Heather A Carlson

Heather A Carlson

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Heather A Carlson

Heather A Carlson

Publications by authors named "Heather A Carlson"

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

J Mol Biol 2019 Jun 22;431(13):2423-2433. Epub 2019 May 22.

Department of Medicinal Chemistry, University of Michigan-Ann Arbor, 428 Church Street, Ann Arbor, MI 48109-1065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.05.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6589129PMC
June 2019

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

J Chem Inf Model 2019 May 2;59(5):2035-2045. Epub 2019 May 2.

Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States.

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http://pubs.acs.org/doi/10.1021/acs.jcim.8b00925
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http://dx.doi.org/10.1021/acs.jcim.8b00925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6549510PMC
May 2019

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

PLoS Comput Biol 2019 01 30;15(1):e1006705. Epub 2019 Jan 30.

Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006705DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6370239PMC
January 2019

Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics.

J Chem Inf Model 2018 02 16;58(2):305-314. Epub 2018 Jan 16.

Department of Biophysics and ‡Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States.

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http://dx.doi.org/10.1021/acs.jcim.7b00268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6190669PMC
February 2018

Multi-targeting Drug Community Challenge.

Cell Chem Biol 2017 12;24(12):1434-1435

Department of Cell, Developmental and Regenerative Biology and School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2017.12.006DOI Listing
December 2017

Comparing pharmacophore models derived from crystallography and NMR ensembles.

J Comput Aided Mol Des 2017 Nov 19;31(11):979-993. Epub 2017 Oct 19.

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, MI, 48109-1065, USA.

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http://dx.doi.org/10.1007/s10822-017-0077-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6549502PMC
November 2017

Are there physicochemical differences between allosteric and competitive ligands?

PLoS Comput Biol 2017 Nov 10;13(11):e1005813. Epub 2017 Nov 10.

Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005813DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5699844PMC
November 2017

Driving Structure-Based Drug Discovery through Cosolvent Molecular Dynamics.

J Med Chem 2016 12 17;59(23):10383-10399. Epub 2016 Aug 17.

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States.

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http://dx.doi.org/10.1021/acs.jmedchem.6b00399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217181PMC
December 2016

ChemTreeMap: an interactive map of biochemical similarity in molecular datasets.

Bioinformatics 2016 12 11;32(23):3584-3592. Epub 2016 Aug 11.

Department of Computational Medicine and Bioinformatics.

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http://dx.doi.org/10.1093/bioinformatics/btw523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5181537PMC
December 2016

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

J Comput Aided Mol Des 2016 09 30;30(9):651-668. Epub 2016 Sep 30.

Drug Design Data Resource, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.

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http://dx.doi.org/10.1007/s10822-016-9946-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5562487PMC
September 2016

Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems.

J Phys Chem B 2016 08 17;120(33):8685-95. Epub 2016 Jun 17.

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States.

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http://pubs.acs.org/doi/10.1021/acs.jpcb.6b03515
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http://dx.doi.org/10.1021/acs.jpcb.6b03515DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5214548PMC
August 2016

Prevalence of CTX-M extended-spectrum beta-lactamases and sequence type 131 in Korean blood, urine, and rectal Escherichia coli isolates.

Infect Genet Evol 2016 07 19;41:292-295. Epub 2016 Apr 19.

Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, United States. Electronic address:

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http://dx.doi.org/10.1016/j.meegid.2016.04.020DOI Listing
July 2016

CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma.

J Chem Inf Model 2016 06 17;56(6):1063-77. Epub 2016 May 17.

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States.

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http://dx.doi.org/10.1021/acs.jcim.5b00523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5228621PMC
June 2016

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

J Chem Inf Model 2016 06;56(6):951-4

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States.

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http://dx.doi.org/10.1021/acs.jcim.6b00182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217176PMC
June 2016

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

Protein Sci 2016 May 31;25(5):1021-9. Epub 2016 Mar 31.

Department of Biophysics, University of Michigan, Ann Arbor, Michigan, 48109-1055.

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http://dx.doi.org/10.1002/pro.2912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838653PMC
May 2016

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

Biopolymers 2016 Jan;105(1):21-34

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St., Ann Arbor, MI, 48109-1065.

