Lee G. Pedersen - Publications

Affiliations: 
University of North Carolina, Chapel Hill, Chapel Hill, NC 
Area:
Theoretical Chemistry and Biology
Website:
http://www.chem.unc.edu/people/faculty/pedersen/index.html

221 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
2020 Perera L, Beard WA, Pedersen LG, Shock DD, Wilson SH. Preferential DNA Polymerase β Reverse Reaction with Imidodiphosphate. Acs Omega. 5: 15317-15324. PMID 32637805 DOI: 10.1021/acsomega.0c01345  0.96
2019 Shizu R, Yokobori K, Perera L, Pedersen L, Negishi M. Ligand induced dissociation of the AR homodimer precedes AR monomer translocation to the nucleus. Scientific Reports. 9: 16734. PMID 31723170 DOI: 10.1038/S41598-019-53139-9  0.96
2019 Cooley B, Broze G, Mann DM, Lin FC, Pedersen LG, Stafford DW. Dysfunctional Endogenous FIX Impairs Prophylaxis in a Mouse Hemophilia B Model. Blood. PMID 30992271 DOI: 10.1182/Blood.2018884015  1
2018 Wu S, Chen X, Jin DY, Stafford DW, Pedersen LG, Tie JK. Warfarin and vitamin K epoxide reductase: a molecular accounting for observed inhibition. Blood. PMID 29743176 DOI: 10.1182/Blood-2018-01-830901  1
2017 Perera L, Freudenthal BD, Beard WA, Pedersen LG, Wilson SH. Revealing the role of the product metal in DNA polymerase β catalysis. Nucleic Acids Research. PMID 28108654 DOI: 10.1093/Nar/Gkw1363  0.96
2016 Perera L, Beard WA, Pedersen LG, Wilson SH. Hiding in Plain Sight: The Bimetallic Magnesium Covalent Bond in Enzyme Active Sites. Inorganic Chemistry. PMID 27976880 DOI: 10.1021/Acs.Inorgchem.6B02189  0.96
2015 Perera L, Freudenthal BD, Beard WA, Shock DD, Pedersen LG, Wilson SH. Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse. Proceedings of the National Academy of Sciences of the United States of America. 112: E5228-36. PMID 26351676 DOI: 10.1073/Pnas.1511207112  0.76
2015 Wu S, Shim JY, Lee CJ, Pedersen LG. Do the crystallographic forms of prethrombin-2 revert to a single form in solution? Biophysical Chemistry. 203: 28-32. PMID 26025788 DOI: 10.1016/J.Bpc.2015.05.005  1
2015 Shim JY, Lee CJ, Wu S, Pedersen LG. A model for the unique role of factor Va A2 domain extension in the human ternary thrombin-generating complex. Biophysical Chemistry. 199: 46-50. PMID 25736537 DOI: 10.1016/J.Bpc.2015.02.003  1
2014 Perera L, Beard WA, Pedersen LG, Wilson SH. Applications of quantum mechanical/molecular mechanical methods to the chemical insertion step of DNA and RNA polymerization. Advances in Protein Chemistry and Structural Biology. 97: 83-113. PMID 25458356 DOI: 10.1016/Bs.Apcsb.2014.10.001  1
2014 Wu S, Jun Lee C, Pedersen LG. Analysis on long-range residue-residue communication using molecular dynamics. Proteins. 82: 2896-901. PMID 24935629 DOI: 10.1002/Prot.24629  1
2014 Wu S, Tie JK, Stafford DW, Pedersen LG. Membrane topology for human vitamin K epoxide reductase. Journal of Thrombosis and Haemostasis : Jth. 12: 112-4. PMID 24406068 DOI: 10.1111/Jth.12450  1
2014 Wu S, Beard WA, Pedersen LG, Wilson SH. Structural comparison of DNA polymerase architecture suggests a nucleotide gateway to the polymerase active site. Chemical Reviews. 114: 2759-74. PMID 24359247 DOI: 10.1021/Cr3005179  1
2013 Mutoh S, Sobhany M, Moore R, Perera L, Pedersen L, Sueyoshi T, Negishi M. Phenobarbital indirectly activates the constitutive active androstane receptor (CAR) by inhibition of epidermal growth factor receptor signaling. Science Signaling. 6: ra31. PMID 23652203 DOI: 10.1126/Scisignal.2003705  1
2013 Batra VK, Perera L, Lin P, Shock DD, Beard WA, Pedersen LC, Pedersen LG, Wilson SH. Amino acid substitution in the active site of DNA polymerase β explains the energy barrier of the nucleotidyl transfer reaction. Journal of the American Chemical Society. 135: 8078-88. PMID 23647366 DOI: 10.1021/Ja403842J  1
2012 Wu S, Liu S, Sim S, Pedersen LG. Weakly Antiferromagentic Coupling Via Superexchange Interaction Between Mn(II)-Mn(II) Atoms: A QM/MM Study of the Active Site of Human Cytosolic X-Propyl Aminopeptidase P. The Journal of Physical Chemistry Letters. 3: 2293-2297. PMID 23145216 DOI: 10.1021/Jz300768G  1
2012 Lee CJ, Wu S, Bartolotti LJ, Pedersen LG. Molecular dynamic simulations of the binary complex of human tissue factor (TF(1-242) ) and factor VIIa (TF(1-242) /FVIIa) on a 4:1 POPC/POPS lipid bilayer. Journal of Thrombosis and Haemostasis : Jth. 10: 2402-5. PMID 22967237 DOI: 10.1111/J.1538-7836.2012.04920.X  1
2012 Elking DM, Perera L, Pedersen LG. HPAM: Hirshfeld Partitioned Atomic Multipoles. Computer Physics Communications. 183: 390-397. PMID 22140274 DOI: 10.1016/J.Cpc.2011.10.003  1
2012 Lee CJ, Wu S, Pedersen LG. A revisit to the one-form kinetic model of prothrombinase: A comment on the rebuttal Biophysical Chemistry. 160: 77-78. DOI: 10.1016/J.Bpc.2011.09.005  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
2011 Lee CJ, Wu S, Pedersen LG. A proposed ternary complex model of prothrombinase with prothrombin: protein-protein docking and molecular dynamics simulations. Journal of Thrombosis and Haemostasis : Jth. 9: 2123-6. PMID 21827606 DOI: 10.1111/J.1538-7836.2011.04463.X  1
2011 Cavanaugh NA, Beard WA, Batra VK, Perera L, Pedersen LG, Wilson SH. Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. The Journal of Biological Chemistry. 286: 31650-60. PMID 21733843 DOI: 10.1074/Jbc.M111.253401  1
