Thomas A. Darden
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Thomas A. Darden's AcademicInfluence.com Rankings
Thomas A. Dardenchemistry Degrees
Chemistry
#2782
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#3744
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Computational Chemistry
#24
World Rank
#24
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Physical Chemistry
#341
World Rank
#390
Historical Rank
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Chemistry Physics
Thomas A. Darden's Degrees
- Bachelors Chemistry University of North Carolina at Chapel Hill
Why Is Thomas A. Darden Influential?
(Suggest an Edit or Addition)Thomas A. Darden's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems (1993) (22111)
- A smooth particle mesh Ewald method (1995) (16130)
- The Amber biomolecular simulation programs (2005) (7188)
- Making optimal use of empirical energy functions: Force‐field parameterization in crystal space (2004) (787)
- Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins (1995) (684)
- Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method (2001) (677)
- The effect of long‐range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods (1993) (548)
- New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. (1999) (545)
- Molecular dynamics simulations of biomolecules: long-range electrostatic effects. (1999) (516)
- Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions (2000) (363)
- Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. (2007) (302)
- Gene assessment and sample classification for gene expression data using a genetic algorithm/k-nearest neighbor method. (2001) (212)
- Differential Transactivation by the p53 Transcription Factor Is Highly Dependent on p53 Level and Promoter Target Sequence (2002) (190)
- Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations. (2004) (188)
- Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. (2006) (173)
- Towards a force field based on density fitting. (2006) (162)
- Heparan/Chondroitin Sulfate Biosynthesis (2000) (160)
- Atomic-level accuracy in simulations of large protein crystals. (1994) (151)
- NMDA Receptor Activation by HIV-Tat Protein Is Clade Dependent (2008) (137)
- Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics (1995) (137)
- ORAC: A Molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions (1997) (130)
- Biased distribution of inverted and direct Alus in the human genome: implications for insertion, exclusion, and genome stability. (2001) (127)
- Role of glutamine-61 in the hydrolysis of GTP by p21H-ras: an experimental and theoretical study. (1994) (126)
- Reduced Frameshift Fidelity and Processivity of HIV-1 Reverse Transcriptase Mutants Containing Alanine Substitutions in Helix H of the Thumb Subdomain (*) (1995) (117)
- Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility. (2009) (115)
- Ionic charging free energies: Spherical versus periodic boundary conditions (1998) (111)
- A minor groove binding track in reverse transcriptase (1997) (107)
- An Atomic Model for the Pleated β-Sheet Structure of Aβ Amyloid Protofilaments (1999) (104)
- Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods. (2006) (97)
- Gaussian induced dipole polarization model (2007) (93)
- Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program (1997) (92)
- A Multipole-Based Algorithm for Efficient Calculation of Forces and Potentials in Macroscopic Period (1996) (84)
- Molecular modeling: an experimental tool. (1993) (78)
- Gaussian Multipole Model (GMM). (2010) (75)
- Structure and dynamics of zymogen human blood coagulation factor X. (2002) (74)
- Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution. (1993) (73)
- A Very Fast Molecular Dynamics Method To Simulate Biomolecular Systems with Realistic Electrostatic Interactions (1996) (72)
- Structural flexibility and functional versatility of mammalian P450 enzymes (1996) (68)
- Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues. (2009) (67)
- Crystal Structure of β1,3-Glucuronyltransferase I in Complex with Active Donor Substrate UDP-GlcUA* (2002) (63)
- Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hybrid Quantum Mechanical/Molecular Mechanical Embedding. (2008) (53)
- p53 mutants exhibiting enhanced transcriptional activation and altered promoter selectivity are revealed using a sensitive, yeast-based functional assay (2001) (52)
- Intermolecular electrostatic energies using density fitting. (2005) (52)
- Residues in the αH and αI Helices of the HIV-1 Reverse Transcriptase Thumb Subdomain Required for the Specificity of RNase H-catalyzed Removal of the Polypurine Tract Primer* (1999) (50)
- Glucosaminylglycan biosynthesis: what we can learn from the X-ray crystal structures of glycosyltransferases GlcAT1 and EXTL2. (2003) (50)
- Engineering mouse P450coh to a novel corticosterone 15 alpha-hydroxylase and modeling steroid-binding orientation in the substrate pocket. (1993) (48)
