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.


Listing Row

Friday, October 3, 2014
Friday, October 3, 2014