: 274-285. DOI: 10.1006/Jcph.1996.0137  1
1996 Procacci P, Darden T, Marchi M. A very fast molecular dynamics method to simulate biomolecular systems with realistic electrostatic interactions Journal of Physical Chemistry. 100: 10464-10468.  1
1996 Li L, Darden T, Hiskey R, Pedersen L. Homology modeling and molecular dynamics simulations of the Gla domains of human coagulation factor IX and its G[12]A mutant Journal of Physical Chemistry. 100: 2475-2479.  1
1995 Iwasaki M, Davis DG, Darden TA, Pedersen LG, Negishi M. Multiple steroid-binding orientations: alteration of regiospecificity of dehydroepiandrosterone 2- and 7-hydroxylase activities of cytochrome P-450 2a-5 by mutation of residue 209. The Biochemical Journal. 306: 29-33. PMID 7864823 DOI: 10.1042/Bj3060029  1
1995 Iwasaki M, Darden TA, Pedersen LG, Negishi M. Altering the regiospecificity of androstenedione hydroxylase activity in P450s 2a-4/5 by a mutation of the residue at position 481. Biochemistry. 34: 5054-9. PMID 7711025 DOI: 10.1021/Bi00015A016  1
1995 Bebenek K, Beard WA, Casas-Finet JR, Kim HR, Darden TA, Wilson SH, Kunkel TA. Reduced frameshift fidelity and processivity of HIV-1 reverse transcriptase mutants containing alanine substitutions in helix H of the thumb subdomain. The Journal of Biological Chemistry. 270: 19516-23. PMID 7543900 DOI: 10.1074/Jbc.270.33.19516  1
1995 Lee H, Darden TA, Pedersen LG. Molecular dynamics simulation studies of a high resolution Z-DNA crystal The Journal of Chemical Physics. 102: 3830-3834. DOI: 10.1063/1.468564  1
1995 Cheatham TE, Miller JL, Fox T, Darden TA, Kollman PA. Molecular dynamics simulations on solvated biomolecular systems: The particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins Journal of the American Chemical Society. 117: 4193-4194. DOI: 10.1021/Ja00119A045  1
1994 Frech M, Darden TA, Pedersen LG, Foley CK, Charifson PS, Anderson MW, Wittinghofer A. Role of glutamine-61 in the hydrolysis of GTP by p21H-ras: an experimental and theoretical study. Biochemistry. 33: 3237-44. PMID 8136358 DOI: 10.1021/Bi00177A014  1
1994 Iwasaki M, Darden TA, Parker CE, Tomer KB, Pedersen LG, Negishi M. Inherent versatility of P-450 oxygenase. Conferring dehydroepiandrosterone hydroxylase activity to P-450 2a-4 by a single amino acid mutation at position 117. The Journal of Biological Chemistry. 269: 9079-83. PMID 8132645  1
1994 York DM, Wlodawer A, Pedersen LG, Darden TA. Atomic-level accuracy in simulations of large protein crystals. Proceedings of the National Academy of Sciences of the United States of America. 91: 8715-8. PMID 7521533 DOI: 10.1073/Pnas.91.18.8715  1
1994 York DM, Bartolotti LJ, Darden TA, Pedersen LG, Anderson MW. Simulations of the solution structure of HIV‐1 protease in the presence and absence of bound zinc Journal of Computational Chemistry. 15: 61-71. DOI: 10.1002/Jcc.540150108  0.6
1993 York DM, Darden TA, Pedersen LG, Anderson MW. Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution. Biochemistry. 32: 1443-53. PMID 8431424 DOI: 10.1021/Bi00057A007  1
1993 Iwasaki M, Darden TA, Pedersen LG, Davis DG, Juvonen RO, Sueyoshi T, Negishi M. Engineering mouse P450coh to a novel corticosterone 15 alpha-hydroxylase and modeling steroid-binding orientation in the substrate pocket. The Journal of Biological Chemistry. 268: 759-62. PMID 8419350  1
1993 York DM, Darden TA, Pedersen LG, Anderson MW. Molecular modeling studies suggest that zinc ions inhibit HIV-1 protease by binding at catalytic aspartates. Environmental Health Perspectives. 101: 246-50. PMID 8404763 DOI: 10.1289/Ehp.93101246  1
1993 Darden TA, Pedersen LG. Molecular modeling: an experimental tool. Environmental Health Perspectives. 101: 410-2. PMID 8119250  1
1993 York DM, Darden TA, Pedersen LG. The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods The Journal of Chemical Physics. 99: 8345-8348. DOI: 10.1063/1.465608  1
1992 Foley CK, Pedersen LG, Charifson PS, Darden TA, Wittinghofer A, Pai EF, Anderson MW. Simulation of the solution structure of the H-ras p21-GTP complex. Biochemistry. 31: 4951-9. PMID 1599919 DOI: 10.1021/Bi00136A005  1
1991 Foley CK, Pedersen LG, Darden TA, Glickman BW, Anderson MW. Theoretical and experimental measures of DNA helix stability and their relation to sequence specific repair of O6-ethylguanine lesions. Mutation Research. 255: 89-93. PMID 2067552 DOI: 10.1016/0921-8777(91)90021-G  1
1989 Darden T, Kaplan NL, Hudson RR. A numerical method for calculating moments of coalescent times in finite populations with selection Journal of Mathematical Biology. 27: 355-368. PMID 2746143 DOI: 10.1007/Bf00275818  1
1988 Pedersen LG, Darden TA, Deerfield DW, Anderson MW, Hoel DG. A theoretical study of the effect of methylation or ethylation at O6-guanine in the structure and energy of DNA double strands. Carcinogenesis. 9: 1553-62. PMID 3409460 DOI: 10.1093/Carcin/9.9.1553  1
1986 Lipkowitz K, Landwer JM, Darden T. Theoretical studies of a chiral stationary phase used in column chromatography Analytical Chemistry. 58: 1611-1617. PMID 3752500 DOI: 10.1021/Ac00121A006  1
1986 Pedersen LG, Darden TA, Oatley SJ, McKinney JD. A theoretical study of the binding of polychlorinated biphenyls (PCBs), dibenzodioxins, and dibenzofuran to human plasma prealbumin. Journal of Medicinal Chemistry. 29: 2451-7. PMID 3097319  1
1986 Lipkowitz KB, Malik DJ, Darden T. Conformational analysis of the covalent pirkle chiral stationary phases Tetrahedron Letters. 27: 1759-1762. DOI: 10.1016/S0040-4039(00)84367-1  1
1985 Day MV, Darden TA. Some regularity results on the Ventcel-Freidlin quasi-potential function Applied Mathematics & Optimization. 13: 259-282. DOI: 10.1007/Bf01442211  1
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