Alex MacKerell
Curriculum Vitae
Alexander D. MacKerell Jr.
Department of Pharmaceutical Sciences
School of Pharmacy
University of Maryland, Baltimore
20 Penn Street
Baltimore, MD 21201
USA
Telephone: 410-706-7442
FAX: 410-706-5017
http://www.pharmacy.umaryland.edu/faculty/amackere/
http://www.pharmacy.umaryland.edu/cadd/
Education
Ph.D.:Biochemistry, Rutgers University, New Brunswick, NJ
Advisor: Professor Regina Pietruszko
Degree conferred: August, 1985
B.S.:Chemistry, University of Hawaii, Honolulu, HI
Degree conferred: May, 1981
A.S.:Biology, Gloucester County College, Sewell, NJ
Degree conferred: May, 1979
Employment Experience
5/04 to PresentProfessor, University of Maryland, Baltimore, School of
Pharmacy, Department of Pharmaceutical Sciences, 20 Penn Street,
Baltimore, MD 21201, USA
8/02 to PresentDirector, Computer-Aided Drug Design Center, University of Maryland,
School of Pharmacy, 20 Penn Street, Baltimore, MD 21201, USA
6/97 to 5/04Associate Professor, University of Maryland, Baltimore, School of
Pharmacy, Department of Pharmaceutical Sciences
1/02 to 6/02Visiting Professor, The Scripps Research Institute, Department of
Molecular Biology, TPC6, 10550 North Torrey Pines Road, LaJolla, CA 92037, USA
9/95 to PresentMember of the Program in Experimental Therapeutics, Greenebaum Cancer Center, University of Maryland, Baltimore, MD 21201, USA
6/93 to 6/97Assistant Professor: University of Maryland at Baltimore, School of
Pharmacy, Department of Pharmaceutical Sciences, 20 North Pine Street,
Baltimore, MD 21201, USA
9/92 to 6/93Visiting Assistant Professor: Swarthmore College, Department of
Chemistry, 500 College Ave., Swathmore, PA 19081, USA
4/88 to 7/92Research Associate: Harvard University, Department of Chemistry, 12
Oxford Street, Cambridge, MA 02138, USA Supervisor: Prof. Martin Karplus
9/90 to 6/93Consultant: Polygen Corporation, 200 Fifth Avenue, Waltham, MA
02254, USA
1/86 to 3/88Postdoctoral Fellow: Karolinska Institutet, Department of Medical
Biophysics, S104-01, Stockholm, Sweden. Supervisor: Prof. Rudolf Rigler
9/81 to 12/85Biochemistry Research Assistant: Rutgers University, Biochemistry
Graduate Program, New Brunswick, NJ, USA,
Supervisor: Prof. Regina Pietruszko
11/79 to 6/81Lab Assistant: University of Hawaii, Hawaii Institute of Geophysics,
Honolulu, HI, USA. Supervisor: Prof. Donald Thomas
Advisory Boards
Lawrence Livermore National Laboratory Biosciences Directorate
Unihart Biotech Pharma N.V.
Pittsburgh Supercomputing Center
Scientific, Professional and Scholarly Organizations
Federation of American Societies for Experimental Biologies (1988-present)
American Society for Biochemistry and Molecular Biology (1988-1999)
Biophysical Society (2000-present)
American Chemical Society (1992-present)
American Association of Colleges of Pharmacy (1992-1998)
International Society of Quantum Biology and Pharmacology (1992-present)
Vice President: 2004
President: 2005-2006
American Association for the Advancement of Science (1995-present)
Rho Chi Honor Society (1993-present)
Editorial Board Member
Proteins: Structure, Function, and Bioinformatics
Journal of Computational Chemistry
Drug Design Reviews, 2002 to 2005
Honors and Awards
NSF NATO Postdoctoral Research Fellowship, 1987
Karolinska Fellowship for Foreign Researchers, 1986-1987
NIH Postdoctoral Fellowship, 1988-1990
Alumnus of the Years, Gloucester County College, Sewell, NJ, ca. 1992
NSF European Centre for Atomic and Molecular Computations Fellowship, 1997
Maryland Chemist of the Year 2006: MD Chapter of the American Chemical Society
Invited Lectures
1. “Dynamics of ribonuclease T1 and horse liver alcohol dehydrogenase: Combining experimental and theoretical information,” European Society for Photobiology Meeting, Padova, Italy, 1987
2. “Structural and dynamics differences in the free and 2’GMP enzyme forms of ribonuclease T1,”First International Meeting on the Structure and Chemistry of Ribonucleases, Moscow, USSR, 1988
3. “Motivation and Validation for the use of Empirical Force Fields for Computational Studies of Biological Systems,” First World Congress on Medicine, Public Health and Biotechnology. Austin, Texas, 1994.
