Heather A. Carlson - Publications

Chemistry University of Michigan, Ann Arbor, Ann Arbor, MI 
protein-ligand recognition, protein flexibility, and new methods for computer-aided drug discovery

82 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Smith RD, Clark JJ, Ahmed A, Orban ZJ, Dunbar JB, Carlson HA. Updates to Binding MOAD (Mother of All Databases): Polypharmacology Tools and Their Utility in Drug Repurposing. Journal of Molecular Biology. PMID 31125569 DOI: 10.1016/j.jmb.2019.05.024  0.96
2019 Ghanakota P, DasGupta D, Carlson HA. Free energies and entropies of binding sites identified by MixMD cosolvent simulations. Journal of Chemical Information and Modeling. PMID 31017411 DOI: 10.1021/acs.jcim.8b00925  0.36
2019 Clark JJ, Benson ML, Smith RD, Carlson HA. Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. Plos Computational Biology. 15: e1006705. PMID 30699115 DOI: 10.1371/journal.pcbi.1006705  0.96
2018 Graham S, Leja N, Carlson HA. MixMD Probeview: Robust Binding Site Prediction from Cosolvent Simulations. Journal of Chemical Information and Modeling. PMID 29905479 DOI: 10.1021/acs.jcim.8b00265  0.36
2017 Graham S, Smith RD, Carlson HA. Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics. Journal of Chemical Information and Modeling. PMID 29286658 DOI: 10.1021/acs.jcim.7b00268  0.96
2017 Smith RD, Lu J, Carlson HA. Are there physicochemical differences between allosteric and competitive ligands? Plos Computational Biology. 13: e1005813. PMID 29125840 DOI: 10.1371/journal.pcbi.1005813  0.96
2017 Ghanakota P, Carlson HA. Comparing pharmacophore models derived from crystallography and NMR ensembles. Journal of Computer-Aided Molecular Design. PMID 29047011 DOI: 10.1007/s10822-017-0077-7  0.36
2016 Gathiaka S, Liu S, Chiu M, Yang H, Stuckey JA, Kang YN, Delproposto J, Kubish G, Dunbar JB, Carlson HA, Burley SK, Walters WP, Amaro RE, Feher VA, Gilson MK. D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. Journal of Computer-Aided Molecular Design. 30: 651-668. PMID 27696240 DOI: 10.1007/s10822-016-9946-8  0.72
2016 Lu J, Carlson HA. ChemTreeMap: An Interactive Map of Biochemical Similarity in Molecular Datasets. Bioinformatics (Oxford, England). PMID 27515740 DOI: 10.1093/bioinformatics/btw523  0.6
2016 Ghanakota P, Carlson HA. Driving Structure Based Drug Discovery through Cosolvent Molecular Dynamics. Journal of Medicinal Chemistry. PMID 27486927 DOI: 10.1021/acs.jmedchem.6b00399  0.36
2016 Ghanakota P, Carlson HA. Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems. The Journal of Physical Chemistry. B. PMID 27258368 DOI: 10.1021/acs.jpcb.6b03515  0.36
2016 Carlson HA, Smith RD, Damm-Ganamet KL, Stuckey JA, Ahmed A, Convery MA, Somers DO, Kranz M, Elkins PA, Cui G, Peishoff CE, Lambert MH, Dunbar JB. CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma. Journal of Chemical Information and Modeling. PMID 27149958 DOI: 10.1021/acs.jcim.5b00523  1
2016 Graham SE, Zhang L, Ali I, Cho YK, Ismail MD, Carlson HA, Foxman B. Prevalence of CTX-M extended-spectrum beta-lactamases and O25b sequence type 131 in Korean blood, urine, and rectal Escherichia coli isolates. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. PMID 27101781 DOI: 10.1016/j.meegid.2016.04.020  0.36
2016 Graham SE, Tweedy SE, Carlson HA. Dynamic Behavior of the Post-SET Loop Region of NSD1: Implications for Histone Binding and Drug Development. Protein Science : a Publication of the Protein Society. PMID 26940890 DOI: 10.1002/pro.2912  1
2015 Smith RD, Damm-Ganamet KL, Dunbar JB, Ahmed A, Chinnaswamy K, Delproposto JE, Kubish GM, Tinberg CE, Khare SD, Dou J, Doyle L, Stuckey JA, Baker D, Carlson HA. CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. Journal of Chemical Information and Modeling. PMID 26419257 DOI: 10.1021/acs.jcim.5b00387  1
