H. Carlson

H. Carlson, Ihsan Ali, B. Foxman, 2016, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

Argonaute 2 modulates EGFR–RAS signaling to promote mutant HRAS and NRAS-driven malignancies

A. Chinnaiyan, H. Carlson, Xuhong Cao, 2022, PNAS nexus.

The structure and characterization of human cytochrome P450 8B1 supports future drug design for nonalcoholic fatty liver disease and diabetes

H. Carlson, E. Scott, Jinghan Liu, 2022, The Journal of biological chemistry.

Investigations into the stereochemistry of cyclophane-steroid complexes via Monte Carlo simulations

W. L. Jorgensen, H. Carlson, 1995 .

A poke in the eye: inhibiting HIV-1 protease through its flap-recognition pocket.

H. Carlson, J. Gestwicki, P. Ung, 2008, Biopolymers.

Cosolvent Simulations with Fragment-Bound Proteins Identify Hot Spots to Direct Lead Growth.

H. Carlson, Pancham Lal Gupta, 2022, Journal of chemical theory and computation.

Monte Carlo Investigations of Solvent Effects on the Chorismate to Prephenate Rearrangement

W. L. Jorgensen, H. Carlson, 1996 .

Chemical validation of a druggable site on Hsp27/HSPB1 using in silico solvent mapping and biophysical methods.

H. Carlson, T. Cierpicki, Phani Ghanakota, 2021, Bioorganic & medicinal chemistry.

Small molecule inhibitors of the MDM2-p53 interaction discovered by ensemble-based receptor models.

Heather A Carlson, Anna L. Bowman, H. Carlson, 2007, Journal of the American Chemical Society.

Quantum mechanical models of the resting state of the vanadium-dependent haloperoxidase.

Heather A Carlson, Piercarlo Fantucci, C. E. Webster, 2004, Inorganic chemistry.

Binding to the open conformation of HIV‐1 protease

Katrina W. Lexa, H. Carlson, 2011, Proteins.

Computational studies and peptidomimetic design for the human p53–MDM2 complex

H. Carlson, Haizhen A. Zhong, 2004, Proteins.

Secondary structural preferences of 2,2-disubstituted pyrrolidine-4-carboxylic acid oligomers: beta-peptide foldamers that cannot form internal hydrogen bonds.

H. Carlson, S. Gellman, B. Huck, 2003, Journal of the American Chemical Society.

Development of polyphosphate parameters for use with the AMBER force field

Heather A. Carlson, Kristin L. Meagher, Luke T. Redman, 2003, J. Comput. Chem..

Differences between high- and low-affinity complexes of enzymes and nonenzymes.

Heather A Carlson, Mark L. Benson, James B Dunbar, 2008, Journal of medicinal chemistry.

Substrate-Competitive Activity-Based Profiling of Ester Prodrug Activating Enzymes.

Brent R. Martin, H. Carlson, G. Amidon, 2015, Molecular pharmaceutics.

Binding MOAD, a high-quality protein–ligand database

Richard D. Smith, Heather A. Carlson, John E. Beaver, 2007, Nucleic Acids Res..

Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge

Kristen K. Dang, Robert J. Allaway, R. Abagyan, 2021, bioRxiv.

Dynamic behavior of the post‐SET loop region of NSD1: Implications for histone binding and drug development

H. Carlson, Sarah E. Graham, S. Tweedy, 2016, Protein science : a publication of the Protein Society.

Binding of a small molecule at a protein-protein interface regulates the chaperone activity of hsp70-hsp40.

H. Carlson, P. Wipf, E. Zuiderweg, 2010, ACS chemical biology.

Molecular dynamics studies on the HIV-1 integrase catalytic domain.

J A McCammon, H A Carlson, J M Briggs, 1999, Biophysical journal.

Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures.

Heather A Carlson, H. Carlson, Kelly L. Damm, 2006, Biophysical journal.

CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys

Richard D. Smith, Heather A. Carlson, Emilio Xavier Esposito, 2013, J. Chem. Inf. Model..

