Heather A. Carlson

34 papers Journal 34

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2016	J	`jnl`	CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma.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