2015 Ung PM, Ghanakota P, Graham SE, Lexa KW, Carlson HA. Identifying binding hot spots on protein surfaces by mixed-solvent MD: HIV-1 protease as a test case. Biopolymers. PMID 26385317 DOI: 10.1002/bip.22742  1
2015 Xu H, Majmudar JD, Davda D, Ghanakota P, Kim KH, Carlson HA, Showalter HD, Martin BR, Amidon GL. Substrate-Competitive Activity-Based Profiling of Ester Prodrug Activating Enzymes. Molecular Pharmaceutics. 12: 3399-407. PMID 26262434 DOI: 10.1021/acs.molpharmaceut.5b00414  0.36
2015 Ahmed A, Smith RD, Clark JJ, Dunbar JB, Carlson HA. Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures. Nucleic Acids Research. 43: D465-9. PMID 25378330 DOI: 10.1093/nar/gku1088  1
2015 Xu H, Majmudar JD, Davda D, Ghanakota P, Kim KH, Carlson HA, Showalter HD, Martin BR, Amidon GL. Substrate-Competitive Activity-Based Profiling of Ester Prodrug Activating Enzymes Molecular Pharmaceutics. 12: 3399-3407. DOI: 10.1021/acs.molpharmaceut.5b00414  0.36
2014 Ung PM, Dunbar JB, Gestwicki JE, Carlson HA. An allosteric modulator of HIV-1 protease shows equipotent inhibition of wild-type and drug-resistant proteases. Journal of Medicinal Chemistry. 57: 6468-78. PMID 25062388 DOI: 10.1021/jm5008352  1
2014 Lexa KW, Goh GB, Carlson HA. Parameter choice matters: validating probe parameters for use in mixed-solvent simulations. Journal of Chemical Information and Modeling. 54: 2190-9. PMID 25058662 DOI: 10.1021/ci400741u  1
2013 Khazanov NA, Carlson HA. Exploring the composition of protein-ligand binding sites on a large scale. Plos Computational Biology. 9: e1003321. PMID 24277997 DOI: 10.1371/journal.pcbi.1003321  1
2013 Ung PM, Thompson AD, Chang L, Gestwicki JE, Carlson HA. Identification of key hinge residues important for nucleotide-dependent allostery in E. coli Hsp70/DnaK. Plos Computational Biology. 9: e1003279. PMID 24277995 DOI: 10.1371/journal.pcbi.1003279  1
2013 Carlson HA. Check your confidence: size really does matter. Journal of Chemical Information and Modeling. 53: 1837-41. PMID 23909878 DOI: 10.1021/ci4004249  1
2013 Dunbar JB, Smith RD, Damm-Ganamet KL, Ahmed A, Esposito EX, Delproposto J, Chinnaswamy K, Kang YN, Kubish G, Gestwicki JE, Stuckey JA, Carlson HA. CSAR data set release 2012: ligands, affinities, complexes, and docking decoys. Journal of Chemical Information and Modeling. 53: 1842-52. PMID 23617227 DOI: 10.1021/ci4000486  1
2013 Damm-Ganamet KL, Smith RD, Dunbar JB, Stuckey JA, Carlson HA. CSAR benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series. Journal of Chemical Information and Modeling. 53: 1853-70. PMID 23548044 DOI: 10.1021/ci400025f  1
2013 Davidson AE, Siddiqui FM, Lopez MA, Lunt P, Carlson HA, Moore BE, Love S, Born DE, Roper H, Majumdar A, Jayadev S, Underhill HR, Smith CO, von der Hagen M, Hubner A, et al. Novel deletion of lysine 7 expands the clinical, histopathological and genetic spectrum of TPM2-related myopathies. Brain : a Journal of Neurology. 136: 508-21. PMID 23413262 DOI: 10.1093/brain/aws344  1
2013 Lexa KW, Carlson HA. Improving protocols for protein mapping through proper comparison to crystallography data. Journal of Chemical Information and Modeling. 53: 391-402. PMID 23327200 DOI: 10.1021/ci300430v  1
2012 Khazanov NA, Damm-Ganamet KL, Quang DX, Carlson HA. Overcoming sequence misalignments with weighted structural superposition. Proteins. 80: 2523-35. PMID 22733542 DOI: 10.1002/prot.24134  1
2012 Smith RD, Engdahl AL, Dunbar JB, Carlson HA. Biophysical limits of protein-ligand binding. Journal of Chemical Information and Modeling. 52: 2098-106. PMID 22713103 DOI: 10.1021/ci200612f  1
