Accuracy of free energies of hydration for organic molecules from 6-31g*-derived partial charges. - Heather A. Carlson; Toan B. Nguyen; Modesto Orozco; William L. Jorgensen (J. Comput. Chem., 1993)

Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model. - Michael J. Potter; Paul D. Kirchhoff; Heather A. Carlson; James Andrew McCammon (J. Comput. Chem., 1999)

Development of polyphosphate parameters for use with the AMBER force field. - Kristin L. Meagher; Luke T. Redman; Heather A. Carlson (J. Comput. Chem., 2003)

Incorporating Dynamics in E. coli Dihydrofolate Reductase Enhances Structure-Based Drug Discovery. - Michael G. Lerner; Anna L. Bowman; Heather A. Carlson (J. Chem. Inf. Model., 2007)

Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design. - Michael G. Lerner; Kristin L. Meagher; Heather A. Carlson (J. Comput. Aided Mol. Des., 2008)

Binding MOAD, a high-quality protein-ligand database. - Mark L. Benson; Richard D. Smith; Nickolay A. Khazanov; Brandon Dimcheff; John E. Beaver; Peter Dresslar; Jason Nerothin; Heather A. Carlson (Nucleic Acids Res., 2008)

A Call to Arms: What You Can Do for Computational Drug Discovery. - Heather A. Carlson; James B. Dunbar Jr. (J. Chem. Inf. Model., 2011)

CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes. - James B. Dunbar Jr.; Richard D. Smith; Chao-Yie Yang; Peter Man-Un Ung; Katrina W. Lexa; Nickolay A. Khazanov; Jeanne A. Stuckey; Shaomeng Wang; Heather A. Carlson (J. Chem. Inf. Model., 2011)

Correction to CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes. - James B. Dunbar Jr.; Richard D. Smith; Chao-Yie Yang; Peter Man-Un Ung; Katrina W. Lexa; Nickolay A. Khazanov; Jeanne A. Stuckey; Shaomeng Wang; Heather A. Carlson (J. Chem. Inf. Model., 2011)

CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions. - Richard D. Smith; James B. Dunbar Jr.; Peter Man-Un Ung; Emilio Xavier Esposito; Chao-Yie Yang; Shaomeng Wang; Heather A. Carlson (J. Chem. Inf. Model., 2011)

Biophysical Limits of Protein-Ligand Binding. - Richard D. Smith; Alaina L. Engdahl; James B. Dunbar Jr.; Heather A. Carlson (J. Chem. Inf. Model., 2012)

Check Your Confidence: Size Really Does Matter. - Heather A. Carlson (J. Chem. Inf. Model., 2013)

CSAR Benchmark Exercise 2011-2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series. - Kelly L. Damm-Ganamet; Richard D. Smith; James B. Dunbar Jr.; Jeanne A. Stuckey; Heather A. Carlson (J. Chem. Inf. Model., 2013)

CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys. - James B. Dunbar Jr.; Richard D. Smith; Kelly L. Damm-Ganamet; Aqeel Ahmed; Emilio Xavier Esposito; James Delproposto; Krishnapriya Chinnaswamy; You-Na Kang; Ginger Kubish; Jason E. Gestwicki; Jeanne A. Stuckey; Heather A. Carlson (J. Chem. Inf. Model., 2013)

Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data. - Katrina W. Lexa; Heather A. Carlson (J. Chem. Inf. Model., 2013)

Exploring the Composition of Protein-Ligand Binding Sites on a Large Scale. - Nickolay A. Khazanov; Heather A. Carlson (PLoS Comput. Biol., 2013)

Identification of Key Hinge Residues Important for Nucleotide-Dependent Allostery in E. coli Hsp70/DnaK. - Peter Man-Un Ung; Andrea D. Thompson; Lyra Chang; Jason E. Gestwicki; Heather A. Carlson (PLoS Comput. Biol., 2013)

Parameter Choice Matters: Validating Probe Parameters for Use in Mixed-Solvent Simulations. - Katrina W. Lexa; Garrett B. Goh; Heather A. Carlson (J. Chem. Inf. Model., 2014)

Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures. - Aqeel Ahmed; Richard D. Smith; Jordan J. Clark; James B. Dunbar Jr.; Heather A. Carlson (Nucleic Acids Res., 2015)

ChemTreeMap: an interactive map of biochemical similarity in molecular datasets. - Jing Lu; Heather A. Carlson (Bioinform., 2016)

D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. - Symon Gathiaka; Shuai Liu; Michael Chiu; Huanwang Yang; Jeanne A. Stuckey; You-Na Kang; Jim Delproposto; Ginger Kubish; James B. Dunbar Jr.; Heather A. Carlson; Stephen K. Burley; W. Patrick Walters; et al. (J. Comput. Aided Mol. Des., 2016)

Lessons Learned over Four Benchmark Exercises from the Community Structure-Activity Resource. - Heather A. Carlson (J. Chem. Inf. Model., 2016)

CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma. - Heather A. Carlson; Richard D. Smith; Kelly L. Damm-Ganamet; Jeanne A. Stuckey; Aqeel Ahmed; Maire A. Convery; Donald O. Somers; Michael Kranz; Patricia A. Elkins; Guanglei Cui; Catherine E. Peishoff; Millard H. Lambert; et al. (J. Chem. Inf. Model., 2016)

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. - Richard D. Smith; Kelly L. Damm-Ganamet; James B. Dunbar Jr.; Aqeel Ahmed; Krishnapriya Chinnaswamy; James Delproposto; Ginger Kubish; Christine E. Tinberg; Sagar D. Khare; Jiayi Dou; Lindsey Doyle; Jeanne A. Stuckey; et al. (J. Chem. Inf. Model., 2016)

Comparing pharmacophore models derived from crystallography and NMR ensembles. - Phani Ghanakota; Heather A. Carlson (J. Comput. Aided Mol. Des., 2017)

Are there physicochemical differences between allosteric and competitive ligands? - Richard D. Smith; Jing Lu; Heather A. Carlson (PLoS Comput. Biol., 2017)

MixMD Probeview: Robust Binding Site Prediction from Cosolvent Simulations. - Sarah E. Graham; Noah Leja; Heather A. Carlson (J. Chem. Inf. Model., 2018)

Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics. - Sarah E. Graham; Richard D. Smith; Heather A. Carlson (J. Chem. Inf. Model., 2018)

Free Energies and Entropies of Binding Sites Identified by MixMD Cosolvent Simulations. - Phani Ghanakota; Debarati DasGupta; Heather A. Carlson (J. Chem. Inf. Model., 2019)

Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. - Jordan J. Clark; Mark L. Benson; Richard D. Smith; Heather A. Carlson (PLoS Comput. Biol., 2019)

Mixed-solvent molecular dynamics simulation-based discovery of a putative allosteric site on regulator of G protein signaling 4. - Wallace K. B. Chan; Debarati DasGupta; Heather A. Carlson; John R. Traynor (J. Comput. Chem., 2021)

Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. - Richard D. Smith; Heather A. Carlson (J. Chem. Inf. Model., 2021)

Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge. - Zhaoping Xiong; Minji Jeon; Robert J. Allaway; Jaewoo Kang; Donghyeon Park; Jinhyuk Lee; Hwisang Jeon; Miyoung Ko; Hualiang Jiang; Mingyue Zheng; Aik Choon Tan; Xindi Guo; et al. (PLoS Comput. Biol., 2021)

Computational Identification of Possible Allosteric Sites and Modulators of the SARS-CoV-2 Main Protease. - Debarati DasGupta; Wallace K. B. Chan; Heather A. Carlson (J. Chem. Inf. Model., 2022)