4. “Validation of the use of Empirical Force Fields for Computational Studies of Biological Systems” Department of Microbiology and Immunology, School of Medicine, University of Maryland at Baltimore, Baltimore, MD, 1994.
5. “Validation of the Use of Empirical Force Fields for Computational Studies of Biological Systems” 8th Middle Atlantic Regional Meeting of the Americal Chemical Society Univeristy of Maryland Baltimore County, Catonsville, MD, 1994.
6. “Empirical Force Field Development and Validation for Computational Studies of Biological Membranes,”208th American Chemical Society National Meeting, Washington D.C., 1994
7. “Molecular Dynamics Simulation Studies of Nucleic Acids,” Research Seminar, University of Maryland Cancer Center, Department of Developmental Therapeutics, School of Medicine, University of Maryland,Baltimore, Baltimore, MD, 1995
8. “Molecular Dynamics Simulation Studies of Nucleic Acids,” Molecular and Cell Biology Graduate Program Seminar Series, University of Maryland at Baltimore, Baltimore, MD, 1995
9. “Molecular Dynamics Simulation Studies of Nucleic Acids,” Department of Chemistry and Biochemistry Seminar Series University of Maryland Baltimore County, Catonsville, MD, 1995
10. “Methodological Developments in the Optimization of Lennard-Jones Parameters for Empirical Force Field Calculations,” Biophysic Laboratory, Center for Biologics Evaluation & Research, Food and Drug Administration and Laboratory of Structural Biology, Division of Computer Research & Technology, NIH, Bethesda, MD, 1995
11. “Empirical Force Field Parameterization and Simulations of Nucleic Acids,” Laboratory of Medicinal Chemistry, National Cancer Institute, NIH, Bethesda, MD, 1995
12. “Molecular Dynamics Simulation Studies of the EcoRI restriction site dodecamer,” Department of Chemistry, University of Houston, Houston, Texas, 1995
13. "An all-atom empirical energy function for the simulation of nucleic acids, " 210th American Chemical Society National Meeting, Chicago, Il,1995.
14. "MD simulations of the EcoRI recognition sequence in solution: Influence of counterions on stability," 210th American Chemical Society National Meeting, Chicago, Il.,1995.
15. "Combined ab initio/empirical approach for the optimization of Lennard-Jones parameters.” 210th American Chemical Society National Meeting, Chicago, Il,1995.
16. “Computational Approaches to the Study of Biological Systems” Department of Chemistry, Towson State University, Towson, MD, 1995
17. “Empirical Force Field Calculations of Nucleic Acids: Parametrization and Application” Center for Structural Biology Department of Bioscience at Novum, Karolinska Institutet, Huddinge, Sweden, 1996.
18. “Empirical Force Field Calculations of Nucleic Acids: Parametrization and Application” Section de Biphysique des Protéines et de Membranes, Commissariat a l’Energie Atomique, CEA-Saclay, Saclay, France, 1996.
19. “Empirical Force Field Calculations of Nucleic Acids: Parametrization and Application” Laboratoire de Chimie Biophysique, Institut le Bel, Universite Louis Pasteur, Strasbourg, France, 1996.