2012 Lexa KW, Carlson HA. Protein flexibility in docking and surface mapping. Quarterly Reviews of Biophysics. 45: 301-43. PMID 22569329 DOI: 10.1017/S0033583512000066  1
2011 Carlson HA, Dunbar JB. A call to arms: what you can do for computational drug discovery. Journal of Chemical Information and Modeling. 51: 2025-6. PMID 21942243 DOI: 10.1021/ci200398g  1
2011 Smith RD, Dunbar JB, Ung PM, Esposito EX, Yang CY, Wang S, Carlson HA. CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions. Journal of Chemical Information and Modeling. 51: 2115-31. PMID 21809884 DOI: 10.1021/ci200269q  1
2011 Dunbar JB, Smith RD, Yang CY, Ung PM, Lexa KW, Khazanov NA, Stuckey JA, Wang S, Carlson HA. CSAR benchmark exercise of 2010: selection of the protein-ligand complexes. Journal of Chemical Information and Modeling. 51: 2036-46. PMID 21728306 DOI: 10.1021/ci200082t  1
2011 Lexa KW, Carlson HA. Binding to the open conformation of HIV-1 protease. Proteins. 79: 2282-90. PMID 21604303 DOI: 10.1002/prot.23054  1
2011 Spronk SA, Carlson HA. The role of tyrosine 71 in modulating the flap conformations of BACE1. Proteins. 79: 2247-59. PMID 21590744 DOI: 10.1002/prot.23050  1
2011 Chang L, Miyata Y, Ung PM, Bertelsen EB, McQuade TJ, Carlson HA, Zuiderweg ER, Gestwicki JE. Chemical screens against a reconstituted multiprotein complex: myricetin blocks DnaJ regulation of DnaK through an allosteric mechanism. Chemistry & Biology. 18: 210-21. PMID 21338918 DOI: 10.1016/j.chembiol.2010.12.010  1
2011 Lexa KW, Carlson HA. Full protein flexibility is essential for proper hot-spot mapping. Journal of the American Chemical Society. 133: 200-2. PMID 21158470 DOI: 10.1021/ja1079332  1
2011 Schuyler AD, Carlson HA, Feldman EL. Computational methods for identifying a layered allosteric regulatory mechanism for ALS-causing mutations of Cu-Zn superoxide dismutase 1. Proteins. 79: 417-27. PMID 21104697 DOI: 10.1002/prot.22892  1
2010 Reinke AA, Ung PM, Quintero JJ, Carlson HA, Gestwicki JE. Chemical probes that selectively recognize the earliest Aβ oligomers in complex mixtures. Journal of the American Chemical Society. 132: 17655-7. PMID 21105683 DOI: 10.1021/ja106291e  1
2010 Wisén S, Bertelsen EB, Thompson AD, Patury S, Ung P, Chang L, Evans CG, Walter GM, Wipf P, Carlson HA, Brodsky JL, Zuiderweg ER, Gestwicki JE. Binding of a small molecule at a protein-protein interface regulates the chaperone activity of hsp70-hsp40. Acs Chemical Biology. 5: 611-22. PMID 20481474 DOI: 10.1021/cb1000422  1
2010 Chang L, Thompson AD, Ung P, Carlson HA, Gestwicki JE. Mutagenesis reveals the complex relationships between ATPase rate and the chaperone activities of Escherichia coli heat shock protein 70 (Hsp70/DnaK). The Journal of Biological Chemistry. 285: 21282-91. PMID 20439464 DOI: 10.1074/jbc.M110.124149  1
2009 Schuyler AD, Carlson HA, Feldman EL. Computational methods for predicting sites of functionally important dynamics. The Journal of Physical Chemistry. B. 113: 6613-22. PMID 19378962 DOI: 10.1021/jp808736c  1
2009 Lexa KW, Damm KL, Quintero JJ, Gestwicki JE, Carlson HA. Clarifying allosteric control of flap conformations in the 1TW7 crystal structure of HIV-1 protease. Proteins. 74: 872-80. PMID 18704936 DOI: 10.1002/prot.22195  1
2008 Carlson HA, Smith RD, Khazanov NA, Kirchhoff PD, Dunbar JB, Benson ML. Differences between high- and low-affinity complexes of enzymes and nonenzymes. Journal of Medicinal Chemistry. 51: 6432-41. PMID 18826206 DOI: 10.1021/jm8006504  1
2008 Lerner MG, Meagher KL, Carlson HA. Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design. Journal of Computer-Aided Molecular Design. 22: 727-36. PMID 18679808 DOI: 10.1007/s10822-008-9231-6  1
