Prof. Carlson’s expertise is in the area of computer simulations, cheminformatics, bioinformatics, and structure-based drug design.  She is a leader in the incorporation of protein flexibility and allosteric control in drug design.  She is also well known for her studies of protein-ligand binding and the biophysics of molecular recognition.  She frequently collaborates with experimental groups on campus to test her models and methods, giving many of her students combined experimental and computational research experiences.

Carlson is also the director of two large, online resources for studying protein-ligand interactions: Binding MOAD ( and the Community Structure-Activity Resource (  These resources are used by numerous research groups around the world.  She also serves the scientific community through NIH review panels and editorial roles for scientific journals.

For a complete listing of Carlson’s professional history, please see her CV.

Research Interests

  • Simulating the dynamic behavior of proteins and ligands

  • Understanding allosteric control and molecular recognition of ligands

  • Developing improved methods for structure-based and computer-aided drug discovery

  • Database mining of molecules and protein systems of biomedical importance

  • Evaluating data quality, statistics in cheminformatics, and database curation


  • 2010 Novartis Chemistry Lectureship, Novartis
  • 2009 Novartis Chemistry Lectureship, Novartis
  • 2008 Corwin Hansch Award, The Cheminformatics and QSAR Society, Cheminformatics and QSAR Society
  • 2006 Wiley International Journal of Quantum Chemistry Young Investigator Award, Chemistry Views
  • 2002 Beckman Young Investigator Award, Arnold and Mabel Beckman Foundation, Arnold and Mabel Beckman Foundation

Selected Publications

  • RD Smith, J Lu, HA Carlson. Are there physicochemical differences between allosteric and competitive ligands? PLoS Comput. Biol. 2017, 13(11), e1005813.

  • P Ghanakota, HA Carlson. Comparing pharmacophore models derived from crystallography and NMR ensembles. J. Comput.-Aided Mol. Des. 2017, 31, 979-993.

  • J Lu, HA Carlson. ChemTreeMap: An interactive map of biochemical similarity in molecular datasets. Bioinformatics 2016, 32, 3584-3592.

  • P Ghanakota, HA Carlson. Moving beyond active-site detection: MixMD applied to allosteric systems. J. Phys. Chem. B 2016, 120, 8685-8695.

  • PMU Ung, P Ghanakota, SE Graham, KW Lexa, HA Carlson. Identifying binding hot spots on protein surfaces by mixed-solvent molecular dynamics: HIV-1 protease as a test case. Biopolymers 2016, 105, 21–34.

  • A Ahmed, RD Smith, JJ Clark, JB Dunbar Jr., HA Carlson. Recent improvements to Binding MOAD: a resource for protein–ligand binding affinities and structures. Nucl. Acids Res. 2015, 43, D465-D469.