20. “Validation of Empirical Force Fields Based on Crystal Calculations” 212th American Chemical Society National Meeting, Orlando, FL, 1996.
21. “Use of Ab Initio Calculations to Aid in the Interpretation of the Influcence of Surface Adsorption on the Vibrational Spectra of Alkoxides” 212th American Chemical Society National Meeting, Orlando, FL. 1996.
22. “Lennard-Jones Parameters of Alkanes and Alkenes Based on a Combined Ab Initio-Empirical Optimization Procedure” 212th American Chemical Society National Meeting, Orlando, FL, 1996.
23. “Relationship of Small Molecule Based Parameter Optimization to Condensed Phase Calculations on Proteins and Nucleic Acids” Center Européen de Calcul Atomique et Moléculaire, Workshop: Potential functions for simulation of biomolecules, Lyon, France, 1996.
24. “MD based Potential of Mean Force Calculations on DNA under Tensile Force.” Chemistry Division, Naval Research Laboratory, Washington, DC. 1997
25. “MD based Potential of Mean Force Calculations on DNA under Tensile Force.” Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 1997
26. “Potential of Mean Force Calculations on DNA under Tensile Force.” Center for Advanced Research in Biotechnology, University of Maryland, Rockville, MD, 1997
27. “Structure, Force and Energy of a Double-Stranded DNA Oligonucleotides Under Tensile Loads” Swiss Federal Institute of Technology, Lausanne, Switzerland, 1997.
28. “Structure, Force and Energy of a Double-Stranded DNA Oligonucleotides Under Tensile Loads” Center Européen de Calcul Atomique et Moléculaire, Workshop: Nucleic Acids, Lyon, France, 1997.
29. “Structure, Force and Energy of a Double-Stranded DNA Oligonucleotides Under Tensile Loads” Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, 1997.
30. “Importance of microscopic contributions to condensed phase macroscopic properties in empirical force field calculations” Computational Chemistry Gordon Conference, Tilton, NH, 1998
31. “Developments in the CHARMM All-Atom Empirical Energy Function for Biological Molecules” 216th American Chemical Society National Meeting, Boston, MA, 1998
32. “Importance of microscopic contributions to condensed phase macroscopic properties in empirical force field calculations” Making and Breaking Potentials, UK Cooperative Computational Project #5 Annual Meeting, Edinburgh, Scotland, 1998
33. “Importance of microscopic contributions to condensed phase macroscopic properties in empirical force field calculations: Application to Nucleic Acids” Department of Chemistry, Georgetown Medical School, Georgetown University, Georgetown, VA, 1998
34. “Mechanical and Environmental Contributions to Opening of Duplex DNA in the TATA Box and Related Oligomers Investigated via Potential of Mean Force Calculations.” Molecular Modeling Interest Group, National Institutes of Health, Bethesda, MD, 1999.
35. “CHARMM empirical force field for biological molecules: Overview of optimization procedures with emphasis on lipid bilayers.” Center Européen de Calcul Atomique et Moléculaire, Workshop: Molecular Dynamics Simulations of Lipid Membranes and Membrane Associated Proteins, Lyon, France, 1999.
36. “Optimization of the CHARMM all-atom nucleic acid force field and investigation of the energetics of DNA deformation.” Department of Biochemistry, University of Zürich, Zürich, Switzerland, 1999.
37. “Optimization of the CHARMM all-atom nucleic acid force field.” Laboratoire de Chimie Biophysique, Institut le Bel, Universite Louis Pasteur, Strasbourg, France, 1999.
38. “HIV Integrase: Identification of Novel Inhibitors and Analysis of Enzyme-Inhibitor Interactions via Ligand Docking.” School of Pharmacy, West Virginia University, Morgantown, WV, 2000.
39. “Balancing Microscopic Contributions with Macroscopic Observables in Empirical Force Fields: Application to Nucleic Acids.” National Institute of Occupational Safety and Health, Morgantown, WV, 2000.