2011 Pedersen LG. Lee Pedersen's work in theoretical and computational chemistry and biochemistry. World Journal of Biological Chemistry. 2: 35-8. PMID 21537488 DOI: 10.4331/Wjbc.V2.I2.35  0.01
2011 Wu S, Liu S, Davis CH, Stafford DW, Kulman JD, Pedersen LG. A hetero-dimer model for concerted action of vitamin K carboxylase and vitamin K reductase in vitamin K cycle. Journal of Theoretical Biology. 279: 143-9. PMID 21453708 DOI: 10.1016/J.Jtbi.2011.03.030  1
2011 Schorzman AN, Perera L, Cutalo-Patterson JM, Pedersen LC, Pedersen LG, Kunkel TA, Tomer KB. Modeling of the DNA-binding site of yeast Pms1 by mass spectrometry. Dna Repair. 10: 454-65. PMID 21354867 DOI: 10.1016/J.Dnarep.2011.01.010  1
2010 Wu S, Liu S, Davis CH, Stafford DW, Pedersen LG. Quantum Chemical Study of the Mechanism of Action of Vitamin K Carboxylase in Solvent. International Journal of Quantum Chemistry. 110: 2744-2751. PMID 21892230 DOI: 10.1002/Qua.22740  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 Lee CJ, Wu S, Eun C, Pedersen LG. A revisit to the one form kinetic model of prothrombinase. Biophysical Chemistry. 149: 28-33. PMID 20435402 DOI: 10.1016/J.Bpc.2010.03.011  1
2010 de Courcy B, Pedersen LG, Parisel O, Gresh N, Silvi B, Pilmé J, Piquemal JP. Understanding selectivity of hard and soft metal cations within biological systems using the subvalence concept. I. Application to blood coagulation: direct cation-protein electronic effects vs. indirect interactions through water networks. Journal of Chemical Theory and Computation. 6: 1048-1063. PMID 20419068 DOI: 10.1021/Ct100089S  1
2010 Liu S, Hu H, Pedersen LG. Steric, quantum, and electrostatic effects on S(N)2 reaction barriers in gas phase. The Journal of Physical Chemistry. A. 114: 5913-8. PMID 20377265 DOI: 10.1021/Jp101329F  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
2010 Lee CJ, Chandrasekaran V, Wu S, Duke RE, Pedersen LG. Recent estimates of the structure of the factor VIIa (FVIIa)/tissue factor (TF) and factor Xa (FXa) ternary complex. Thrombosis Research. 125: S7-S10. PMID 20156644 DOI: 10.1016/J.Thromres.2010.01.022  1
2009 Liu S, Schauer CK, Pedersen LG. Molecular acidity: A quantitative conceptual density functional theory description. The Journal of Chemical Physics. 131: 164107. PMID 19894927 DOI: 10.1063/1.3251124  1
2009 Mutoh S, Osabe M, Inoue K, Moore R, Pedersen L, Perera L, Rebolloso Y, Sueyoshi T, Negishi M. Dephosphorylation of threonine 38 is required for nuclear translocation and activation of human xenobiotic receptor CAR (NR1I3). The Journal of Biological Chemistry. 284: 34785-92. PMID 19858220 DOI: 10.1074/Jbc.M109.048108  1
2009 Wu S, Lee CJ, Pedersen LG. Conformational change path between closed and open forms of C2 domain of coagulation factor V on a two-dimensional free-energy surface. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 79: 041909. PMID 19518258 DOI: 10.1103/Physreve.79.041909  1
2009 Liu S, Pedersen LG. Estimation of molecular acidity via electrostatic potential at the nucleus and valence natural atomic orbitals. The Journal of Physical Chemistry. A. 113: 3648-55. PMID 19317439 DOI: 10.1021/Jp811250R  1
2009 Chandrasekaran V, Lee CJ, Lin P, Duke RE, Pedersen LG. A computational modeling and molecular dynamics study of the Michaelis complex of human protein Z-dependent protease inhibitor (ZPI) and factor Xa (FXa). Journal of Molecular Modeling. 15: 897-911. PMID 19172319 DOI: 10.1007/S00894-008-0444-3  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 Wu S, Chandrasekaran V, Pedersen LG. Free energy correction to rigid body docking: Application to the colicin E7 and Im7 complex Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5545: 221-228. DOI: 10.1007/978-3-642-01973-9_25  1
2008 Liu S, Govind N, Pedersen LG. Exploring the origin of the internal rotational barrier for molecules with one rotatable dihedral angle. The Journal of Chemical Physics. 129: 094104. PMID 19044862 DOI: 10.1063/1.2976767  1
2008 Cisneros GA, Perera L, García-Díaz M, Bebenek K, Kunkel TA, Pedersen LG. Catalytic mechanism of human DNA polymerase lambda with Mg2+ and Mn2+ from ab initio quantum mechanical/molecular mechanical studies. Dna Repair. 7: 1824-34. PMID 18692600 DOI: 10.1016/J.Dnarep.2008.07.007  1
2008 Chandrasekaran V, Lee CJ, Duke RE, Perera L, Pedersen LG. Computational study of the putative active form of protein Z (PZa): sequence design and structural modeling. Protein Science : a Publication of the Protein Society. 17: 1354-61. PMID 18493021 DOI: 10.1110/Ps.034801.108  1
2008 Lin P, Batra VK, Pedersen LC, Beard WA, Wilson SH, Pedersen LG. Incorrect nucleotide insertion at the active site of a G:A mismatch catalyzed by DNA polymerase beta. Proceedings of the National Academy of Sciences of the United States of America. 105: 5670-4. PMID 18391201 DOI: 10.1073/Pnas.0801257105  1
2008 Lee CJ, Lin P, Chandrasekaran V, Duke RE, Everse SJ, Perera L, Pedersen LG. Proposed structural models of human factor Va and prothrombinase. Journal of Thrombosis and Haemostasis : Jth. 6: 83-9. PMID 17973648 DOI: 10.1111/J.1538-7836.2007.02821.X  1
2008 Patterson K, Colina CM, Perera L, Pedersen LG. Human tissue factor: A molecular dynamics study Aiche Annual Meeting, Conference Proceedings 1
2007 Davis CH, Ii DD, Stafford DW, Pedersen LG. Quantum chemical study of the mechanism of action of vitamin K carboxylase (VKC). IV. Intermediates and transition states. The Journal of Physical Chemistry. A. 111: 7257-61. PMID 17503787 DOI: 10.1021/Jp068564Y  1