2008 Damm KL, Ung PM, Quintero JJ, Gestwicki JE, Carlson HA. A poke in the eye: inhibiting HIV-1 protease through its flap-recognition pocket. Biopolymers. 89: 643-52. PMID 18381626 DOI: 10.1002/bip.20993  1
2008 Benson ML, Smith RD, Khazanov NA, Dimcheff B, Beaver J, Dresslar P, Nerothin J, Carlson HA. Binding MOAD, a high-quality protein-ligand database. Nucleic Acids Research. 36: D674-8. PMID 18055497 DOI: 10.1093/nar/gkm911  1
2007 Bowman AL, Nikolovska-Coleska Z, Zhong H, Wang S, Carlson HA. Small molecule inhibitors of the MDM2-p53 interaction discovered by ensemble-based receptor models. Journal of the American Chemical Society. 129: 12809-14. PMID 17902662 DOI: 10.1021/ja073687x  1
2007 Lerner MG, Bowman AL, Carlson HA. Incorporating dynamics in E. coli dihydrofolate reductase enhances structure-based drug discovery. Journal of Chemical Information and Modeling. 47: 2358-65. PMID 17877338 DOI: 10.1021/ci700167n  1
2007 Damm KL, Carlson HA. Exploring experimental sources of multiple protein conformations in structure-based drug design. Journal of the American Chemical Society. 129: 8225-35. PMID 17555316 DOI: 10.1021/ja0709728  1
2007 Bowman AL, Lerner MG, Carlson HA. Protein flexibility and species specificity in structure-based drug discovery: dihydrofolate reductase as a test system. Journal of the American Chemical Society. 129: 3634-40. PMID 17335207 DOI: 10.1021/ja068256d  1
2006 Meagher KL, Lerner MG, Carlson HA. Refining the multiple protein structure pharmacophore method: consistency across three independent HIV-1 protease models. Journal of Medicinal Chemistry. 49: 3478-84. PMID 16759090 DOI: 10.1021/jm050755m  1
2006 Damm KL, Carlson HA. Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures. Biophysical Journal. 90: 4558-73. PMID 16565070 DOI: 10.1529/biophysj.105.066654  1
2006 Smith RD, Hu L, Falkner JA, Benson ML, Nerothin JP, Carlson HA. Exploring protein-ligand recognition with Binding MOAD. Journal of Molecular Graphics & Modelling. 24: 414-25. PMID 16168689 DOI: 10.1016/j.jmgm.2005.08.002  1
2006 Zhong H, Carlson HA. Conformational studies of polyprolines Journal of Chemical Theory and Computation. 2: 342-353. DOI: 10.1021/ct050182t  1
2005 Kravitz JY, Pecoraro VL, Carlson HA. Quantum Mechanics/Molecular Mechanics Calculations of the Vanadium Dependent Chloroperoxidase. Journal of Chemical Theory and Computation. 1: 1265-74. PMID 26631670 DOI: 10.1021/ct050132o  0.6
2005 Tan XJ, Carlson HA. Docking studies and ligand recognition in folylpolyglutamate synthetase. Journal of Medicinal Chemistry. 48: 7764-72. PMID 16302815 DOI: 10.1021/jm0507734  1
2005 Hu L, Benson ML, Smith RD, Lerner MG, Carlson HA. Binding MOAD (Mother Of All Databases). Proteins. 60: 333-40. PMID 15971202 DOI: 10.1002/prot.20512  1
2005 Todorov KA, Tan XJ, Nonekowski ST, Garcia GA, Carlson HA. The role of aspartic acid 143 in E. coli tRNA-guanine transglycosylase: insights from mutagenesis studies and computational modeling. Biophysical Journal. 89: 1965-77. PMID 15951383 DOI: 10.1529/biophysj.105.059576  1
2005 Meagher KL, Carlson HA. Solvation influences flap collapse in HIV-1 protease. Proteins. 58: 119-25. PMID 15521062 DOI: 10.1002/prot.20274  1
2005 Zhong H, Carlson HA. Computational studies and peptidomimetic design for the human p53-MDM2 complex. Proteins. 58: 222-34. PMID 15505803 DOI: 10.1002/prot.20275  1
2005 Kravitz JY, Pecoraro VL, Carlson HA. Quantum mechanics/molecular mechanics calculations of the vanadium dependent chloroperoxidase Journal of Chemical Theory and Computation. 1: 1265-1274. DOI: 10.1021/ct050132o  1
2004 Meagher KL, Carlson HA. Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case. Journal of the American Chemical Society. 126: 13276-81. PMID 15479081 DOI: 10.1021/ja0469378  1