40. “Balancing Microscopic Contributions with Macroscopic Observables in Empirical Force Fields. Application to Nucleic Acids” Department of Chemistry, University of York, York, UK, 2000
41. “Advances in the CHARMM all-atom force field for biological molecules” Canadian Computational Chemistry Conference 4, Bishop University, Quebec, Canada, 2000.
42. “Advances in the CHARMM all-atom force field for biological molecules” 220th American Chemical Society National Meeting, Washington, DC, 2000.
43. “Use of Oligodeoxyribonucleotides with Conformationally Constrained Abasic Sugar Targets to Probe the Mechanism of Base Flipping by HhaI DNA (Cytosine C5)-Methyltransferase” Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 2000
44. “Overview of the CHARMM all-atom force field for biological molecules” 4th Biannual Structural Biology Symposium, Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 2001
45. “Recent Advances in Biomolecular Molecular Dynamics Simulations: DNA Conformational Transitions and the Impact of Protein Binding” School of Chemical Engineering, Purdue University, West Lafayette, IN, 2001.
46. “Computational Studies of Base Flipping In DNA and Impact of Binding with the (Cytosine-5) Methyltransferase from HhaI” Department of Chemistry and Biochemisty, Duquesne University, Pittsburgh, PA, 2001
47. “Base Flipping in DNA and the Impact of Binding to (Cytosine-5) Methyltransferase from HhaI” Department of Chemistry, Kansas University, Lawrence, KS, 2001
48. “Ab initio Quantum Mechanical Analysis of Nucleic Acid Components” DIMACS Workshop on DNA Sequence and Topology, DIMACS Center, Rutgers University, Piscataway, NJ, 2001.
49.”Computational Studies of Base Flipping In DNA” Laboratory of Medicinal Chemistry, National Cancer Institute, National Institutes of Health, Frederick, MD, 2001.
50. “Energetic and Structural Details of Base Flipping from Duplex DNA” Horizons in Biophysics 2001, Royal Swedish Academy of Sciences, Nobel Institute of Chemistry, Stockholm, Sweden, 2001.
51. “Energetic and Structural Details of Base Flipping from Duplex DNA” Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 2001.
52. “Drude Oscillator as a Model for Electronic Polarization in Empirical Force Fields: Application to Dimethylphosphate” Workshop on Polarizability for Biomolecular Simulation, Snowbird, Utah, 2001.
53. “CHARMM Force Fields: Approaches, Recent Developments and the Misery….” Department of Chemistry and Biochemistry, University of California, San Diego, CA, 2002.
54. “ Recent developments in the CHARMM all-atom force field for nucleic acids” 223rd American Chemical Society National Meeting, Orlando, Fl., 2002
55. CHARMM Force Fields: Approaches, Recent Developments and the Misery….” Accelyrs Corporation, San Diego, CA, 2002.
56. “Base Flipping in DNA: Facilitation by the Enzyme Cytosine-5-Methyltransferase” Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, 2002.
57. “Improved representation of protein backbone conformational energetics and condensed phase simulations of dimethylphosphate using the Shell Model to treat electronic polarizability,” CHARMM Meeting, Department of Chemistry, Harvard University, Cambridge MA, 2002.
58. “Computational Studies of Base Flipping Alone and Complexed to the Cytosine-5-Methyltransferase from HhaI” Diffraction Methods In Structural Biology, Gordon Research Conference, New London, CT, 2002
59. “CHARMM biomolecular force field: Recent developments and future directions,” American Chemical Society National Meeting, Boston, MA, 2002
60. “Empirical Force Fields: Overview, parameter optimization & applications,” Department of Physics, University of Cyprus, Nicosia, Cyprus, 2003
61. “Force Fields” Short Course on Force Fields and Molecular Dynamics,” Quantum Theory Project 43rd Sanibel Symposium, University of Florida, St. Augustine, Fl, 2003
62. “Computational Studies of Base Flipping in DNA Alone and Bound to the Cytosine-5-methyltransferase from HhaI,” DNA and beyond: Structure, Dynamics and Interactions, École Polytechnique Fédérale de Lausanne, Laussane, Switzerland, 2003.