2007 Lee CJ, Chandrasekaran V, Duke RE, Perera L, Pedersen LG. A proposed structural model of human protein Z. Journal of Thrombosis and Haemostasis : Jth. 5: 1558-61. PMID 17456189 DOI: 10.1111/J.1538-7836.2007.02597.X  1
2007 Hoffman M, Colina CM, Mcdonald AG, Arepally GM, Pedersen L, Monroe DM. Tissue factor around dermal vessels has bound factor VII in the absence of injury Journal of Thrombosis and Haemostasis. 5: 1403-1408. PMID 17425666 DOI: 10.1111/J.1538-7836.2007.02576.X  1
2007 Davis CH, Deerfield D, Wymore T, Stafford DW, Pedersen LG. A quantum chemical study of the mechanism of action of Vitamin K epoxide reductase (VKOR) II. Transition states. Journal of Molecular Graphics & Modelling. 26: 401-8. PMID 17182266 DOI: 10.1016/J.Jmgm.2006.10.005  1
2007 Davis CH, Deerfield D, Wymore T, Stafford DW, Pedersen LG. A quantum chemical study of the mechanism of action of Vitamin K carboxylase (VKC) III. Intermediates and transition states. Journal of Molecular Graphics & Modelling. 26: 409-14. PMID 17182265 DOI: 10.1016/J.Jmgm.2006.10.006  1
2007 Liu SB, Perera L, Pedersen LG. Binuclear manganese(II) complexes in biological systems Molecular Physics. 105: 2893-2898. DOI: 10.1080/00268970701747199  1
2006 Colina CM, Venkateswarlu D, Duke R, Perera L, Pedersen LG. What causes the enhancement of activity of factor VIIa by tissue factor? Journal of Thrombosis and Haemostasis : Jth. 4: 2726-9. PMID 17002651 DOI: 10.1111/J.1538-7836.2006.02222.X  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 Lin P, Pedersen LC, Batra VK, Beard WA, Wilson SH, Pedersen LG. Energy analysis of chemistry for correct insertion by DNA polymerase beta. Proceedings of the National Academy of Sciences of the United States of America. 103: 13294-9. PMID 16938895 DOI: 10.1073/Pnas.0606006103  1
2006 Pedersen LG, Bartolotti L, Li L. Deuterium and its role in the machinery of evolution. Journal of Theoretical Biology. 238: 914-8. PMID 16098990 DOI: 10.1016/J.Jtbi.2005.07.002  1
2006 Ping L, Yang W, Pedersen LC, Negishi M, Pedersen LG. Searching for the minimum energy path in the sulfuryl transfer reaction catalyzed by human estrogen sulfotransferase: Role of enzyme dynamics International Journal of Quantum Chemistry. 106: 2981-2998. DOI: 10.1002/Qua.21123  1
2006 Deerfield D, Davis CH, Wymore T, Stafford DW, Pedersen LG. Quantum chemical study of the mechanism of action of Vitamin K Epoxide Reductase (VKOR) International Journal of Quantum Chemistry. 106: 2944-2952. DOI: 10.1002/Qua.21119  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 Perera L, Pedersen LG. A reconsideration of the evidence for structural reorganization in FVII zymogen. Journal of Thrombosis and Haemostasis : Jth. 3: 1543-5. PMID 15978118 DOI: 10.1111/J.1538-7836.2005.01433.X  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 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  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 Kakuta Y, Li L, Pedersen LC, Pedersen LG, Negishi M. Heparan sulphate N-sulphotransferase activity: reaction mechanism and substrate recognition. Biochemical Society Transactions. 31: 331-4. PMID 12653630 DOI: 10.1042/Bst0310331  1
2003 Pedersen LC, Dong J, Taniguchi F, Kitagawa H, Krahn JM, Pedersen LG, Sugahara K, Negishi M. Crystal structure of an alpha 1,4-N-acetylhexosaminyltransferase (EXTL2), a member of the exostosin gene family involved in heparan sulfate biosynthesis. The Journal of Biological Chemistry. 278: 14420-8. PMID 12562774 DOI: 10.1074/Jbc.M210532200  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
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 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 Singh P, Jones LA, Foley CK, White PS, Pedersen LG. Structural aspects of phencyclidines: Crystal structure and quantum mechanical calculations for 1-[1-(2-thienyl)cyclohexyl] piperidine and its hydrochloride Journal of Molecular Structure. 608: 55-62. DOI: 10.1016/S0022-2860(01)00932-2  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 Negishi M, Pedersen LG, Petrotchenko E, Shevtsov S, Gorokhov A, Kakuta Y, Pedersen LC. Structure and function of sulfotransferases. Archives of Biochemistry and Biophysics. 390: 149-57. PMID 11396917 DOI: 10.1006/Abbi.2001.2368  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 Jin J, Perera L, Stafford D, Pedersen L. Four loops of the catalytic domain of factor VIIa mediate the effect of the first EGF-like domain substitution on factor VIIa catalytic activity Journal of Molecular Biology. 307: 1503-1517. PMID 11292356 DOI: 10.1006/Jmbi.2001.4556  1
2001 Deerfield DW, Carter CW, Pedersen LG. Models for protein-zinc ion binding sites. II. The catalytic sites International Journal of Quantum Chemistry. 83: 150-165. DOI: 10.1002/Qua.1207  1
2001 Bartolotti LJ, Pedersen LG, Meyer TJ. Quantum mechanical study of the oxidation pathway of the oxygen-evolving catalyst, [(bpy)2(H2O)RuIII-O-RuIII(H 2O)(bpy)2]+4 International Journal of Quantum Chemistry. 83: 143-149. DOI: 10.1002/Qua.1206  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 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 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 Tiraboschi G, Gresh N, Giessner-Prettre C, Pedersen LG, Deerfield DW. Parallel Ab Initio and Molecular Mechanics Investigation of Polycoordinated Zn(II) Complexes with Model Hard and Soft Ligands: Variations of Binding Energy and of Its Components with Number and Charges of Ligands Journal of Computational Chemistry. 21: 1011-1039. DOI: 10.1002/1096-987X(200009)21:12<1011::Aid-Jcc1>3.0.Co;2-B  1
