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

Selected Publications

  • RD Smith, HA Carlson. Identification of cryptic binding sites using MixMD with standard and accelerated molecular dynamics. J. Chem. Info. Model. 2021, 61, 1287-1299. 

  • LN Makley, OT Johnson, P Ghanakota, JN Rauch, D Osborn, TS Wu, T Cierpicki, HA Carlson, JE Gestwicki. Chemical Validation of a Druggable Site on Hsp27/HSPB1 using In Silico Solvent Mapping and Biophysical Methods. Bioorg. & Med. Chem. 2021, 34, 115990.

  • JJ Clark, ZJ Orban, HA Carlson. Predicting binding sites from unbound vs. bound protein structures.  Sci. Reports 2020, 10, 15856.

  • RD Smith, JJ Clark, A Ahmed, ZJ Orban, JB Dunbar Jr., HA Carlson. Updates to Binding MOAD (Mother of All Databases): Polypharmacology tools and their utility in drug repurposing. J. Mol. Biol. 2019, 431, 2423-2433.

  • P Ghanakota, D DasGupta, HA Carlson. Free energies and entropies of binding sites identified by MixMD cosolvent simulations. J. Chem. Info. Model. 2019, 59, 2035-2045.

  • JJ Clark, ML Benson, RD Smith, HA Carlson. Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. PLoS Comput. Biol. 2019, 15, e1006705.

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

  • 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.

  • 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.