- Long-range electrostatic effects in biomolecular simulations (1997) (47)
- Simulation of the solution structure of the H-ras p21-GTP complex. (1992) (46)
- 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. (1997) (46)
- Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions. (2006) (46)
- PCB and Related Compound Binding to the Ah Receptor(s) Theoretical Model Based on Molecular Parameters and Molecular Mechanics (1985) (45)
- Identification of a specific motif of the DSS1 protein required for proteasome interaction and p53 protein degradation. (2008) (43)
- Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: influence of the crystal environment. (2000) (42)
- Accurate crystal molecular dynamics simulations using particle-mesh-Ewald: RNA dinucleotides — ApU and GpC (1995) (42)
- MOLECULAR DYNAMICS SIMULATION STUDIES OF A HIGH RESOLUTION Z-DNA CRYSTAL (1995) (38)
- 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. (2003) (38)
- Molecular modeling of the amino-terminal zinc ring domain of BRCA1. (1996) (38)
- Vertical-scanning Mutagenesis of a Critical Tryptophan in the Minor Groove Binding Track of HIV-1 Reverse Transcriptase (1998) (37)
- QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential. (2018) (34)
- Computational Analysis of Leukemia Microarray Expression Data Using the GA/KNN Method (2002) (34)
- Modeling zymogen protein C. (2000) (34)
- Liquid–vapour equilibrium of n -alkanes using interface simulations (2006) (34)
- Structural flexibility and functional versatility of cytochrome P450 and rapid evolution. (1996) (33)
- A smooth‐particle mesh Ewald method for DL_POLY molecular dynamics simulation package on the Fujitsu VPP700 (2000) (31)
- Model for the catalytic domain of the proofreading epsilon subunit of Escherichia coli DNA polymerase III based on NMR structural data. (2002) (31)
- Elucidation of the epsilon-theta subunit interface of Escherichia coli DNA polymerase III by NMR spectroscopy. (2003) (31)
- An ab Initio Quantum Mechanical Model for the Catalytic Mechanism of HIV-1 Protease (1996) (29)
- Numerical fitting of molecular properties to Hermite Gaussians. (2007) (28)
- Design Of Next Generation Force Fields From AB Initio Computations: Beyond Point Charges Electrostatics (2009) (25)
- A smooth-particle mesh Ewald method for DL_POLY molecular dynamics simulation package on the Fujitsu VPP700 (2000) (25)
- Structural Determinants of Slippage-mediated Mutations by Human Immunodeficiency Virus Type 1 Reverse Transcriptase* (2006) (24)
- An all‐atom solution‐equilibrated model for human extrinsic blood coagulation complex (sTF–VIIa–Xa): a protein–protein docking and molecular dynamics refinement study (2003) (23)
- 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 (2003) (23)
- A finite field method for calculating molecular polarizability tensors for arbitrary multipole rank (2011) (22)
- 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. (2014) (21)
- Modeling Human Zymogen Factor IX (2001) (20)
- Inherent versatility of P-450 oxygenase. Conferring dehydroepiandrosterone hydroxylase activity to P-450 2a-4 by a single amino acid mutation at position 117. (1994) (19)
- Molecular dynamics simulation of bovine prothrombin fragment 1 in the presence of calcium ions. (1992) (19)
- Trans-cis isomerization of proline 22 in bovine prothrombin fragment 1: a surprising result of structural characterization. (1998) (17)
- The interaction of Na(I), Ca(II), and Mg(II) metal ions with duplex DNA: A theoretical modeling study (1992) (17)
- An atomic model for the pleated beta-sheet structure of Abeta amyloid protofilaments. (1999) (17)
- Altering the regiospecificity of androstenedione hydroxylase activity in P450s 2a-4/5 by a mutation of the residue at position 481. (1995) (17)
- Atomic forces for geometry‐dependent point multipole and Gaussian multipole models (2010) (16)
- Predicted solution structure of zymogen human coagulation FVII (2002) (16)
- 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. (1997) (16)
- A theoretical study of the effect of methylation or ethylation at O6-guanine in the structure and energy of DNA double strands. (1988) (16)
- The roles of individual amino acids in altering substrate specificity of the P450 2a4/2a5 enzymes. (1996) (16)
- A theoretical study of the binding of polychlorinated biphenyls (PCBs), dibenzodioxins, and dibenzofuran to human plasma prealbumin. (1986) (15)
- Heparan sulfate biosynthesis: a theoretical study of the initial sulfation step by N-deacetylase/N-sulfotransferase. (2000) (15)
- 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. (1995) (14)
- Homology modeling and molecular dynamics simulation of human prothrombin fragment 1 (1995) (14)
- Explicit water near the catalytic I helix Thr in the predicted solution structure of CYP2A4. (2003) (13)