2000 Mercero JM, Barrett P, Lam CW, Fowler JE, Ugalde JM, Pedersen LG. Quantum Mechanical Calculations on Phosphate Hydrolysis Reactions Journal of Computational Chemistry. 21: 43-51. DOI: 10.1002/(Sici)1096-987X(20000115)21:1<43::Aid-Jcc5>3.0.Co;2-8  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  0.4
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
1999 Dingemans TJ, Bacher A, Thelakkat M, Pedersen LG, Samulski ET, Schmidt HW. Spectral tuning of light emitting diodes with phenyl-thiophenes Synthetic Metals. 105: 171-177. DOI: 10.1016/S0379-6779(99)00073-9  1
1999 Bartolotti L, Kakuta Y, Pedersen L, Negishi M. A quantum mechanical study of the transfer of biological sulfate Journal of Molecular Structure: Theochem. 461: 105-111. DOI: 10.1016/S0166-1280(98)00424-2  0.8
1998 Sueyoshi T, Kakuta Y, Pedersen LC, Wall FE, Pedersen LG, Negishi M. A role of Lys614 in the sulfotransferase activity of human heparan sulfate N-deacetylase/N-sulfotransferase. Febs Letters. 433: 211-4. PMID 9744796 DOI: 10.1016/S0014-5793(98)00913-2  1
1998 Klose TS, Ibeanu GC, Ghanayem BI, Pedersen LG, Li L, Hall SD, Goldstein JA. Identification of residues 286 and 289 as critical for conferring substrate specificity of human CYP2C9 for diclofenac and ibuprofen. Archives of Biochemistry and Biophysics. 357: 240-8. PMID 9735164 DOI: 10.1006/Abbi.1998.0826  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 Shih P, Pedersen LG, Gibbs PR, Wolfenden R. Hydrophobicities of the nucleic acid bases: distribution coefficients from water to cyclohexane. Journal of Molecular Biology. 280: 421-30. PMID 9665846 DOI: 10.1006/Jmbi.1998.1880  1
1998 Chen Z, Blandl T, Prorok M, Warder SE, Li L, Zhu Y, Pedersen LG, Ni F, Castellino FJ. Conformational changes in conantokin-G induced upon binding of calcium and magnesium as revealed by NMR structural analysis. The Journal of Biological Chemistry. 273: 16248-58. PMID 9632684 DOI: 10.1074/Jbc.273.26.16248  1
1998 Kakuta Y, Pedersen LG, Pedersen LC, Negishi M. Conserved structural motifs in the sulfotransferase family. Trends in Biochemical Sciences. 23: 129-30. PMID 9584614 DOI: 10.1016/S0968-0004(98)01182-7  1
1998 Warder SE, Prorok M, Chen Z, Li L, Zhu Y, Pedersen LG, Ni F, Castellino FJ. The roles of individual gamma-carboxyglutamate residues in the solution structure and cation-dependent properties of conantokin-T. The Journal of Biological Chemistry. 273: 7512-22. PMID 9516452 DOI: 10.1074/Jbc.273.13.7512  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
1998 Miller RE, Pedersen L. The infrared spectrum and structure of the nitrous oxide trimer Journal of Chemical Physics. 108: 436-443.  1
1997 Rigby AC, Baleja JD, Li L, Pedersen LG, Furie BC, Furie B. Role of gamma-carboxyglutamic acid in the calcium-induced structural transition of conantokin G, a conotoxin from the marine snail Conus geographus. Biochemistry. 36: 15677-84. PMID 9398296 DOI: 10.1021/Bi9718550  1
1997 Kakuta Y, Pedersen LG, Carter CW, Negishi M, Pedersen LC. Crystal structure of estrogen sulphotransferase. Nature Structural Biology. 4: 904-8. PMID 9360604 DOI: 10.1038/Nsb1197-904  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 King AD, Huh NW, Pedersen LG, Hiskey RG. Studies on the peptide corresponding to residues 34-47 of bovine factor X. The Journal of Peptide Research : Official Journal of the American Peptide Society. 50: 34-8. PMID 9273885 DOI: 10.1111/J.1399-3011.1997.Tb00617.X  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 Deerfield DW, Pedersen LG. Structure and relative acidity for a model zinc finger Journal of Molecular Structure: Theochem. 419: 221-226. DOI: 10.1016/S0166-1280(97)00282-0  1
1997 Miller RE, Pedersen L. The structure of nitrous oxide tetramer from near infrared laser spectroscopy Chemical Physics Letters. 275: 307-313. DOI: 10.1016/S0009-2614(97)00739-2  0.96
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
1997 Miller RE, Pedersen L. The structure of nitrous oxide tetramer from near infrared laser spectroscopy Chemical Physics Letters. 275: 307-313.  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 Wolberg AS, Li L, Cheung WF, Hamaguchi N, Pedersen LG, Stafford DW. Characterization of gamma-carboxyglutamic acid residue 21 of human factor IX. Biochemistry. 35: 10321-7. PMID 8756687 DOI: 10.1021/Bi960502I  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 Ibeanu GC, Ghanayem BI, Linko P, Li L, Pedersen LG, Goldstein JA. Identification of residues 99, 220, and 221 of human cytochrome P450 2C19 as key determinants of omeprazole hydroxylase activity Journal of Biological Chemistry. 271: 12496-12501. PMID 8647857 DOI: 10.1074/jbc.271.21.12496  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 Taylor FB, Rao VM, Rapaport SI, Tracy PB, Allen DH, Worfolk LA, Lawler RR, Hedner U, Roberts HR, Hoffman M, Monroe DM, Mackman N, Tuddenham EGD, Camerer E, Prydz H, ... ... Pedersen LG, et al. Subject Index, Vol. 26 (suppl 1), 1996 Pathophysiology of Haemostasis and Thrombosis. 26: 166-166. DOI: 10.1159/000217262  1