Chemical screens against a reconstituted multiprotein complex: myricetin blocks DnaJ regulation of DnaK through an allosteric mechanism.

H. Carlson, E. Zuiderweg, J. Gestwicki, 2011, Chemistry & biology.

Exploring the Composition of Protein-Ligand Binding Sites on a Large Scale

Heather A. Carlson, Nickolay A. Khazanov, H. Carlson, 2013, PLoS Comput. Biol..

CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes

Richard D. Smith, Heather A. Carlson, Shaomeng Wang, 2011, J. Chem. Inf. Model..

Solvation influences flap collapse in HIV‐1 protease

H. Carlson, Kristin L. Meagher, Heather A. Carlson, 2004, Proteins.

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge

Richard D. Smith, Heather A. Carlson, David Baker, 2016, J. Chem. Inf. Model..

Comparing pharmacophore models derived from crystallography and NMR ensembles

Heather A. Carlson, Phani Ghanakota, H. Carlson, 2017, Journal of Computer-Aided Molecular Design.

Computational methods for predicting sites of functionally important dynamics.

H. Carlson, A. Schuyler, E. Feldman, 2009, The journal of physical chemistry. B.

Incorporating Dynamics in E. coli Dihydrofolate Reductase Enhances Structure-Based Drug Discovery

Heather A. Carlson, Michael G. Lerner, Anna L. Bowman, 2007, J. Chem. Inf. Model..

CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma

Richard D. Smith, Heather A. Carlson, Aqeel Ahmed, 2016, J. Chem. Inf. Model..

CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series

Richard D. Smith, Heather A. Carlson, James B. Dunbar, 2013, J. Chem. Inf. Model..

Accommodating protein flexibility in computational drug design.

J A McCammon, H A Carlson, J. Mccammon, 2000, Molecular pharmacology.

Updates to Binding MOAD (Mother of All Databases): Polypharmacology Tools and Their Utility in Drug Repurposing.

Heather A Carlson, Richard D Smith, Jordan J. Clark, 2019, Journal of molecular biology.

Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case.

Heather A Carlson, H. Carlson, Kristin L Meagher, 2004, Journal of the American Chemical Society.

Protein flexibility in docking and surface mapping

Katrina W Lexa, Heather A Carlson, Katrina W. Lexa, 2012, Quarterly Reviews of Biophysics.

D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions

Shuai Liu, Huanwang Yang, Stephen K. Burley, 2016, Journal of Computer-Aided Molecular Design.

Biophysical Limits of Protein-Ligand Binding

Heather A. Carlson, James B. Dunbar, Richard D. Smith, 2012, Journal of Chemical Information and Modeling.

The role of aspartic acid 143 in E. coli tRNA-guanine transglycosylase: insights from mutagenesis studies and computational modeling.

H. Carlson, G. Garcia, S. Nonekowski, 2005, Biophysical journal.

Accommodating Protein Flexibility in Computational Drug Design 1 , 2

J. Mccammon, H. Carlson, HEATHER A. CARLSON, 2000 .

Free energies of solvation in chloroform and water from a linear response approach

Heather A. Carlson, William L. Jorgensen, W. L. Jorgensen, 1997 .

Accuracy of free energies of hydration for organic molecules from 6‐31g*‐derived partial charges

Heather A. Carlson, William L. Jorgensen, Modesto Orozco, 1993, J. Comput. Chem..

Protein flexibility is an important component of structure-based drug discovery.

Heather A Carlson, H. Carlson, 2002, Current pharmaceutical design.

Parameter Choice Matters: Validating Probe Parameters for Use in Mixed-Solvent Simulations

Heather A. Carlson, Garrett B. Goh, Katrina W. Lexa, 2014, J. Chem. Inf. Model..

Identification of Key Hinge Residues Important for Nucleotide-Dependent Allostery in E. coli Hsp70/DnaK

Heather A. Carlson, Peter Man-Un Ung, Andrea D. Thompson, 2013, PLoS Comput. Biol..

Multi-targeting Drug Community Challenge.

Avner Schlessinger, Ruben Abagyan, Justin Guinney, 2017, Cell chemical biology.

