| 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 |
0.777 |
|
| 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 |
0.767 |
|
| 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 |
0.686 |
|
| 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 |
0.704 |
|
| 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 |
0.44 |
|
| 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 |
0.49 |
|
| 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 |
0.778 |
|
| 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 |
0.375 |
|
| 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 |
0.702 |
|
| 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 |
0.515 |
|
| 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 |
0.753 |
|
| 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 |
0.673 |
|
| 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 |
0.775 |
|
| 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 |
0.312 |
|
| 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 |
0.397 |
|
| 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 |
0.778 |
|
| 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 |
0.726 |
|
| 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 |
0.715 |
|
| 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 |
0.64 |
|
| 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 |
0.752 |
|
| 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 |
0.392 |
|
| 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 |
0.811 |
|
| 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 |
0.722 |
|
| 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 |
0.788 |
|
| 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 |
0.788 |
|
| 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 |
0.65 |
|
| 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 |
0.564 |
|
| 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 |
0.789 |
|
| 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. |
0.662 |
|
| 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 |
0.719 |
|
| 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 |
0.693 |
|
| 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. |
0.632 |
|
| 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 |
0.788 |
|
| 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 |
0.341 |
|
| 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 |
0.686 |
|
| 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 |
0.748 |
|
| 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 |
0.673 |
|
| 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 |
0.666 |
|
| 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 |
0.323 |
|
| 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 |
0.499 |
|
| 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 |
0.637 |
|
| 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 |
0.663 |
|
| 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 |
0.572 |
|
| 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 |
0.673 |
|
| 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 |
0.635 |
|
| 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 |
0.301 |
|
| 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 |
0.469 |
|
| 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 |
0.475 |
|
| 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 |
0.657 |
|
| 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 |
0.63 |
|
| 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 |
0.66 |
|
| 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. |
0.383 |
|
| 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 |
0.667 |
|
| 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 |
0.66 |
|
| 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 |
0.571 |
|
| 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 |
0.64 |
|
| 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 |
0.579 |
|
| 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 |
0.334 |
|
| 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 |
0.657 |
|
| 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 |
0.643 |
|
| 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 |
0.423 |
|
| 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 |
0.526 |
|
| 1998 |
Beard WA, Bebenek K, Darden TA, Li L, Prasad R, Kunkel TA, Wilson SH. Vertical-scanning mutagenesis of a critical tryptophan in the minor groove binding track of HIV-1 reverse transcriptase. Molecular nature of polymerase-nucleic acid interactions. The Journal of Biological Chemistry. 273: 30435-42. PMID 9804810 DOI: 10.1074/Jbc.273.46.30435 |
0.365 |
|
| 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 |
0.678 |
|
| 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 |
0.527 |
|
| 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 |
0.657 |
|
| 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 |
0.499 |
|
| 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 |
0.569 |
|
| 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. |
0.481 |
|
| 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 |
0.533 |
|
| 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 |
0.547 |
|
| 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 |
0.512 |
|
| 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 |
0.454 |
|
| 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 |
0.531 |
|
| 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 |
0.356 |
|
| 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 |
0.442 |
|
| 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 |
0.488 |
|
| 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 |
0.301 |
|
| 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 |
0.612 |
|
| 1995 |
Lee H, Darden T, Pedersen L. Accurate crystal molecular dynamics simulations using particle-mesh-Ewald: RNA dinucleotides — ApU and GpC Chemical Physics Letters. 243: 229-235. DOI: 10.1016/0009-2614(95)00845-U |
0.57 |
|
| 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 |
0.484 |
|
| 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 |
0.423 |
|
| 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 |
0.546 |
|
| 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 |
0.525 |
|
| 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 |
0.524 |
|
| 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 |
0.451 |
|
| 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 |
0.49 |
|
| 1993 |
Darden TA, Pedersen LG. Molecular modeling: an experimental tool. Environmental Health Perspectives. 101: 410-2. PMID 8119250 |
0.478 |
|
| 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 |
0.546 |
|
| 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 |
0.544 |
|
| 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 |
0.511 |
|
| 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 |
0.505 |
|
| 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 |
0.359 |
|
| 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 |
0.478 |
|
| 1983 |
Bursey MM, Harvan DJ, Parker CE, Darden TA, Hass JR. Charge reversal of three alkylamide ions: Free nitrenium ions Organic Mass Spectrometry. 18: 530-533. DOI: 10.1002/Oms.1210181207 |
0.328 |
|
| Show low-probability matches. |