1996 Taylor FB, Rao VM, Rapaport SI, Tracy PB, Allen DH, Worfolk LA, Lawler RR, Hedner U, Roberts HR, Hoffman M, Monroe DM, Mackman N, Tuddenham EGD, Camerer E, Prydz H, ... ... Pedersen LG, et al. Title Page / Table of Contents, Vol. 26, Supplement 1, 1996 Pathophysiology of Haemostasis and Thrombosis. 26. DOI: 10.1159/000217231  1
1996 Singh P, Zottola M, Huang S, Shaw BR, Pedersen LG. 2′-Deoxycytidine-N(3)-cyanoborane monohydrate Acta Crystallographica Section C: Crystal Structure Communications. 52: 693-696. DOI: 10.1107/S0108270195013412  1
1996 Bemish RJ, Rhee WM, Pedersen LG, Miller RE. The structure and intermolecular dynamics of the nitrous oxide-ethylene complex: Experiment and ab initio theory Journal of Chemical Physics. 104: 4411-4418. DOI: 10.1063/1.471193  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 Deerfield DW, Pedersen LG. Enol and deprotonated forms of acetic and malonic acid Journal of Molecular Structure: Theochem. 368: 163-171. DOI: 10.1016/S0166-1280(96)90557-6  1
1996 Bartolotti LJ, Kominos D, Pedersen LG. A model for the tertiary structure of the β-amyloid peptide Alzheimer's Research. 2: 189-193.  1
1995 Cabaniss S, Deerfield DW, Monroe DM, Hiskey RG, Pedersen LG. Is Ca(II) ion binding to prothrombin fragment 1 intrinsically cooperative, or is the cooperative binding accounted for by self-association? Blood Coagulation & Fibrinolysis : An International Journal in Haemostasis and Thrombosis. 6: 464-73. PMID 8589215  1
1995 Li L, Darden T, Foley C, Hiskey R, Pedersen LG. Homology modeling and molecular dynamics simulation of human prothrombin fragment 1 Protein Science. 4: 2341-2348. PMID 8563631 DOI: 10.1002/Pro.5560041112  1
1995 Deerfield DW, Pedersen LG. The first solvation shell of magnesium and calcium ions in a model nucleic acid environment: an ab initio study. Journal of Biomolecular Structure & Dynamics. 13: 167-80. PMID 8527028 DOI: 10.1080/07391102.1995.10508828  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 Deerfield DW, Fox DJ, Head-Gordon M, Hiskey RG, Pedersen LG. The first solvation shell of magnesium ion in a model protein environment with formate, water, and X-NH3, H2S, imidazole, formaldehyde, and chloride as ligands: an Ab initio study. Proteins. 21: 244-55. PMID 7784428 DOI: 10.1002/Prot.340210307  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 Bemish RJ, Block PA, Pedersen LG, Miller RE. The ethylene-carbon dioxide complex: A double internal rotor The Journal of Chemical Physics. 103: 7788-7795. DOI: 10.1063/1.470194  1
1995 Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method The Journal of Chemical Physics. 103: 8577-8593. DOI: 10.1063/1.470117  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 York DM, Yang W, Lee H, Darden T, Pedersen LG. Toward the accurate modeling of DNA: The importance of long-range electrostatics Journal of the American Chemical Society. 117: 5001-5002. DOI: 10.1021/Ja00122A034  1
1995 Deerfield DW, Pedersen LG. An ab initio quantum mechanical study of thioesters Journal of Molecular Structure: Theochem. 358: 99-106. DOI: 10.1016/0166-1280(96)87754-2  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 Amburgey JC, Huh NW, Pedersen LG, Hiskey RG. Small molecule analogs of phospholipid-metal ion binding sites: Potentiometric and spectroscopic studies of Mg(II) and Ca(II) complexes of cyclohexane-1,2,4-triol triphosphates Bioorganic Chemistry. 22: 198-215. DOI: 10.1006/Bioo.1994.1015  1
1994 Amburgey JC, Shuey SW, Pedersen LG, Hiskey RG. Small molecule analogs of phospholipid-metal ion binding sites: Synthesis and molecular modeling of cyclohexane-1,2,4-triol trisphosphates Bioorganic Chemistry. 22: 172-197. DOI: 10.1006/Bioo.1994.1014  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  0.76
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
1993 Bemish RJ, Block PA, Pedersen LG, Weitao Y, Miller RE. The Ar-C2H2 intermolecular potential from high resolution spectroscopy and ab initio theory: A case for multicenter interactions The Journal of Chemical Physics. 99: 8585-8598. DOI: 10.1063/1.465582  1
1993 Block PA, Pedersen LG, Miller RE. The structure of Ar-C2H4 from high resolution infrared spectroscopy and ab initio theory: The twofold barrier to C 2H4 internal rotation The Journal of Chemical Physics. 98: 3754-3762. DOI: 10.1063/1.464054  1
1993 Foley CK, Pedersen LG, Darden TA, Charifson PS, Wittinghofer A, Anderson MW. Molecular Dynamics Studies of H-ras p21-GTP Handbook of Experimental Pharmacology. 108: 235-245. DOI: 10.1007/978-3-642-78267-1_16  1
1993 Shuey SW, Deerfield DW, Amburgey JC, Cabaniss SE, Huh NW, Charifson PS, Pedersen LG, Hiskey RG. Cyclohexanediol bisphosphates as models for phospholipid-metal ion binding sites Bioorganic Chemistry. 21: 95-108. DOI: 10.1006/Bioo.1993.1011  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
1992 Weber DJ, Berkowitz P, Panek MG, Huh NW, Pedersen LG, Hiskey RG. Modifications of bovine prothrombin fragment 1 in the presence and absence of Ca(II) ions. Loss of positive cooperativity in Ca(II) ion binding for the modified proteins. The Journal of Biological Chemistry. 267: 4564-9. PMID 1531656  1
1992 Balbes LM, Pedersen LG, Hiskey RG. Predicted secondary structure of bovine prothrombin fragment 1 and related proteins in different environments by circular dichroism spectroscopy. International Journal of Peptide and Protein Research. 40: 127-33. PMID 1446970 DOI: 10.1111/J.1399-3011.1992.Tb01460.X  1
