Heather A. Carlson

Publication Activity (10 Years)

Years Active: 1993-2022
Publications (10 Years): 15

Top Topics

Protein Protein

Molecular Dynamics

Top Venues

J. Chem. Inf. Model.

PLoS Comput. Biol.

J. Comput. Aided Mol. Des.

Publications

Debarati DasGupta, Wallace K. B. Chan, Heather A. Carlson
Computational Identification of Possible Allosteric Sites and Modulators of the SARS-CoV-2 Main Protease. J. Chem. Inf. Model. 62 (3) (2022)
Wallace K. B. Chan, Debarati DasGupta, Heather A. Carlson, John R. Traynor
Mixed-solvent molecular dynamics simulation-based discovery of a putative allosteric site on regulator of G protein signaling 4. J. Comput. Chem. 42 (30) (2021)
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, Multi-Targeting Drug DREAM Challenge Community, Kristen K. Dang, Alex Tropsha, Chana Hecht, Tirtha K. Das, Heather A. Carlson, Ruben Abagyan, Justin Guinney, Avner Schlessinger, Ross Cagan
Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge. PLoS Comput. Biol. 17 (9) (2021)
Richard D. Smith, Heather A. Carlson
Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. J. Chem. Inf. Model. 61 (3) (2021)
Phani Ghanakota, Debarati DasGupta, Heather A. Carlson
Free Energies and Entropies of Binding Sites Identified by MixMD Cosolvent Simulations. J. Chem. Inf. Model. 59 (5) (2019)
Jordan J. Clark, Mark L. Benson, Richard D. Smith, Heather A. Carlson
Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. PLoS Comput. Biol. 15 (1) (2019)
Sarah E. Graham, Richard D. Smith, Heather A. Carlson
Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics. J. Chem. Inf. Model. 58 (2) (2018)
Sarah E. Graham, Noah Leja, Heather A. Carlson
MixMD Probeview: Robust Binding Site Prediction from Cosolvent Simulations. J. Chem. Inf. Model. 58 (7) (2018)
Phani Ghanakota, Heather A. Carlson
Comparing pharmacophore models derived from crystallography and NMR ensembles. J. Comput. Aided Mol. Des. 31 (11) (2017)
Richard D. Smith, Jing Lu, Heather A. Carlson
Are there physicochemical differences between allosteric and competitive ligands? PLoS Comput. Biol. 13 (11) (2017)
Heather A. Carlson
Lessons Learned over Four Benchmark Exercises from the Community Structure-Activity Resource. J. Chem. Inf. Model. 56 (6) (2016)
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, David Baker, Heather A. Carlson
CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. J. Chem. Inf. Model. 56 (6) (2016)
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, Rommie E. Amaro, Victoria A. Feher, Michael K. Gilson
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. J. Comput. Aided Mol. Des. 30 (9) (2016)
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, James B. Dunbar Jr.
CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma. J. Chem. Inf. Model. 56 (6) (2016)
Jing Lu, Heather A. Carlson
ChemTreeMap: an interactive map of biochemical similarity in molecular datasets. Bioinform. 32 (23) (2016)
Aqeel Ahmed, Richard D. Smith, Jordan J. Clark, James B. Dunbar Jr., Heather A. Carlson
Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures. Nucleic Acids Res. 43 (Database-Issue) (2015)
Katrina W. Lexa, Garrett B. Goh, Heather A. Carlson
Parameter Choice Matters: Validating Probe Parameters for Use in Mixed-Solvent Simulations. J. Chem. Inf. Model. 54 (8) (2014)
Nickolay A. Khazanov, Heather A. Carlson
Exploring the Composition of Protein-Ligand Binding Sites on a Large Scale. PLoS Comput. Biol. 9 (11) (2013)
Heather A. Carlson
Matter. J. Chem. Inf. Model. 53 (8) (2013)
Kelly L. Damm-Ganamet, Richard D. Smith, James B. Dunbar Jr., Jeanne A. Stuckey, Heather A. Carlson
CSAR Benchmark Exercise 2011-2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series. J. Chem. Inf. Model. 53 (8) (2013)
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
CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys. J. Chem. Inf. Model. 53 (8) (2013)
Peter Man-Un Ung, Andrea D. Thompson, Lyra Chang, Jason E. Gestwicki, Heather A. Carlson
Hsp70/DnaK. PLoS Comput. Biol. 9 (11) (2013)
Katrina W. Lexa, Heather A. Carlson
Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data. J. Chem. Inf. Model. 53 (2) (2013)
Richard D. Smith, Alaina L. Engdahl, James B. Dunbar Jr., Heather A. Carlson
Biophysical Limits of Protein-Ligand Binding. J. Chem. Inf. Model. 52 (8) (2012)
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
Correction to CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes. J. Chem. Inf. Model. 51 (9) (2011)
Richard D. Smith, James B. Dunbar Jr., Peter Man-Un Ung, Emilio Xavier Esposito, Chao-Yie Yang, Shaomeng Wang, Heather A. Carlson
CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions. J. Chem. Inf. Model. 51 (9) (2011)
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
CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes. J. Chem. Inf. Model. 51 (9) (2011)
Heather A. Carlson, James B. Dunbar Jr.
A Call to Arms: What You Can Do for Computational Drug Discovery. J. Chem. Inf. Model. 51 (9) (2011)
Mark L. Benson, Richard D. Smith, Nickolay A. Khazanov, Brandon Dimcheff, John E. Beaver, Peter Dresslar, Jason Nerothin, Heather A. Carlson
Binding MOAD, a high-quality protein-ligand database. Nucleic Acids Res. 36 (Database-Issue) (2008)
Michael G. Lerner, Kristin L. Meagher, Heather A. Carlson
Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design. J. Comput. Aided Mol. Des. 22 (10) (2008)
Michael G. Lerner, Anna L. Bowman, Heather A. Carlson
Dihydrofolate Reductase Enhances Structure-Based Drug Discovery. J. Chem. Inf. Model. 47 (6) (2007)
Kristin L. Meagher, Luke T. Redman, Heather A. Carlson
Development of polyphosphate parameters for use with the AMBER force field. J. Comput. Chem. 24 (9) (2003)
Michael J. Potter, Paul D. Kirchhoff, Heather A. Carlson, James Andrew McCammon
Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model. J. Comput. Chem. 20 (9) (1999)
Heather A. Carlson, Toan B. Nguyen, Modesto Orozco, William L. Jorgensen
Accuracy of free energies of hydration for organic molecules from 6-31g*-derived partial charges. J. Comput. Chem. 14 (10) (1993)