List of works - Heather A Carlson

A call to arms: what you can do for computational drug discovery

scientific article published on 01 September 2011

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

scientific article

An allosteric modulator of HIV-1 protease shows equipotent inhibition of wild-type and drug-resistant proteases

scientific article

Association of common genetic variants in GPCPD1 with scaling of visual cortical surface area in humans

scientific article published on 16 February 2012

Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design.

scientific article

Binding MOAD (Mother Of All Databases)

scientific article published on 01 August 2005

Binding MOAD, a high-quality protein-ligand database.

scientific article

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

scientific article

Binding to the open conformation of HIV-1 protease

scientific article

Biophysical Limits of Protein–Ligand Binding ⬇️

scientific article published on July 18, 2012

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

scientific article published on May 10, 2013

CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions.

scientific article

CSAR benchmark exercise of 2010: selection of the protein-ligand complexes.

scientific article

CSAR data set release 2012: ligands, affinities, complexes, and docking decoys

scientific article

Check Your Confidence: Size Really Does Matter ⬇️

scientific article published on 08 August 2013

Chemical Screens against a Reconstituted Multiprotein Complex: Myricetin Blocks DnaJ Regulation of DnaK through an Allosteric Mechanism ⬇️

scientific article published on February 25, 2011

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

scientific article published on 24 November 2010

Clarifying allosteric control of flap conformations in the 1TW7 crystal structure of HIV-1 protease.

scientific article published on March 2009

Comparing pharmacophore models derived from crystallography and NMR ensembles

scientific article

Computational methods for identifying a layered allosteric regulatory mechanism for ALS‐causing mutations of Cu‐Zn superoxide dismutase 1 ⬇️

scientific article published on February 1, 2011

Computational methods for predicting sites of functionally important dynamics.

scientific article published on May 2009

Conformational Studies of Polyprolines

scientific article published on 01 March 2006

Conformational behavior of beta-proline oligomers.

scientific article published in December 2003

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

scientific article published on 09 May 2022

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

scientific article published on 14 September 2021

Development of polyphosphate parameters for use with the AMBER force field.

scientific article published in July 2003

Docking studies and ligand recognition in folylpolyglutamate synthetase.

scientific article

Exploring experimental sources of multiple protein conformations in structure-based drug design.

scientific article

Exploring protein-ligand recognition with Binding MOAD

scientific article published on 15 September 2005

Exploring the composition of protein-ligand binding sites on a large scale

scientific article (publication date: 2013)

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

scientific article published on 02 May 2019

Full protein flexibility is essential for proper hot-spot mapping.

scientific article

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

scientific article published on 18 February 2021

Identification of key hinge residues important for nucleotide-dependent allostery in E. coli Hsp70/DnaK

scientific article (publication date: 2013)

Identifying binding hot spots on protein surfaces by mixed-solvent molecular dynamics: HIV-1 protease as a test case

scientific article

Improving protocols for protein mapping through proper comparison to crystallography data

scientific article

Incorporating dynamics in E. coli dihydrofolate reductase enhances structure-based drug discovery.

scientific article published on 18 September 2007

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

scientific article published on 01 October 2004

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

scientific article published on 30 January 2019

MixMD Probeview: Robust Binding Site Prediction from Cosolvent Simulations

scientific article published on 26 June 2018

Novel deletion of lysine 7 expands the clinical, histopathological and genetic spectrum of TPM2-related myopathies.

scientific article published on February 2013

Parameter choice matters: validating probe parameters for use in mixed-solvent simulations.

scientific article

Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics

scientific article

Protein flexibility and drug design: how to hit a moving target.

scientific article

Protein flexibility in docking and surface mapping

scientific article

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

scientific article

Quantum Mechanics/Molecular Mechanics Calculations of the Vanadium Dependent Chloroperoxidase

scientific article published on 01 November 2005

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

scientific article

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

scientific article published on 01 July 2003

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

scientific article

Solvation influences flap collapse in HIV-1 protease

scientific article published on 01 January 2005

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

scientific article

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

scientific article

The role of tyrosine 71 in modulating the flap conformations of BACE1.

scientific article published on 16 May 2011

List of works by Heather A Carlson

A call to arms: what you can do for computational drug discovery

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

An allosteric modulator of HIV-1 protease shows equipotent inhibition of wild-type and drug-resistant proteases

Association of common genetic variants in GPCPD1 with scaling of visual cortical surface area in humans

Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design.

Binding MOAD (Mother Of All Databases)

Binding MOAD, a high-quality protein-ligand database.

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

Binding to the open conformation of HIV-1 protease

Biophysical Limits of Protein–Ligand Binding ⬇️

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

CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions.

CSAR benchmark exercise of 2010: selection of the protein-ligand complexes.

CSAR data set release 2012: ligands, affinities, complexes, and docking decoys

Check Your Confidence: Size Really Does Matter ⬇️

Chemical Screens against a Reconstituted Multiprotein Complex: Myricetin Blocks DnaJ Regulation of DnaK through an Allosteric Mechanism ⬇️

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

Clarifying allosteric control of flap conformations in the 1TW7 crystal structure of HIV-1 protease.

Comparing pharmacophore models derived from crystallography and NMR ensembles

Computational methods for identifying a layered allosteric regulatory mechanism for ALS‐causing mutations of Cu‐Zn superoxide dismutase 1 ⬇️

Computational methods for predicting sites of functionally important dynamics.

Conformational Studies of Polyprolines

Conformational behavior of beta-proline oligomers.

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

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

Development of polyphosphate parameters for use with the AMBER force field.

Docking studies and ligand recognition in folylpolyglutamate synthetase.

Exploring experimental sources of multiple protein conformations in structure-based drug design.

Exploring protein-ligand recognition with Binding MOAD

Exploring the composition of protein-ligand binding sites on a large scale

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

Full protein flexibility is essential for proper hot-spot mapping.

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

Identification of key hinge residues important for nucleotide-dependent allostery in E. coli Hsp70/DnaK

Identifying binding hot spots on protein surfaces by mixed-solvent molecular dynamics: HIV-1 protease as a test case

Improving protocols for protein mapping through proper comparison to crystallography data

Incorporating dynamics in E. coli dihydrofolate reductase enhances structure-based drug discovery.

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

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

MixMD Probeview: Robust Binding Site Prediction from Cosolvent Simulations

Novel deletion of lysine 7 expands the clinical, histopathological and genetic spectrum of TPM2-related myopathies.

Parameter choice matters: validating probe parameters for use in mixed-solvent simulations.

Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics

Protein flexibility and drug design: how to hit a moving target.

Protein flexibility in docking and surface mapping

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

Quantum Mechanics/Molecular Mechanics Calculations of the Vanadium Dependent Chloroperoxidase

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

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

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

Solvation influences flap collapse in HIV-1 protease

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

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

The role of tyrosine 71 in modulating the flap conformations of BACE1.