1992 Hamaguchi N, Charifson P, Darden T, Xiao L, Padmanabhan K, Tulinsky A, Hiskey R, Pedersen L. Molecular dynamics simulation of bovine prothrombin fragment 1 in the presence of calcium ions. Biochemistry. 31: 8840-8. PMID 1390671 DOI: 10.1021/Bi00152A021  1
1992 Berkowitz P, Huh NW, Brostrom KE, Panek MG, Weber DJ, Tulinsky A, Pedersen LG, Hiskey RG. A metal ion-binding site in the kringle region of bovine prothrombin fragment 1. The Journal of Biological Chemistry. 267: 4570-6. PMID 1311313  1
1992 Block PA, Marshall MD, Pedersen LG, Miller RE. Wide amplitude motion in the water–carbon dioxide and water–acetylene complexes Journal of Chemical Physics. 96: 7321-7332. DOI: 10.1063/1.462435  0.96
1992 Dayton DC, Pedersen LG, Miller RE. Structural determinations for two isomeric forms of N2O-HCN Journal of Physical Chemistry. 96: 1087-1095.  1
1992 Block PA, Marshall MD, Pedersen LG, Miller RE. Wide amplitude motion in the water-carbon dioxide and water-acetylene complexes The Journal of Chemical Physics. 96: 7321-7332.  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
1991 Charifson PS, Darden T, Tulinsky A, Hughey JL, Hiskey RG, Pedersen LG. Solution conformations of the gamma-carboxyglutamic acid domain of bovine prothrombin fragment 1, residues 1-65. Proceedings of the National Academy of Sciences of the United States of America. 88: 424-8. PMID 1988943 DOI: 10.1073/Pnas.88.2.424  1
1991 Hamaguchi N, Charifson PS, Pedersen LG, Brayer GD, Smith KJ, Stafford DW. Expression and characterization of human factor IX. Factor IXthr-397 and factor IXval-397. The Journal of Biological Chemistry. 266: 15213-20. PMID 1907972  1
1991 Huh NW, Berkowitz P, Hiskey RG, Pedersen LG. Determination of strontium binding to macromolecules. Analytical Biochemistry. 198: 391-3. PMID 1799227 DOI: 10.1016/0003-2697(91)90445-Y  1
1991 Cabaniss SE, Pugh KC, Pedersen LG, Hiskey RG. Proton, calcium, and magnesium binding by peptides containing gamma-carboxyglutamic acid. International Journal of Peptide and Protein Research. 37: 33-8. PMID 1646183 DOI: 10.1111/J.1399-3011.1991.Tb00730.X  1
1991 Deerfield DW, Fox DJ, Head-Gordon M, Hiskey RG, Pedersen LG. Interaction of Calcium and Magnesium Ions with Malonate and the Role of the Waters of Hydration: A Quantum Mechanical Study Journal of the American Chemical Society. 113: 1892-1899. DOI: 10.1021/Ja00006A004  1
1991 Bartolotti LJ, Pedersen LG, Charifson PS. Long range nonbonded attractive constants for some charged atoms Journal of Computational Chemistry. 12: 1125-1128. DOI: 10.1002/Jcc.540120910  0.76
1990 Cabaniss SE, Pugh KC, Charifson PS, Pedersen LG, Hiskey RG. Synthesis and characterization of 1,1,4,4-butanetetracarboxylic acid. A di-gamma-carboxyglutamic acid (GlaGla) analogue. International Journal of Peptide and Protein Research. 36: 79-85. PMID 2401602 DOI: 10.1111/J.1399-3011.1990.Tb00085.X  1
1990 Cain JD, Deerfield DW, Hiskey RG, Pedersen LG. Divalent metal ion mediated interaction of proteins with negatively charged membranes. A model study employing molecular mechanics. International Journal of Peptide and Protein Research. 35: 111-6. PMID 2323886 DOI: 10.1111/J.1399-3011.1990.Tb00244.X  1
1990 Lapadat MA, Deerfield DW, Pedersen LG, Spremulli LL. Generation of potential structures for the G-domain of chloroplast EF-Tu using comparative molecular modeling. Proteins. 8: 237-50. PMID 2281086 DOI: 10.1002/Prot.340080306  1
1990 Monroe DM, Deerfield DW, Olson DL, Stewart TN, Treanor RE, Roberts HR, Hiskey RG, Pedersen LG. Calcium ion binding to human and bovine factor X. Blood Coagulation & Fibrinolysis : An International Journal in Haemostasis and Thrombosis. 1: 633-40. PMID 2133243  1
1990 Dayton DC, Pedersen LG, Miller RE. Infrared spectroscopy and ab initio theory of the structural isomers of CO2-HCN The Journal of Chemical Physics. 93: 4560-4570. DOI: 10.1063/1.458696  1
1989 Deerfield DW, Lapadat MA, Spremulli LL, Hiskey RG, Pedersen LG. The role of hydrated divalent metal ions in the bridging of two anionic groups. An ab initio quantum chemical and molecular mechanics study of dimethyl phosphate and formate bridged by calcium and magnesium ions. Journal of Biomolecular Structure & Dynamics. 6: 1077-91. PMID 2818858 DOI: 10.1080/07391102.1989.10506538  1
1989 Deerfield DW, Nicholas HB, Hiskey RG, Pedersen LG. Salt or ion bridges in biological systems: a study employing quantum and molecular mechanics. Proteins. 6: 168-92. PMID 2622904 DOI: 10.1002/Prot.340060207  1
1989 Block PA, Jucks KW, Pedersen LG, Miller RE. The linear and T-shaped isomers of C2H2HCN: Vibrational dynamics from infrared spectroscopy and ab initio theory Chemical Physics. 139: 15-30. DOI: 10.1016/0301-0104(89)90002-5  1
1989 Cornish TJ, Baer T, Pedersen LG. The n → 3s Rydberg transition of jet-cooled tetrahydropyran, 1,4-dioxane, and 1,4-dioxane-d8 studied by 2 + 1 resonance-enhanced multiphoton ionization Journal of Physical Chemistry. 93: 6064-6069.  1
1988 Weber DJ, Pollock JS, Pedersen LG, Hiskey RG. The determination of a calcium-dependent binding constant of the bovine prothrombin Gla domain (residues 1-45) to phospholipid vesicles. Biochemical and Biophysical Research Communications. 155: 230-5. PMID 3415682 DOI: 10.1016/S0006-291X(88)81073-8  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
