Publications by authors named "James B Dunbar"

16Publications

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

Authors:
Richard D Smith Jordan J Clark Aqeel Ahmed Zachary J Orban James B Dunbar Heather A Carlson

J Mol Biol 2019 06 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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June 2019

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

Authors:
Symon Gathiaka Shuai Liu Michael Chiu Huanwang Yang Jeanne A Stuckey You Na Kang Jim Delproposto Ginger Kubish James B Dunbar Heather A Carlson Stephen K Burley W Patrick Walters Rommie E Amaro Victoria A Feher Michael K Gilson

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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September 2016

CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma.

Authors:
Heather A Carlson Richard D Smith Kelly L Damm-Ganamet Jeanne A Stuckey Aqeel Ahmed Maire A Convery Donald O Somers Michael Kranz Patricia A Elkins Guanglei Cui Catherine E Peishoff Millard H Lambert James B Dunbar

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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June 2016

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

Authors:
Richard D Smith Kelly L Damm-Ganamet James B Dunbar Aqeel Ahmed Krishnapriya Chinnaswamy James E Delproposto Ginger M Kubish Christine E Tinberg Sagar D Khare Jiayi Dou Lindsey Doyle Jeanne A Stuckey David Baker Heather A Carlson

J Chem Inf Model 2016 06 9;56(6):1022-31. Epub 2015 Oct 9.

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

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June 2016

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

Authors:
Aqeel Ahmed Richard D Smith Jordan J Clark James B Dunbar Heather A Carlson

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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January 2015

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

Authors:
Peter M-U Ung James B Dunbar Jason E Gestwicki Heather A Carlson

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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August 2014

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

Authors:
James B Dunbar Richard D Smith Kelly L Damm-Ganamet Aqeel Ahmed Emilio Xavier Esposito James Delproposto Krishnapriya Chinnaswamy You-Na Kang Ginger Kubish Jason E Gestwicki Jeanne A Stuckey Heather A Carlson

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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August 2013

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

Authors:
Kelly L Damm-Ganamet Richard D Smith James B Dunbar Jeanne A Stuckey Heather A Carlson

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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August 2013

Biophysical limits of protein-ligand binding.

Authors:
Richard D Smith Alaina L Engdahl James B Dunbar Heather A Carlson

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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August 2012

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

Authors:
Heather A Carlson James B Dunbar

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

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September 2011

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

Authors:
Richard D Smith James B Dunbar Peter Man-Un Ung Emilio X Esposito Chao-Yie Yang Shaomeng Wang Heather A Carlson

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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September 2011

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

Authors:
James B Dunbar Richard D Smith Chao-Yie Yang Peter Man-Un Ung Katrina W Lexa Nickolay A Khazanov Jeanne A Stuckey Shaomeng Wang Heather A Carlson

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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September 2011

Benzothiophene piperazine and piperidine urea inhibitors of fatty acid amide hydrolase (FAAH).

Authors:
Douglas S Johnson Kay Ahn Suzanne Kesten Scott E Lazerwith Yuntao Song Mark Morris Lorraine Fay Tracy Gregory Cory Stiff James B Dunbar Marya Liimatta David Beidler Sarah Smith Tyzoon K Nomanbhoy Benjamin F Cravatt

Bioorg Med Chem Lett 2009 May 24;19(10):2865-9. Epub 2009 Mar 24.

Pfizer Global Research and Development, Ann Arbor, MI 48105, USA.

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May 2009

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

Authors:
Heather A Carlson Richard D Smith Nickolay A Khazanov Paul D Kirchhoff James B Dunbar Mark L Benson

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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October 2008

Thermodynamic and structure guided design of statin based inhibitors of 3-hydroxy-3-methylglutaryl coenzyme A reductase.

Authors:
Ronald W Sarver Elizabeth Bills Gary Bolton Larry D Bratton Nicole L Caspers James B Dunbar Melissa S Harris Richard H Hutchings Robert M Kennedy Scott D Larsen Alexander Pavlovsky Jeffrey A Pfefferkorn Graeme Bainbridge

J Med Chem 2008 Jul 10;51(13):3804-13. Epub 2008 Jun 10.

Pfizer Global Research & Development, Ann Arbor, Michigan 48105, USA.

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July 2008

CLIP: similarity searching of 3D databases using clique detection.

Authors:
Nicholas Rhodes Peter Willett Alain Calvet James B Dunbar Christine Humblet

J Chem Inf Comput Sci 2003 Mar-Apr;43(2):443-8

Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom.

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June 2003