2004 Zampella G, Kravitz JY, Webster CE, Fantucci P, Hall MB, Carlson HA, Pecoraro VL, De Luca L. Quantum mechanical models of the resting state of the vanadium-dependent haloperoxidase. Inorganic Chemistry. 43: 4127-36. PMID 15236524 DOI: 10.1021/ic0353256  1
2003 Huck BR, Fisk JD, Guzei IA, Carlson HA, Gellman SH. Secondary structural preferences of 2,2-disubstituted pyrrolidine-4-carboxylic acid oligomers: beta-peptide foldamers that cannot form internal hydrogen bonds. Journal of the American Chemical Society. 125: 9035-7. PMID 15369358 DOI: 10.1021/ja034561c  1
2003 Sandvoss LM, Carlson HA. Conformational behavior of beta-proline oligomers. Journal of the American Chemical Society. 125: 15855-62. PMID 14677977 DOI: 10.1021/ja036471d  1
2003 Meagher KL, Redman LT, Carlson HA. Development of polyphosphate parameters for use with the AMBER force field. Journal of Computational Chemistry. 24: 1016-25. PMID 12759902 DOI: 10.1002/jcc.10262  1
2002 Carlson HA. Protein flexibility and drug design: how to hit a moving target. Current Opinion in Chemical Biology. 6: 447-52. PMID 12133719 DOI: 10.1016/S1367-5931(02)00341-1  1
2002 Carlson HA. Protein flexibility is an important component of structure-based drug discovery. Current Pharmaceutical Design. 8: 1571-8. PMID 12052201 DOI: 10.2174/1381612023394232  1
2000 Carlson HA, Masukawa KM, Rubins K, Bushman FD, Jorgensen WL, Lins RD, Briggs JM, McCammon JA. Developing a dynamic pharmacophore model for HIV-1 integrase. Journal of Medicinal Chemistry. 43: 2100-14. PMID 10841789 DOI: 10.1021/jm990322h  1
2000 Carlson HA, McCammon JA. Accommodating protein flexibility in computational drug design. Molecular Pharmacology. 57: 213-8. PMID 10648630  1
1999 Lins RD, Briggs JM, Straatsma TP, Carlson HA, Greenwald J, Choe S, McCammon JA. Molecular dynamics studies on the HIV-1 integrase catalytic domain. Biophysical Journal. 76: 2999-3011. PMID 10354426  1
1999 Carlson HA, Briggs JM, McCammon JA. Calculation of the pKa values for the ligands and side chains of Escherichia coli D-alanine:D-alanine ligase. Journal of Medicinal Chemistry. 42: 109-17. PMID 9888837 DOI: 10.1021/jm980351c  1
1999 Carlson HA, Masukawa KM, McCammon JA. Method for including the dynamic fluctuations of a protein in computer-aided drug design Journal of Physical Chemistry A. 103: 10213-10219.  1
1999 Potter MJ, Kirchhoff PD, Carlson HA, Mccammon JA. Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model Journal of Computational Chemistry. 20: 956-970.  1
1997 McDonald NA, Carlson HA, Jorgensen WL. Free energies of solvation in chloroform and water from a linear response approach Journal of Physical Organic Chemistry. 10: 563-576.  1
1996 Carlson HA, Jorgensen WL. Monte Carlo investigations of solvent effects on the chorismate to prephenate rearrangement Journal of the American Chemical Society. 118: 8475-8484. DOI: 10.1021/ja961500o  1
1995 Carlson HA, Jorgensen WL. Investigations into the stereochemistry of cyclophane-steroid complexes via Monte Carlo simulations Tetrahedron. 51: 449-472. DOI: 10.1016/0040-4020(94)00908-D  1
1995 Carlson HA, Jorgensen WL. An extended linear response method for determining free energies of hydration Journal of Physical Chemistry. 99: 10667-10673.  1
1993 Carlson HA, Nguyen TB, Orozco M, Jorgensen WL. Accuracy of free energies of hydration for organic molecules from 6-31G-derived partial charges Journal of Computational Chemistry. 14: 1240-1249.  1
1992 Carlson HA, Quelch GE, Schaefer HF. How "stable" is cyclobutyne? The activation energy for the unimolecular rearrangement to butatriene Journal of the American Chemical Society. 114: 5344-5348.  1
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