1988 Maynard AT, Eastman MA, Darden T, Deerfield DW, Hiskey RG, Pedersen L. 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. International Journal of Peptide and Protein Research. 31: 137-49. PMID 3366547 DOI: 10.1111/J.1399-3011.1988.Tb00016.X  1
1988 Lewis MR, Deerfield DW, Hoke RA, Koehler KA, Pedersen LG, Hiskey RG. Studies on Ca(II) binding to gamma-carboxyglutamic acid. Use of thermal decarboxylation to probe metal ion/gamma-carboxyglutamic acid interactions. The Journal of Biological Chemistry. 263: 1358-63. PMID 3335547  1
1988 Pollock JS, Shepard AJ, Weber DJ, Olson DL, Klapper DG, Pedersen LG, Hiskey RG. Phospholipid binding properties of bovine prothrombin peptide residues 1-45. The Journal of Biological Chemistry. 263: 14216-23. PMID 3170544  1
1988 Zapata GA, Berkowitz P, Noyes CM, Pollock JS, Deerfield DW, Pedersen LG, Hiskey RG. Chemical modification of bovine prothrombin fragment 1 in the presence of Tb3+ ions. Sequence studies on 3-gamma-MGlu-fragment. The Journal of Biological Chemistry. 263: 8150-6. PMID 3131340  1
1987 Deerfield DW, Olson DL, Berkowitz P, Koehler KA, Pedersen LG, Hiskey RG. Relative affinity of Ca(II) and Mg(II) ions for human and bovine prothrombin and fragment 1. Biochemical and Biophysical Research Communications. 144: 520-7. PMID 3579923 DOI: 10.1016/S0006-291X(87)80540-5  1
1987 Olson DL, Deerfield DW, Berkowitz P, Hiskey RG, Pedersen LG. Determination of magnesium binding to macromolecules. Analytical Biochemistry. 160: 468-70. PMID 3578772 DOI: 10.1016/0003-2697(87)90077-7  1
1987 Deerfield DW, Olson DL, Berkowitz P, Byrd PA, Koehler KA, Pedersen LG, Hiskey RG. Mg(II) binding by bovine prothrombin fragment 1 via equilibrium dialysis and the relative roles of Mg(II) and Ca(II) in blood coagulation. The Journal of Biological Chemistry. 262: 4017-23. PMID 3558405  1
1987 McKinney JD, Pedersen LG. Do residue levels of polychlorinated biphenyls (PCBs) in human blood produce mild hypothyroidism? Journal of Theoretical Biology. 129: 231-41. PMID 3138502 DOI: 10.1016/S0022-5193(87)80015-2  1
1987 Koehler LS, Jarnagin F, Hiskey RG, Pedersen LG, Koehler KA. Estimation of apparent quadrupolar coupling constants for complexes of magnesium ions with mono- and dicarboxylic acid ligands. Applications to magnesium ion: protein interactions. Journal of Inorganic Biochemistry. 29: 153-64. PMID 3104538 DOI: 10.1016/0162-0134(87)80022-3  1
1987 McKinney J, Fannin R, Jordan S, Chae K, Rickenbacher U, Pedersen L. Polychlorinated biphenyls and related compound interactions with specific binding sites for thyroxine in rat liver nuclear extracts. Journal of Medicinal Chemistry. 30: 79-86. PMID 3100800 DOI: 10.1021/Jm00384A014  1
1986 Hoke RA, Deerfield DW, Pedersen LG, Koehler KA, Hiskey RG. Synthesis of a gamma-carboxyglutamic acid containing heptapeptide corresponding to bovine prothrombin residues 17-23. International Journal of Peptide and Protein Research. 28: 569-78. PMID 3818174 DOI: 10.1111/J.1399-3011.1986.Tb03294.X  1
1986 Deerfield DW, Hoke RA, Pedersen LG, Darden T, Hiskey RG. Relative spectral response as a function of sequential ligand binding. Biochemical and Biophysical Research Communications. 141: 1207-12. PMID 3814120 DOI: 10.1016/S0006-291X(86)80173-5  1
1986 Wright SF, Berkowitz P, Deerfield DW, Byrd PA, Olson DL, Larson RS, Hinn GC, Koehler KA, Pedersen LG, Hiskey RG. Chemical modification of bovine prothrombin fragment 1 in the presence of Tb3+ ions. The Journal of Biological Chemistry. 261: 10598-605. PMID 3755435  1
1986 Deerfield DW, Berkowitz P, Olson DL, Wells S, Hoke RA, Koehler KA, Pedersen LG, Hiskey RG. The effect of divalent metal ions on the electrophoretic mobility of bovine prothrombin and bovine prothrombin fragment 1. The Journal of Biological Chemistry. 261: 4833-9. PMID 3754256  1
1986 Eastman MA, Pedersen LG, Hiskey RG, Pique M, Koehler KA, Gottschalk KE, Némethy G, Scheraga HA. Conformation of the 18-23 loop region of bovine prothrombin in the absence and presence of a model Ca2+ ion. An energy minimization study. International Journal of Peptide and Protein Research. 27: 530-53. PMID 3733321  1
1986 Maynard AT, Pedersen LG, Posner HS, McKinney JD. An Ab initio study of the relationship between nitroarene mutagenicity and electron affinity Molecular Pharmacology. 29: 629-636. PMID 3520290  1
1986 McKinney JD, Pedersen LG. Biological activity of polychlorinated biphenyls related to conformational structure. The Biochemical Journal. 240: 621-2. PMID 3101675  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 Darden T, McKinney JD, Gottschalk K, Maynard AT, Pedersen LG. A theoretical study of the minimum energy structures of diethylstilbestrol and its analogues by molecular mechanics (MM2p), MNDO, and ab initio calculations Journal of the American Chemical Society. 108: 207-211. DOI: 10.1021/Ja00262A004  1
1986 Marsh HC, Hoke RA, Deerfield DW, Pedersen LG, Hiskey RG, Koehler KA. Terbium ion binding to a synthetic .gamma.-carboxyglutamic acid containing heptapeptide corresponding to bovine prothrombin residues 17-23 Inorganic Chemistry. 25: 4503-4506. DOI: 10.1021/Ic00245A011  1
1986 Kiplinger JP, Pedersen LG, Bursey MM. Direct observation of new antimony-containing anions: SbH2O-, Sb3 -, and monomeric Sb3O5 - Inorganica Chimica Acta. 115: 203-205. DOI: 10.1016/S0020-1693(00)84415-1  1