63. “Computational Studies of Base Flipping in DNA Alone and Bound to the Cytosine-5-methyltransferase from HhaI,” Laboratory of Biophysical Chemistry Seminar Series, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, 2003.
64. “Computer-Aided Drug Design: Ligand- and Target-Based Applications,” Chemistry Group, National Institute of Drug Abuse, NIH, Baltimore, MD, 2003.
65. “CHARMM biomolecular force field: Recent developments and future directions,” Annual CHARMM Developers Meeting, The Scripps Reseach Institute, LaJolla, CA, 2003.
66. “Improved Treatment of the Protein Backbone Conformation in the CHARMM All-atom Force Field,” Computing for Biology, IBM-BNL Blue-Gene Science Workshop, Stony Brook, NY, 2003.
67. “CHARMM all-atom empirical force field for biomolecules: Recent enhancements and progress towards inclusion of electronic polarizability” Theoretical and Computational Biophysics Seminar, Beckman Institute, University of Illinois, Urbana-Champaign, IL, 2003
68. “Computational Studies of Base Flipping in DNA Alone and Bound to the Cytosine-5-methyltransferase from HhaI,” Department of Chemistry Seminar Series, Pennsylvania State University, State College, PA, 2003
69. “Computational methods used in drug discovery” Department of Medical and Research Technology, University of Maryland School of Medicine, Continuing Education Credits, Baltimore, MD, 2003
70. “Base Flipping in DNA: Accessing Millisecond Events via MD-based Potential of Mean Force Calculations,” 48th Annual Meeting of the Biophysical Society, Baltmore, MD, USA, February 2004
71. “Computational Studies of Base Flipping in DNA Alone and Bound to the Cytosine-5-methyltransferase from HhaI,” 2004 President's Meeting, International Society of Quantum Biology and Pharmacology, Como, Italy, June 2004.
72. “Parameters, parameters, parameters,” Annual CHARMM Developers Meeting, Harvard University, Cambridge, MA, July 2004
73. “Enhancements and Extensions of the CHARMM Biological Empirical Force Fields” Frontiers in Computational Biophysics and Drug Design, Army Research Laboratories Workshop, Beltsville, MD, October 2004
74. “Enhancements and Extensions of the CHARMM Biological Empirical Force Fields” Keck Computational and Theoretical Biology Symposium, Rice University, Houston, TX, December, 2004
75. “Computational Studies of Base Flipping in DNA Alone and Bound to the Cytosine-5-methyltransferase from HhaI” World Association of Theoretically Oriented Chemists, 2005 International Meeting, Cape Town, South Africa, January, 2005
76. “Computer-Aided Drug Design: Ligand- and Target-Based Approaches” Howard University, School of Pharmacy, Department of Pharmaceutical Sciences Seminar, March 2005
77. “Computational Studies of Base Flipping in DNA Alone and Bound to the Cytosine-5-methyltransferase from HhaI” Molecular Biophysics Seminar Series, Wesleyan University, Middletown, CT, April 2005.
78. “Progress in the CHARMM force fields; Extension to polarizable model based on the classical Drude oscillator,” Annual CHARMM meeting, Weill Medical College, Cornell University, New York, NY, July 2005
79. “Improvements in the CHARMM all-atom force fields for biomolecules” 230th National American Chemical Society Meeting, Washington, DC, August 2005
80. “MD simulation Studies of Base Flipping in DNA,” International Society of Quantum Biology and Pharmacology Gilda Lowe Memorial Meeting, Staten Island, New York, October 2005.
81. “Structure-function relationships of nucleic acids and protein-nucleic acid complexes studied via MD simulations” Bioinformatics Institute Visiting Scientist Lecture Series, Singapore, March 2006.
