CADD Centerhttp://mackerell.umaryland.edu/CADD/CADD_center.html
PSC Departmenthttp://www2.pharmacy.umaryland.edu
 

Active areas of research include the development of parameters for empirical force field calculations of molecules of biological and pharmaceutical interest and the application of theoretical approaches towards the elucidation of biochemical mechanisms and the rational design of drugs. Specific areas of interest include the structural determinants of DNA, structure-function relationships of opioid analgesics, structure-function relationships of DNA and RNA, DNA-protein interactions, including base flipping by the 5-methyltransferase from HhaI, and Computer-Aided Drug Design studies.

From Publications

Lee, G.U., MacKerell, Jr., A.D. Force Energy and Structure of Double-Stranded DNA Oligonucleotides under Tensile Load. European Biophysical Journal, 1999, 28: 415-426.[DNA stick representation][DNA space filling][DNA w/solvent at 10.1 nm]

Yang, B., Wright, J., Eldefrawi, M.E., Poi, S.,and MacKerell Jr., A.D. Conformational, aqueous solvation and pKa contributions to the binding of cocaine, WIN and a WIN vinyl analog. Journal of the American Chemical Society, 1994, 116:8722-8732.[Cocaine stick representation]

Huang, N. Banavali, N.K., and MacKerell, Jr., A.D. "Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase." Proceedings of the National Academy of Sciences, USA, 100: 68-73, 2003 [Base flipping images of MHhai DNA]

Obtain Cartesian Coordinates of Published Structures

Foloppe, N. and MacKerell, A.D., Jr. Intrinsic Conformational Properties of Deoxyribonucleosides: Implicated Role for Cytosine in the Equilibrium Among the A, B, and Z Forms of DNA. Biophysical Journal, 1999, 76: 3206-3218.[HTML][TXT]

MacKerell, Jr., A.D. Molecular dynamics simulation analysis of a sodium dodecyl sulfate micelle in aqueous solution: Decreased fluiditiy of the micelle hydrophobic interior. Journal of Physical Chemistry, 1995, 99:1846-1855.[Image of Sodium dodecyl sulfate micelle][SDS_PDB.gz][SDS_CRD.gz]

Computer-Aided Drug Design Projects

Binding response program

Miscellaneous Images

ASV integrase
DNA and cytosine-5-methyltransferasefig_DNA_tensor.htmlfig_DNA_tensor_2.htmlfig_DNA_tensor_2.htmlfig_DNA_tensor_3.htmlfig_cocaine.htmlfig_MHhai.htmlfig_MHhai.htmlhttp://www.pharmacy.umaryland.edu/faculty/amackere/supplem/B81012_appendixb.htmlhttp://www.pharmacy.umaryland.edu/faculty/amackere/supplem/B81012_appendixb.txtfig_micelle.htmlResearch_files/SDS_PDB.gzResearch_files/SDS_CRD.gzhttp://mackerell.umaryland.edu/CADD/CADD_resources_files/binding_response.tar.gzfig_ASV.htmlfig_DNA_cytosine.htmlfig_cocaine.htmlshapeimage_5_link_0shapeimage_5_link_1shapeimage_5_link_2shapeimage_5_link_3shapeimage_5_link_4shapeimage_5_link_5shapeimage_5_link_6shapeimage_5_link_7shapeimage_5_link_8shapeimage_5_link_9shapeimage_5_link_10shapeimage_5_link_11shapeimage_5_link_12shapeimage_5_link_13shapeimage_5_link_14

View from the interior of the protein Erk with a bound inhibitor (red) , where the ribbons represent the protein backbone and the mesh represents the protein surface

“Erk-side out, #17”

            Research Interest

Images from Selected Publication

Lab Wikihttp://dogmans.umaryland.edu/pmwiki/pmwiki.php
Group MembersGroup_Members.html
Research
PublicationsPublications.html
CHARMM Force FieldsCHARMM_ff_params.html
Force Field Development ResourcesEmpirical_FF_Dev.html
Contact InformationContact.html

LINKS

CHARMM LINKS

CHARMM Links/ForumCHARMM_links.html
CHARMM TutorialsCHARMM_tutor.html
HOMEMacKerell_Lab.html