1986 Lehman TA, Hass JR, Crow FW, Tomer KB, Pedersen LG. Isotope effects in collision-activated dissociations of simple ions International Journal of Mass Spectrometry and Ion Processes. 69: 85-96. DOI: 10.1016/0168-1176(86)87043-4  1
1986 Bursey MM, Harvan DJ, Pedersen LG, Maynard AT. Direct Observation of the HTiO3-Ion. Cheminform. 17. DOI: 10.1002/Chin.198616003  1
1986 Marsh HC, Hoke RA, Deerfield DW, Pedersen LG, Hiskey RG, Koehler KA. Terbium ion binding to a synthetic γ-carboxyglutamic acid containing heptapeptide corresponding to bovine prothrombin residues 17-23 Inorganic Chemistry. 25: 4503-4506.  1
1985 McKinney JD, Darden T, Lyerly MA, Pedersen LG. PCB and related compound binding to the Ah receptor(s) theoretical model based on molecular parameters and molecular mechanics Quantitative Structure-Activity Relationships. 4: 166-172. DOI: 10.1002/Qsar.19850040405  1
1985 Bursey MM, Harvan DJ, Pedersen LG, Maynard AT. Direct observation of the HTiO3 - ion Inorganic Chemistry. 24: 4748-4749.  1
1984 Washington K, Sarasua MM, Koehler LS, Koehler KA, Schultz JA, Pedersen LG, Hiskey RG. Utilization of heavy-atom effect quenching of pyrene fluorescence to determine the intramembrane distribution of halothane. Photochemistry and Photobiology. 40: 693-701. PMID 6549213 DOI: 10.1111/J.1751-1097.1984.Tb04639.X  1
1984 Long GA, Hiskey RG, Pedersen LG, Koehler KA. The role of γ-carboxyclutamic acid (Gla) in blood clotting proteins: A theoretical study of Mg-malonate complexes Journal of Molecular Structure: Theochem. 108: 173-178. DOI: 10.1016/0166-1280(84)85003-4  1
1983 Bursey MM, Cerny RL, Pedersen LG, Gottschalk KE, Tomer KB, Lehman TA. Direct observation of the H2NO2– ion Journal of the Chemical Society, Chemical Communications. 517-518. DOI: 10.1039/C39830000517  1
1983 McKinney JD, Gottschalk KE, Pedersen L. The polarizability of planar aromatic systems. An application to polychlorinated biphenyls (PCB's), dioxins and polyaromatic hydrocarbons Journal of Molecular Structure: Theochem. 105: 427-438. DOI: 10.1016/0166-1280(83)80220-6  1
1983 McKinney JD, Gottschalk KE, Pedersen L. A theoretical investigation of the conformation of polychlorinated biphenyls (PCB's) Journal of Molecular Structure: Theochem. 104: 445-450. DOI: 10.1002/Chin.198401065  1
1982 Schultz JA, Gates SM, Pedersen LG, Jarnagin RC. Surface complexes formed by monohydric alcohols on lithium Surface Science. 118: 634-648. DOI: 10.1016/0039-6028(82)90212-6  1
1982 Gottschalk KE, Hiskey RG, Pedersen LG, Koehler KA. A theoretical study of the chelation complex comprising formate ions, calcium ion and water of hydration Journal of Molecular Structure. 90: 265-269. DOI: 10.1016/0022-2860(82)90226-5  1
1982 Fraley DF, Pedersen LG, Bursey MM. Resistive heating of emitter wires for field desorption and ionization: A theory International Journal of Mass Spectrometry and Ion Physics. 43: 99-129. DOI: 10.1016/0020-7381(82)80002-8  1
1981 Youngless TL, Bursey MM, Pedersen LG. Field ionization at a surface modified by chemically bound carboxylic acid groups International Journal of Mass Spectrometry and Ion Physics. 38: 223-239. DOI: 10.1016/0020-7381(81)80069-1  1
1980 Schultz JA, Gates S, Pedersen LG, Jarnagin RC. Methoxide surface complexes on lithium Chemical Physics Letters. 72: 156-161. DOI: 10.1016/0009-2614(80)80263-6  1
1979 McLean W, Schultz JA, Pedersen LG, Jarnagin RC. The structure and formation of methyllithium ionic fragments Journal of Organometallic Chemistry. 175: 1-9. DOI: 10.1016/S0022-328X(00)82294-9  1
1979 McLean W, Schultz JA, Pedersen LG, Jarnagin RC. Surface complexes between O2, H2O and lithium Surface Science. 83: 354-366. DOI: 10.1016/0039-6028(79)90049-9  1
1979 Schultz JA, McLean W, Pedersen L, Jarnagin RC. H2O on Lin clusters: a theoretical study Chemical Physics Letters. 64: 230-233. DOI: 10.1016/0009-2614(79)80502-3  1
1978 Eslava LA, Putnam JB, Pedersen L. An AB initio investigation of molecules with a disulfide bond: (HS)2, (CH3S)2 and cystine. International Journal of Peptide and Protein Research. 11: 149-53. PMID 640773 DOI: 10.1111/J.1399-3011.1978.Tb02833.X  0.32
1976 Putnam JB, Pedersen LG. Discovery of a 3',5'-guanosine monophosphate simulating factor in amoebae of Dictyostelium discoideum. Biochimica Et Biophysica Acta. 411: 168-70. PMID 170997 DOI: 10.1016/0304-4165(75)90296-2  0.36
1975 Bursey MM, Greenberg RS, Pedersen LG. Position of protonation of the cresols: Semi-empirical and ab initio calculations Chemical Physics Letters. 36: 470-474. DOI: 10.1016/0009-2614(75)80282-X  1
1973 Parker CE, Hass JR, Bursey MM, Pedersen LG. The ortho effect in mass spectra. Insight into the tightening of activated complexes for the loss of ketene from phenyl acetates and ethylene from phenetoles from INDO molecular orbital calculations Organic Mass Spectrometry. 7: 1189-1195. DOI: 10.1002/Oms.1210071008  0.6
1971 Pedersen L, Gammon K, Hoskins D. Rotational relaxation in the H2,Ar system: A Monte Carlo trajectory calculation Chemical Physics Letters. 11: 407-410. DOI: 10.1016/0009-2614(71)80371-8  1
1968 Morokuma K, Pedersen L, Karplus M. Structure of CH3 and CF3 The Journal of Chemical Physics. 48: 4801-4802. DOI: 10.1063/1.1668076  0.52
1967 Morokuma K, Pedersen L, Karplus M. Vibrational vs. translational activation in the H2,H2 and H2,D2 exchange reactions Journal of the American Chemical Society. 89: 5064-5065. DOI: 10.1021/Ja00995A055  0.52
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