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http://doi.wiley.com/10.1002/bip.22742
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http://dx.doi.org/10.1002/bip.22742DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4623995PMC
January 2016

The 12-minute journey.

Narrat Inq Bioeth 2014 ;4(3):192-3

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http://dx.doi.org/10.1353/nib.2014.0060DOI Listing
November 2015

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

Mol Pharm 2015 Sep 17;12(9):3399-407. Epub 2015 Aug 17.

Department of Medicinal Chemistry, College of Pharmacy, ‡Department of Pharmaceutical Sciences, College of Pharmacy, §Department of Chemistry, and ⊥Program in Chemical Biology, University of Michigan , Ann Arbor, Michigan 48109, United States.

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http://dx.doi.org/10.1021/acs.molpharmaceut.5b00414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4694564PMC
September 2015

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

Nucleic Acids Res 2015 Jan 6;43(Database issue):D465-9. Epub 2014 Nov 6.

Department of Medicinal Chemistry, University of Michigan, 428 Church St, Ann Arbor, MI 48109-1065, USA

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http://dx.doi.org/10.1093/nar/gku1088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383918PMC
January 2015

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

J Chem Inf Model 2014 Aug 1;54(8):2190-9. Epub 2014 Aug 1.

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor , 428 Church St., Ann Arbor, Michigan 48109-1065, United States.

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http://dx.doi.org/10.1021/ci400741uDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4144759PMC
August 2014

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

J Med Chem 2014 Aug 1;57(15):6468-78. Epub 2014 Aug 1.

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States.

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http://dx.doi.org/10.1021/jm5008352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136727PMC
August 2014

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

PLoS Comput Biol 2013 21;9(11):e1003279. Epub 2013 Nov 21.

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1003279
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http://dx.doi.org/10.1371/journal.pcbi.1003279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836694PMC
July 2014

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

PLoS Comput Biol 2013 21;9(11):e1003321. Epub 2013 Nov 21.

Bioinformatics Graduate Program, University of Michigan, Ann Arbor, Michigan, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836696PMC
July 2014

CSAR benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series.

J Chem Inf Model 2013 Aug 10;53(8):1853-70. Epub 2013 May 10.

Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1065, USA.

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http://dx.doi.org/10.1021/ci400025fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753884PMC
August 2013

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

J Chem Inf Model 2013 Aug 10;53(8):1842-52. Epub 2013 May 10.

Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, Michigan 48109-1065, USA.

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http://dx.doi.org/10.1021/ci4000486DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753885PMC
August 2013

Check your confidence: size really does matter.

J Chem Inf Model 2013 Aug 8;53(8):1837-41. Epub 2013 Aug 8.

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St., Ann Arbor, Michigan 48109-1065, USA.

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http://dx.doi.org/10.1021/ci4004249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3821705PMC
August 2013

Improving protocols for protein mapping through proper comparison to crystallography data.

J Chem Inf Model 2013 Feb 13;53(2):391-402. Epub 2013 Feb 13.

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, USA.

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http://dx.doi.org/10.1021/ci300430vDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3581705PMC
February 2013

Overcoming sequence misalignments with weighted structural superposition.

Proteins 2012 Nov 28;80(11):2523-35. Epub 2012 Jul 28.

Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA.

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http://doi.wiley.com/10.1002/prot.24134
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http://dx.doi.org/10.1002/prot.24134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464347PMC
November 2012

Protein flexibility in docking and surface mapping.

Q Rev Biophys 2012 Aug 9;45(3):301-43. Epub 2012 May 9.

Department of Medicinal Chemistry, University of Michigan, Ann Arbor, 48109-1065, USA.

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http://www.journals.cambridge.org/abstract_S0033583512000066
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http://dx.doi.org/10.1017/S0033583512000066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4272345PMC
August 2012

Biophysical limits of protein-ligand binding.

J Chem Inf Model 2012 Aug 18;52(8):2098-106. Epub 2012 Jul 18.

Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1065, USA.

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http://dx.doi.org/10.1021/ci200612fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3428497PMC
August 2012

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

J Chem Inf Model 2011 Sep 22;51(9):2036-46. Epub 2011 Jul 22.

Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1065, United States.

