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Author Details

Heather A Carlson
University of Michigan ann arbor
1999
88
35
PMIDPaper TitleJournal TitlePublished Year
37141501Identifying Potential Ligand Binding Sites on Glycogen Synthase Kinase 3 Using Atomistic Cosolvent Simulations.ACS Appl Bio Mater2024
36868791Application of Mixed-Solvent Molecular Dynamics Simulations for Prediction of Allosteric Sites on G Protein-Coupled Receptors.Mol Pharmacol2023
36810894Sunsetting Binding MOAD with its last data update and the addition of 3D-ligand polypharmacology tools.Sci Rep2023
35107014Computational Identification of Possible Allosteric Sites and Modulators of the SARS-CoV-2 Main Protease.J Chem Inf Model2022
35351926In silico analysis of SARS-CoV-2 proteins as targets for clinically available drugs.Sci Rep2022
35533286Cosolvent Simulations with Fragment-Bound Proteins Identify Hot Spots to Direct Lead Growth.J Chem Theory Comput2022
35923912Argonaute 2 modulates EGFR-RAS signaling to promote mutant <i>HRAS</i> and <i>NRAS-</i>driven malignancies.PNAS Nexus2022
35944583The structure and characterization of human cytochrome P450 8B1 supports future drug design for nonalcoholic fatty liver disease and diabetes.J Biol Chem2022
34520464Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge.PLoS Comput Biol2021
33599485Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics.J Chem Inf Model2021
33549906Chemical validation of a druggable site on Hsp27/HSPB1 using in silico solvent mapping and biophysical methods.Bioorg Med Chem2021
34494289Mixed-solvent molecular dynamics simulation-based discovery of a putative allosteric site on regulator of G protein signaling 4.J Comput Chem2021
32985584Predicting binding sites from unbound versus bound protein structures.Sci Rep2020
30699115Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures.PLoS Comput Biol2019
31017411Free Energies and Entropies of Binding Sites Identified by MixMD Cosolvent Simulations.J Chem Inf Model2019
31125569Updates to Binding MOAD (Mother of All Databases): Polypharmacology Tools and Their Utility in Drug Repurposing.J Mol Biol2019
29286658Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics.J Chem Inf Model2018
29905479MixMD Probeview: Robust Binding Site Prediction from Cosolvent Simulations.J Chem Inf Model2018
29047011Comparing pharmacophore models derived from crystallography and NMR ensembles.J Comput Aided Mol Des2017
29125840Are there physicochemical differences between allosteric and competitive ligands?PLoS Comput Biol2017
29272700Multi-targeting Drug Community Challenge.Cell Chem Biol2017
27101781Prevalence of CTX-M extended-spectrum beta-lactamases and sequence type 131 in Korean blood, urine, and rectal Escherichia coli isolates.Infect Genet Evol2016
26385317Identifying binding hot spots on protein surfaces by mixed-solvent molecular dynamics: HIV-1 protease as a test case.Biopolymers2016
26419257CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge.J Chem Inf Model2016
27696240D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.J Comput Aided Mol Des2016
27149958CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma.J Chem Inf Model2016
27258368Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems.J Phys Chem B2016
27345761Lessons Learned over Four Benchmark Exercises from the Community Structure-Activity Resource.J Chem Inf Model2016
27515740ChemTreeMap: an interactive map of biochemical similarity in molecular datasets.Bioinformatics2016
27486927Driving Structure-Based Drug Discovery through Cosolvent Molecular Dynamics.J Med Chem2016
26940890Dynamic behavior of the post-SET loop region of NSD1: Implications for histone binding and drug development.Protein Sci2016
25378330Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures.Nucleic Acids Res2015
26262434Substrate-Competitive Activity-Based Profiling of Ester Prodrug Activating Enzymes.Mol Pharm2015
25058662Parameter choice matters: validating probe parameters for use in mixed-solvent simulations.J Chem Inf Model2014
25481987The 12-minute journey.Narrat Inq Bioeth2014
25062388An allosteric modulator of HIV-1 protease shows equipotent inhibition of wild-type and drug-resistant proteases.J Med Chem2014
23327200Improving protocols for protein mapping through proper comparison to crystallography data.J Chem Inf Model2013
24277997Exploring the composition of protein-ligand binding sites on a large scale.PLoS Comput Biol2013
24277995Identification of key hinge residues important for nucleotide-dependent allostery in E. coli Hsp70/DnaK.PLoS Comput Biol2013
23909878Check your confidence: size really does matter.J Chem Inf Model2013
23617227CSAR data set release 2012: ligands, affinities, complexes, and docking decoys.J Chem Inf Model2013
23413262Novel deletion of lysine 7 expands the clinical, histopathological and genetic spectrum of TPM2-related myopathies.Brain2013
23548044CSAR benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series.J Chem Inf Model2013
22569329Protein flexibility in docking and surface mapping.Q Rev Biophys2012
22733542Overcoming sequence misalignments with weighted structural superposition.Proteins2012
22713103Biophysical limits of protein-ligand binding.J Chem Inf Model2012
21158470Full protein flexibility is essential for proper hot-spot mapping.J Am Chem Soc2011
21809884CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions.J Chem Inf Model2011
21942243A call to arms: what you can do for computational drug discovery.J Chem Inf Model2011
21590744The role of tyrosine 71 in modulating the flap conformations of BACE1.Proteins2011
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Collaborators

Jason E Gestwicki
Institute for Neurodegenerative Diseases, University of California San Francisco
Co-authored papers 10
Peter Man-Un Ung
Co-authored papers 10
James Andrew McCammon
Co-authored papers 4
Kristen K Dang
Benaroya Research Institute at Virginia Mason
Co-authored papers 2
Ruben Abagyan
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California
Co-authored papers 2
Justin Guinney
University of Washington
Co-authored papers 2
Ross L Cagan
University of Glasgow
Co-authored papers 2
Avner Schlessinger
Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai
Co-authored papers 2
Stephen K Burley
The State University of New Jersey
Co-authored papers 1
Rommie E Amaro
University of California
Co-authored papers 1
Sagar D Khare
The State University of New Jersey
Co-authored papers 1
Chana Hecht
Icahn School of Medicine at Mount Sinai
Co-authored papers 1
Xuhong Cao
Michigan Center for Translational Pathology.
Co-authored papers 1
David Baker
University of Washington
Co-authored papers 1
Mingyue Zheng
Shanghai Institute of Materia Medica, Chinese Academy of Sciences
Co-authored papers 1
Tirtha K Das
Icahn School of Medicine at Mount Sinai
Co-authored papers 1
Huanwang Yang
The State University of New Jersey
Co-authored papers 1
Hwisang Jeon
Korea University
Co-authored papers 1
Aik Choon Tan
Huntsman Cancer Institute, The University of Utah
Co-authored papers 1
Victoria A Feher
University of California San Diego
Co-authored papers 1
Tjerk P Straatsma
Co-authored papers 1
Michael K Gilson
University of California
Co-authored papers 1
Frederic D Bushman
Perelman School of Medicine, University of Pennsylvania
Co-authored papers 1
Jaewoo Kang
Korea University
Co-authored papers 1
Jinhyuk Lee
Korea University
Co-authored papers 1
Donghyeon Park
Korea University
Co-authored papers 1
Shuai Liu
XtalPi Inc.
Co-authored papers 1
Minji Jeon
Korea University College of Medicine
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Zhaoping Xiong
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Release 1.2