Literature DB >> 21537488

Lee Pedersen's work in theoretical and computational chemistry and biochemistry.

Lee G Pedersen1.   

Abstract

Nature at the lab level in biology and chemistry can be described by the application of quantum mechanics. In many cases, a reasonable approximation to quantum mechanics is classical mechanics realized through Newton's equations of motion. Dr. Pedersen began his career using quantum mechanics to describe the properties of small molecular complexes that could serve as models for biochemical systems. To describe large molecular systems required a drop-back to classical means and this led surprisingly to a major improvement in the classical treatment of electrostatics for all molecules, not just biological molecules. Recent work has involved the application of quantum mechanics for the putative active sites of enzymes to gain greater insight into the key steps in enzyme catalysis.

Keywords:  Blood coagulation cascade; Classical mechanics; DNA repair enzymes; Particle mesh Ewald; Quantum mechanical/molecular mechanical; Quantum mechanics

Year:  2011        PMID: 21537488      PMCID: PMC3083993          DOI: 10.4331/wjbc.v2.i2.35

Source DB:  PubMed          Journal:  World J Biol Chem        ISSN: 1949-8454


  10 in total

1.  Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method.

Authors:  L Li; C R Weinberg; T A Darden; L G Pedersen
Journal:  Bioinformatics       Date:  2001-12       Impact factor: 6.937

2.  Gene assessment and sample classification for gene expression data using a genetic algorithm/k-nearest neighbor method.

Authors:  L Li; T A Darden; C R Weinberg; A J Levine; L G Pedersen
Journal:  Comb Chem High Throughput Screen       Date:  2001-12       Impact factor: 1.339

3.  Incorrect nucleotide insertion at the active site of a G:A mismatch catalyzed by DNA polymerase beta.

Authors:  Ping Lin; Vinod K Batra; Lars C Pedersen; William A Beard; Samuel H Wilson; Lee G Pedersen
Journal:  Proc Natl Acad Sci U S A       Date:  2008-04-07       Impact factor: 11.205

4.  Molecular acidity: A quantitative conceptual density functional theory description.

Authors:  Shubin Liu; Cynthia K Schauer; Lee G Pedersen
Journal:  J Chem Phys       Date:  2009-10-28       Impact factor: 3.488

5.  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.

Authors:  L Li; T A Darden; S J Freedman; B C Furie; B Furie; J D Baleja; H Smith; R G Hiskey; L G Pedersen
Journal:  Biochemistry       Date:  1997-02-25       Impact factor: 3.162

6.  Energy analysis of chemistry for correct insertion by DNA polymerase beta.

Authors:  Ping Lin; Lars C Pedersen; Vinod K Batra; William A Beard; Samuel H Wilson; Lee G Pedersen
Journal:  Proc Natl Acad Sci U S A       Date:  2006-08-28       Impact factor: 11.205

Review 7.  Recent estimates of the structure of the factor VIIa (FVIIa)/tissue factor (TF) and factor Xa (FXa) ternary complex.

Authors:  Chang Jun Lee; Vasu Chandrasekaran; Sangwook Wu; Robert E Duke; Lee G Pedersen
Journal:  Thromb Res       Date:  2010-02-13       Impact factor: 3.944

8.  An all-atom solution-equilibrated model for human extrinsic blood coagulation complex (sTF-VIIa-Xa): a protein-protein docking and molecular dynamics refinement study.

Authors:  D Venkateswarlu; R E Duke; L Perera; T A Darden; L G Pedersen
Journal:  J Thromb Haemost       Date:  2003-12       Impact factor: 5.824

9.  Estimation of molecular acidity via electrostatic potential at the nucleus and valence natural atomic orbitals.

Authors:  Shubin Liu; Lee G Pedersen
Journal:  J Phys Chem A       Date:  2009-04-16       Impact factor: 2.781

10.  Proposed structural models of human factor Va and prothrombinase.

Authors:  C J Lee; P Lin; V Chandrasekaran; R E Duke; S J Everse; L Perera; L G Pedersen
Journal:  J Thromb Haemost       Date:  2007-10-29       Impact factor: 5.824

  10 in total
  1 in total

1.  Accelerated molecular dynamics simulation analysis of MSI-594 in a lipid bilayer.

Authors:  Shruti Mukherjee; Rajiv K Kar; Ravi Prakash Reddy Nanga; Kamal H Mroue; Ayyalusamy Ramamoorthy; Anirban Bhunia
Journal:  Phys Chem Chem Phys       Date:  2017-07-26       Impact factor: 3.676

  1 in total

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