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


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

Selected Publications

  • HA Carlson. Check your confidence: Size really does matter. J. Chem. Info. Model. 2013, 53, 1837-1841. [Highlighted on the cover of JCIM]

  • KW Lexa, HA Carlson. Improving protocols for protein mapping through proper comparison to crystallography data. J. Chem. Info. Model. 2013, 53, 391-402.

  • RD Smith, AE Engdahl, JB Dunbar Jr., HA Carlson. Biophysical limits of protein-ligand binding. J. Chem. Info. Model. 2012, 52: 2098-2106. [2012's 10th most-read paper in JCIM, despite appearing only half-way through the year]

  • NA Khazanov, KL Damm-Ganamet, DX Quang, HA Carlson. Overcoming sequence misalignments with weighted structural superposition. Prot. Struct. Func. Bioinf. 2012, 80, 2523-2535. [Highlighted on the cover of Proteins]

  • KW Lexa, HA Carlson. Full protein flexibility is essential for proper hot-spot mapping. J. Am. Chem. Soc. 2011, 133, 200-202.