- Reciprocal size-effect relationship of the key residues in determining regio- and stereospecificities of DHEA hydroxylase activity in P450 2a5. (1997) (13)
- Mapping the dimer interface in the C-terminal domains of the yeast MLH1-PMS1 heterodimer. (2006) (11)
- Molecular modeling studies suggest that zinc ions inhibit HIV-1 protease by binding at catalytic aspartates. (1993) (11)
- Obligatory role in GTP hydrolysis for the amide carbonyl oxygen of the Mg2+-coordinating Thr of regulatory GTPases (2010) (11)
- Probing the structural changes in the light chain of human coagulation factor VIIa due to tissue factor association. (1999) (10)
- Solution conformations of the gamma-carboxyglutamic acid domain of bovine prothrombin fragment 1, residues 1-65. (1991) (9)
- A Molecular Dynamics Model of HIV-1 Reverse Transcriptase Complexed with DNA: Comparison with Experimental Structures (2000) (9)
- 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 (2010) (8)
- Structural characterization of the conformational change in calbindin-D28k upon calcium binding using differential surface modification analyzed by mass spectrometry. (2009) (8)
- A theoretical study of the minimum energy structures of diethylstilbestrol and its analogues by molecular mechanics (MM2p), MNDO, and ab initio calculations (1986) (7)
- Progress Towards Accurate Molecular Modeling of Metal Complexes Using Polarizable Force Fields (2009) (7)
- Particle-Mesh Based Methods for Fast Ewald Summation in Molecular Dynamics Simulations (1997) (7)
- Extensions of the Ewald method for Coulomb interactions in crystals (2010) (7)
- Homology Modeling and Molecular Dynamics Simulations of the Gla Domains of Human Coagulation Factor IX and Its G[12]A Mutant (1996) (6)
- CRYSTAL STRUCTURE OF BETA1,3-GLUCURONYLTRANSFERASE I IN COMPLEX WITH THE ACTIVE UDP-GLCUA DONOR (2002) (6)
- Effect of calcium (II) and magnesium (II) ions on the 18-23 gamma-carboxyglutamic acid containing cyclic peptide loop of bovine prothrombin. An AMBER molecular mechanics study. (2009) (6)
- Three-dimensional solution structure of Tropidechis carinatus venom extract trocarin: a structural homologue of Xa and prothrombin activator (2002) (5)
- A method for fitting a smooth ribbon to curved DNA (1989) (5)
- Selected new developments in computational chemistry. (1996) (5)
- Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution. [Erratum to document cited in CA118(21):208404x] (1993) (4)
- Relative spectral response as a function of sequential ligand binding. (1986) (4)
- Simulations of the solution structure of HIV‐1 protease in the presence and absence of bound zinc (1994) (3)
- Molecular Dynamics: Techniques and Applications to Proteins (2002) (3)
- Computational studies of human prothrombin fragment 1, the Gla domain of factor IX and several biological interesting mutants. (1996) (3)
- Ionic Charging Free Energies Using Ewald Summation (1999) (2)
- Theoretical and experimental measures of DNA helix stability and their relation to sequence specific repair of O6-ethylguanine lesions. (1991) (2)
- Molecular dynamics simulations using particle-mesh ewald methods (1999) (1)
- Crystal Structure-Based Analysis of Human Glucuronyltransferase 1 (2001) (1)
- Subject Index, Vol. 26 (suppl 1), 1996 (1996) (1)
- The Effect of Hydrostatic Pressure on Protein Crystals Investigated by Molecular Simulation (1995) (1)
- DNA fragment mass distributions following molecular recombination (1985) (1)
- Molecular Dynamics Studies of H-ras p21-GTP (1993) (1)
- Incorporating Charge Polarization in Classical Force Fields (2006) (0)
- O XI A.1 Structure-function studies of DNA polymerase error specificity (1997) (0)
- Molecular Dynamics Studies of Hras p 21-GTP c (0)
- Development of Yeast as an In Vivo Test Tube to Characterize a Broad Spectrum of p53 Mutations Associated with Breast Cancer (2002) (0)
- Implementing Advanced Force Fields for Simulation of Physical and Biological Processes (0)
- Title Page / Table of Contents, Vol. 26, Supplement 1, 1996 (1996) (0)
- Early Unfolding Response of a Stable Protein Domain to Environmental Changes (2004) (0)
- Molecular mechanics studies of sequence-specific repair of DNA alkylated by EMS in the lacI gene of escherichia coli (2009) (0)
- The TPS algorithm & the Evolutionary Path of Protein Structures (0)
- A Molecular Mechanics Study (AMBER) of the Displacement of Thyroxine from the Binding Pocket of Prealbumin by PCBs and PCB Analogues (1986) (0)
- A Theoretical Study of the Minimum Energy Structures of Diethylstilbestrol (I) and Its Analogues (II), (III) by Molecular Mechanics (MM2p), MNDO, and ab initio Calculations. (1986) (0)
- p53 Transactivation from response element sequences within cells may not reflect in vitro DNA binding ability (2006) (0)
- CRYSTAL STRUCTURE OF 1,3-GLUCURONYLTRANSFERASE I (GLCAT-I) COMPLEXED WITH GAL-GAL-XYL, UDP, AND MN2+ (2001) (0)
- Atomic Mutipoles in Macromolecular Simulations (2003) (0)
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