Postdoctoral Fellow, University of California, San Diego with J. Andrew McCammon (1997-2000)
Ph.D., Physical Chemistry, Yale University with William L. Jorgensen (1997)
M.S., Physical Chemistry, Yale University (1992)
B.S., Magna Cum Laude, Mathematics, Chemistry, and Physics, North Central College (1991)
Prof. Carlson focuses on understanding protein-ligand complexes, from the basic biophysics of molecular recognition to applied drug design. Her lab uses molecular mechanics simulations and database mining to pursue two major goals: (1) developing new methods that incorporate protein flexibility into computer-aided drug design and (2) creating Binding MOAD (Mother of All Databases), the definitive database for protein-ligand recognition. Understanding protein binding sites and protein-protein interactions is fundamental to chemistry, biology, and medicine.
RD Smith, KL Damm-Ganamet, JB Dunbar Jr, A Ahmed, K Chinnaswamy, JE Delproposto, GM Kubish, CE Tinberg, SD Khare, J Dou, L Doyle, JA Stuckey, D Baker, HA Carlson. CSAR Benchmark Exercise 2013: Evaluation of results from a combined computational protein design, docking, and scoring/ranking challenge. J. Chem. Info. Model. 2015, in press.
PM‐U Ung, P Ghanakota, SE Graham, KW Lexa, HA Carlson. Identifying binding hot spots on protein surfaces by mixed-solvent MD: HIV -1 protease as a test case. Biopolymers 2015, in press.
PM-U Ung, JB Dunbar Jr, JE Gestwicki, HA Carlson. An allosteric modulator of HIV-1 protease shows equipotent inhibition of wild-type and drug-resistant pro teases. J. Med. Chem. 2014, 57, 6468-6478.
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. 2014, 43, D465-D469.
NA Khazanov, HA Carlson. Exploring the composition of protein-ligand binding sites on a large scale. PLoS Comput. Biol. 9, e1003321.
HA Carlson. Check your confidence: Size really does matter. J. Chem. Info. Model. 2013, 53, 1837-1841. [highlighted on cover]
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]
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 cover]
- KW Lexa, HA Carlson. Full protein flexibility is essential for proper hot-spot mapping. J. Am. Chem. Soc. 2011, 133, 200-202.