82. “Computer-aided drug design: Ligand-based approaches on -opioid ligands” Bioinformatics Institute Visiting Scientist Lecture Series, Singapore, March 2006.
83. “Computer-aided drug design: Target-based approaches with emphasis on protein-protein interactions” Bioinformatics Institute Visiting Scientist Lecture Series, Singapore, March 2006.
84. “Overview of the CHARMM all-atom force fields including the additive and classical Drude polarizable models,” Validating Modeling and Experimental Methods to Enable Drug Discovery, National Institute of Standards and Technology, Gaithersburg, MD., April, 2006.
85. “Overview of the CHARMM all-atom force fields including the additive and classical Drude polarizable models” Center for Bioinformatics, University of Kansas, Lawrence, Kansas, April, 2006.
86. “MD simulation studies of base flipping in DNA alone and in the presence
of the (cytosine-C5)-methyltransferase from HhaI” Department of Chemistry, University of Kansas , Lawrence, Kansas, April, 2006.
87. “CHARMM force fields: 2006” Annual CHARMM Developers Meeting, Harvard University, Cambridge, MA, July 2006.
88. “MD simulation studies of base flipping in DNA alone and in the presence
of the (cytosine-C5)-methyltransferase from HhaI” MMTSB Workshop, The Scripps Research Institute, LaJolla, California, August, 2006.
89. “Polarizable empirical force field based on the classical Drude oscillator model” Computational Chemistry Gordon Conference, Les Diablerets, Switzerland, October 2006.
90. “Computer-Aided Drug Design; Targeting the Tyrosine Kinase p56Lck SH2 Domain” Structure Biology Program, St. Jude Children’s Hospital, Memphis, Tennessee. October 2006.
91. “Ligand-based drug discovery using CHARMM; Conformationally sampled pharmacophore (CSP)” Accelyrs User Meeting and Conference 2006, Baltimore, Maryland, November 2006.
92. “Overview of CHARMM force fields and extension to drug-like molecules” Accelyrs User Meeting and Conference 2006, Baltimore, Maryland, November 2006.
93. “Polarizable empirical force field based on the classical Drude oscillator model” Florida State University Workshop 2007 on “Quantitative Computational Biophysics”, Florida State University, Tallahassee, Florida, February 2007.
94. “Computational studies of base flipping in DNA alone and bound to the cytosine-5-methyltransferase from HhaI” Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, Illinois, USA, March 2007
95. “Optimization and validation of a polarizable force field based on the classical Drude oscillator” 233rd American Chemical Society National Meeting, Chicago, Illinois, USA, March 2007
96. “Ongoing developments in the CHARMM force fields for lipids” Semiannual Membrane Meeting, University of Utah, Park City, Utah, June 2007
97. “CHARMM force fields: 2007,” Annual CHARMM Developers Meeting, University of Maryland, School of Pharmacy, Baltimore, Maryland, USA, July 2007.
98. “Towards a Polarizable Force Field for Macromolecules: Optimization of a Force Field Based on the Classical Drude Oscillator,” Modeling Interactions in Biomolecules III, Prague, Czech Republic, September, 2007
99. “Computational studies of base flipping in DNA bound to the cytosine-5-methyltransferase from HhaI” FEBS Workshop on “DNA and RNA Modification Enzymes,” Centre Paul Langevin, Aussois, France, September 2007
100. “Advances in the CHARMM force fields for biological and pharmaceutical compounds” Accelrys Science Forum, Cambridge, MA, USA, October 2007.
101. “Development of a polarizable force field based on the classical Drude oscillator” 16th Conference on Current Trends in Computational Chemistry (CCTCC), Jackson State University, Jackson, MS, USA, November, 2007.
102. “Computational studies of base flipping in DNA alone and bound to the cytosine-5-methyltransferase from HhaI,” Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA, USA, November, 2007.
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