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http://dx.doi.org/10.1021/ci200082tDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3180202PMC
September 2011

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

J Chem Inf Model 2011 Sep 29;51(9):2115-31. Epub 2011 Aug 29.

Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1065, United States.

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http://dx.doi.org/10.1021/ci200269qDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3186041PMC
September 2011

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

J Chem Inf Model 2011 Sep;51(9):2025-6

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http://dx.doi.org/10.1021/ci200398gDOI Listing
September 2011

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

Proteins 2011 Jul 16;79(7):2247-59. Epub 2011 May 16.

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA.

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http://dx.doi.org/10.1002/prot.23050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577374PMC
July 2011

Binding to the open conformation of HIV-1 protease.

Proteins 2011 Jul 20;79(7):2282-90. Epub 2011 May 20.

Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1065, USA.

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http://doi.wiley.com/10.1002/prot.23054
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http://dx.doi.org/10.1002/prot.23054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3124008PMC
July 2011

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

Proteins 2011 Feb;79(2):417-27

Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.

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http://dx.doi.org/10.1002/prot.22892DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058251PMC
February 2011

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

J Am Chem Soc 2011 Jan 15;133(2):200-2. Epub 2010 Dec 15.

Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1065, United States.

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http://dx.doi.org/10.1021/ja1079332DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3081398PMC
January 2011

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

J Am Chem Soc 2010 Dec 24;132(50):17655-7. Epub 2010 Nov 24.

Department of Biological Chemistry, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216, United States.

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http://pubs.acs.org/doi/abs/10.1021/ja106291e
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http://dx.doi.org/10.1021/ja106291eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3005376PMC
December 2010

Computational methods for predicting sites of functionally important dynamics.

J Phys Chem B 2009 May;113(19):6613-22

Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109, USA.

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http://dx.doi.org/10.1021/jp808736cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761153PMC
May 2009

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

Proteins 2009 Mar;74(4):872-80

Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1065, USA.

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http://dx.doi.org/10.1002/prot.22195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2635929PMC
March 2009

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 2008 Oct 5;22(10):727-36. Epub 2008 Aug 5.

Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA.

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http://dx.doi.org/10.1007/s10822-008-9231-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2856601PMC
October 2008

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

J Med Chem 2008 Oct 1;51(20):6432-41. Epub 2008 Oct 1.

Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.

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http://pubs.acs.org/doi/abs/10.1021/jm8006504
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http://dx.doi.org/10.1021/jm8006504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2692211PMC
October 2008

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

Biopolymers 2008 Aug;89(8):643-52

Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, USA.

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http://dx.doi.org/10.1002/bip.20993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859825PMC
August 2008

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

J Chem Inf Model 2007 Nov-Dec;47(6):2358-65. Epub 2007 Sep 18.

Biophysics Research Division and Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, USA.

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http://pubs.acs.org/doi/abs/10.1021/ci700167n
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http://dx.doi.org/10.1021/ci700167nDOI Listing
February 2008

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

Nucleic Acids Res 2008 Jan 30;36(Database issue):D674-8. Epub 2007 Nov 30.

Bioinformatics Graduate Program, Biophysics Research Division, University of Michigan, Ann Arbor, MI 48109, Torrey Path LLC, Ann Arbor, MI 48104, USA.

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http://dx.doi.org/10.1093/nar/gkm911DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238910PMC
January 2008

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

J Am Chem Soc 2007 Oct 29;129(42):12809-14. Epub 2007 Sep 29.

Department of Medicinal Chemistry and the Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1021/ja073687xDOI Listing
October 2007

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

J Am Chem Soc 2007 Jul 8;129(26):8225-35. Epub 2007 Jun 8.

Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, USA.

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http://dx.doi.org/10.1021/ja0709728DOI Listing
July 2007

Protein flexibility and species specificity in structure-based drug discovery: dihydrofolate reductase as a test system.

J Am Chem Soc 2007 Mar 3;129(12):3634-40. Epub 2007 Mar 3.

Department of Medicinal Chemistry and Biophysics Research Division, University of Michigan, Ann Arbor, Michigan 48109-1065, USA.

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http://pubs.acs.org/doi/abs/10.1021/ja068256d
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http://dx.doi.org/10.1021/ja068256dDOI Listing
March 2007

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

Biophys J 2006 Jun 24;90(12):4558-73. Epub 2006 Mar 24.

Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1065, USA.

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http://dx.doi.org/10.1529/biophysj.105.066654DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1471868PMC
June 2006

Refining the multiple protein structure pharmacophore method: consistency across three independent HIV-1 protease models.

J Med Chem 2006 Jun;49(12):3478-84

Department of Medicinal Chemistry, College of Pharmacy, 428 Church St., University of Michigan, Ann Arbor, 48109-1065, USA.

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http://dx.doi.org/10.1021/jm050755mDOI Listing
June 2006

Exploring protein-ligand recognition with Binding MOAD.

J Mol Graph Model 2006 May 15;24(6):414-25. Epub 2005 Sep 15.

Biophysics Research Division, University of Michigan, Ann Arbor, MI 48109-1055, USA.

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http://dx.doi.org/10.1016/j.jmgm.2005.08.002DOI Listing
May 2006

Conformational Studies of Polyprolines.

J Chem Theory Comput 2006 Mar;2(2):342-53

Department of Medicinal Chemistry, College of Pharmacy, The University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065.

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http://dx.doi.org/10.1021/ct050182tDOI Listing
March 2006

Docking studies and ligand recognition in folylpolyglutamate synthetase.

J Med Chem 2005 Dec;48(24):7764-72

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St., Ann Arbor, Michigan 48109-1065, USA.

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http://dx.doi.org/10.1021/jm0507734DOI Listing
December 2005

Quantum Mechanics/Molecular Mechanics Calculations of the Vanadium Dependent Chloroperoxidase.

J Chem Theory Comput 2005 Nov;1(6):1265-74

Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, and Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065.

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http://dx.doi.org/10.1021/ct050132oDOI Listing
November 2005

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

Biophys J 2005 Sep 10;89(3):1965-77. Epub 2005 Jun 10.

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065, USA.

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http://dx.doi.org/10.1529/biophysj.105.059576DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1366699PMC
September 2005

Binding MOAD (Mother Of All Databases).

Proteins 2005 Aug;60(3):333-40

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065, USA.

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http://dx.doi.org/10.1002/prot.20512DOI Listing
August 2005

Computational studies and peptidomimetic design for the human p53-MDM2 complex.

Proteins 2005 Jan;58(1):222-34

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor 48109-1065, USA.

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http://dx.doi.org/10.1002/prot.20275DOI Listing
January 2005

Solvation influences flap collapse in HIV-1 protease.

Proteins 2005 Jan;58(1):119-25

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor 48109-1065, USA.

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http://dx.doi.org/10.1002/prot.20274DOI Listing
January 2005

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

J Am Chem Soc 2004 Oct;126(41):13276-81

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, USA.

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http://dx.doi.org/10.1021/ja0469378DOI Listing
October 2004

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

Inorg Chem 2004 Jul;43(14):4127-36

Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy.

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http://dx.doi.org/10.1021/ic0353256DOI Listing
July 2004

Conformational behavior of beta-proline oligomers.

J Am Chem Soc 2003 Dec;125(51):15855-62

Department of Medicinal Chemistry, College of Pharmacy, 428 Church St., Ann Arbor, Michigan 48109-1065, USA.

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http://dx.doi.org/10.1021/ja036471dDOI Listing
December 2003

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

J Comput Chem 2003 Jul;24(9):1016-25

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St, Ann Arbor, Michigan 48109-1065, USA.

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http://dx.doi.org/10.1002/jcc.10262DOI Listing
July 2003

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

J Am Chem Soc 2003 Jul;125(30):9035-7

Department of Chemistry and Graduate Program in Biophysics, University of Wisconsin, Madison, WI 53706, USA.

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http://pubs.acs.org/doi/abs/10.1021/ja034561c
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http://dx.doi.org/10.1021/ja034561cDOI Listing
July 2003

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

Curr Pharm Des 2002 ;8(17):1571-8

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St., Ann Arbor, MI 48109-1065, USA.

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http://dx.doi.org/10.2174/1381612023394232DOI Listing
December 2002

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

Curr Opin Chem Biol 2002 Aug;6(4):447-52

Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, USA.

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http://dx.doi.org/10.1016/s1367-5931(02)00341-1DOI Listing
August 2002