Conformational Studies of Polyprolines.

H. Carlson, Haizhen A. Zhong, 2006, Journal of chemical theory and computation.

Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures

Heather A Carlson, Richard D Smith, Jordan J. Clark, 2019, PLoS Comput. Biol..

In silico analysis of SARS-CoV-2 proteins as targets for clinically available drugs

H. Carlson, J. Traynor, Wallace K. B. Chan, 2022, Scientific Reports.

Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data

Heather A. Carlson, Katrina W. Lexa, H. Carlson, 2013, J. Chem. Inf. Model..

Recent improvements to Binding MOAD: a resource for protein–ligand binding affinities and structures

Richard D. Smith, Heather A. Carlson, Aqeel Ahmed, 2014, Nucleic Acids Res..

Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics

Heather A. Carlson, Richard D. Smith, H. Carlson, 2021, J. Chem. Inf. Model..

Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics

Heather A. Carlson, Richard D. Smith, Sarah E. Graham, 2018, J. Chem. Inf. Model..

Free Energies and Entropies of Binding Sites Identified by MixMD Cosolvent Simulations

Heather A Carlson, Debarati DasGupta, Phani Ghanakota, 2019, J. Chem. Inf. Model..

MixMD Probeview: Robust Binding Site Prediction from Cosolvent Simulations

Heather A Carlson, Sarah E Graham, Noah Leja, 2018, J. Chem. Inf. Model..

Chemical probes that selectively recognize the earliest Aβ oligomers in complex mixtures.

H. Carlson, J. Gestwicki, P. Ung, 2010, Journal of the American Chemical Society.

Docking studies and ligand recognition in folylpolyglutamate synthetase.

H. Carlson, Xiao-Jian Tan, 2005, Journal of medicinal chemistry.

ChemTreeMap: an interactive map of biochemical similarity in molecular datasets

Jing Lu, Heather A. Carlson, H. Carlson, 2016, Bioinform..

CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions

Richard D. Smith, Heather A. Carlson, Emilio Xavier Esposito, 2011, J. Chem. Inf. Model..

Identifying Potential Ligand Binding Sites on Glycogen Synthase Kinase 3 Using Atomistic Cosolvent Simulations.

H. Carlson, Sumit Sharma, Ramin Mehrani, 2023, ACS applied bio materials.

Computational Identification of Possible Allosteric Sites and Modulators of the SARS-CoV-2 Main Protease

H. Carlson, Wallace K. B. Chan, Debarati DasGupta, 2022, J. Chem. Inf. Model..

Sunsetting Binding MOAD with its last data update and the addition of 3D-ligand polypharmacology tools

H. Carlson, S. Tripathi, Swapnil Wagle, 2023, Scientific Reports.

Are there physicochemical differences between allosteric and competitive ligands?

Jing Lu, Richard D. Smith, Heather A. Carlson, 2017, PLoS Comput. Biol..

Mutagenesis Reveals the Complex Relationships between ATPase Rate and the Chaperone Activities of Escherichia coli Heat Shock Protein 70 (Hsp70/DnaK)*

H. Carlson, J. Gestwicki, P. Ung, 2010, The Journal of Biological Chemistry.

Differences between high- and low-affinity complexes of enzymes and nonenzymes.

Mark L. Benson, Richard D. Smith, H. Carlson, 2008, Journal of Medicinal Chemistry.

Biophysical Limits of Protein-Ligand Binding

Alaina L. Engdahl, Richard D. Smith, H. Carlson, 2012, J. Chem. Inf. Model..

Lessons Learned over Four Benchmark Exercises from the Community Structure-Activity Resource

Heather A. Carlson, H. Carlson, 2016, J. Chem. Inf. Model..

Check Your Confidence: Size Really Does Matter

Heather A. Carlson, H. Carlson, 2013, J. Chem. Inf. Model..

UPDATING BINDING MOAD — DATA MANAGEMENT AND INFORMATION WORKFLOW

Heather A. Carlson, Nickolay A. Khazanov, Richard D. Smith, 2010 .