A. D. Clark

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Two Introductory Experiments in Electromagnetics

A. D. Clark, R. Freer, 1986 .

Structures of HIV-1 RT–DNA complexes before and after incorporation of the anti-AIDS drug tenofovir

Roger A. Jones, A. D. Clark, G. Wang, 2004, Nature Structural &Molecular Biology.

Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants.

H. M. Vinkers, A. D. Clark, R. Pauwels, 2004, Journal of medicinal chemistry.

Crystal structure of HIV‐1 reverse transcriptase in complex with a polypurine tract RNA:DNA

A. D. Clark, Jianping Ding, S. Sarafianos, 2001, The EMBO journal.

Structure of unliganded HIV-1 reverse transcriptase at 2.7 A resolution: implications of conformational changes for polymerization and inhibition mechanisms.

A. D. Clark, Jianping Ding, E. Arnold, 1996, Structure.

The Lys103Asn mutation of HIV-1 RT: a novel mechanism of drug resistance.

A. D. Clark, Jianping Ding, P. Boyer, 2001, Journal of molecular biology.

In search of a novel anti-HIV drug: multidisciplinary coordination in the discovery of 4-[[4-[[4-[(1E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2- pyrimidinyl]amino]benzonitrile (R278474, rilpivirine).

Stephen H Hughes, Peter Williams, Paul J Lewi, 2005, Journal of medicinal chemistry.

Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design

Joseph D. Bauman, Aaron J. Shatkin, Stephen H. Hughes, 2008, Nucleic acids research.

Crystal structures for HIV-1 reverse transcriptase in complexes with three pyridinone derivatives: a new class of non-nucleoside inhibitors effective against a broad range of drug-resistant strains.

Christophe Meyer, Stephen H Hughes, Eddy Arnold, 2005, Journal of medicinal chemistry.

Crystallization of human immunodeficiency virus type 1 reverse transcriptase with and without nucleic acid substrates, inhibitors, and an antibody Fab fragment.

A. D. Clark, P. Clark, S. Hughes, 1995, Methods in enzymology.

Structure of HIV-1 reverse transcriptase with the inhibitor beta-Thujaplicinol bound at the RNase H active site.

A. D. Clark, S. Hughes, E. Arnold, 2009, Structure.

Inhibition of human immunodeficiency virus type 1 integrase by the Fab fragment of a specific monoclonal antibody suggests that different multimerization states are required for different enzymatic functions

A. D. Clark, P. Clark, S. Hughes, 1996, Journal of virology.

HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site.

Jennifer L. Knight, A. D. Clark, R. Levy, 2006, ACS chemical biology.

Crystals of a ternary complex of human immunodeficiency virus type 1 reverse transcriptase with a monoclonal antibody Fab fragment and double-stranded DNA diffract x-rays to 3.5-A resolution.

A. D. Clark, P. Clark, S. Hughes, 1991, Proceedings of the National Academy of Sciences of the United States of America.

Crystal structures of arginine deiminase with covalent reaction intermediates; implications for catalytic mechanism.

A. D. Clark, E. Arnold, K. Das, 2004, Structure.

Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA.

A. D. Clark, Jianping Ding, Roger L. Williams, 1993, Proceedings of the National Academy of Sciences of the United States of America.

Crystal structures of clinically relevant Lys103Asn/Tyr181Cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-nucleoside inhibitor HBY 097.

A. D. Clark, S. Sarafianos, P. Boyer, 2007, Journal of molecular biology.

High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: Strategic flexibility explains potency against resistance mutations

Stephen H Hughes, Paul J Lewi, Eddy Arnold, 2008, Proceedings of the National Academy of Sciences.

Crystal structures of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT drug-resistant mutant.

A. D. Clark, Jianping Ding, R. Pauwels, 1996, Journal of molecular biology.

Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with beta-branched amino acids.

A. D. Clark, Jianping Ding, S. Sarafianos, 1999, Proceedings of the National Academy of Sciences of the United States of America.

Inhibition of Bacterial RNA Polymerase by Streptolydigin: Stabilization of a Straight-Bridge-Helix Active-Center Conformation

A. D. Clark, R. Ebright, S. Tuske, 2005, Cell.

Structures of HIV‐1 reverse transcriptase with pre‐ and post‐translocation AZTMP‐terminated DNA

A. D. Clark, S. Tuske, S. Sarafianos, 2002, The EMBO journal.

Crystal structure of tert-butyldimethylsilyl-spiroaminooxathioledioxide-thymine (TSAO-T) in complex with HIV-1 reverse transcriptase (RT) redefines the elastic limits of the non-nucleoside inhibitor-binding pocket.

A. D. Clark, E. Arnold, K. Das, 2011, Journal of medicinal chemistry.

Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution.

A. D. Clark, Jianping Ding, S. Sarafianos, 1998, Journal of molecular biology.

Sarafianos, S.G. et al. Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with -branched amino acids. Proc. Natl. Acad. Sci. USA 96, 10027-10032

A. D. Clark, Jianping Ding, S. Sarafianos, 1999 .

Trapping HIV-1 Reverse Transcriptase Before and After Translocation on DNA*

A. D. Clark, S. Tuske, S. Sarafianos, 2003, The Journal of Biological Chemistry.

HIV-1 reverse transcriptase purified from a recombinant strain of Escherichia coli.

A. D. Clark, P. Clark, K. W. Kim, 1990, AIDS research and human retroviruses.

Structural basis of HIV-1 resistance to AZT by excision

Roger A. Jones, A. D. Clark, S. Sarafianos, 2010, Nature Structural &Molecular Biology.

Structural Basis for the Role of the K65R Mutation in HIV-1 Reverse Transcriptase Polymerization, Excision Antagonism, and Tenofovir Resistance*

Roger A. Jones, A. D. Clark, S. Tuske, 2009, The Journal of Biological Chemistry.

Structure of HIV-1 reverse transcriptase/DNA complex at 7 Å resolution showing active site locations

A. D. Clark, Jianping Ding, Roger L. Williams, 1992, Nature.

Insights into DNA polymerization mechanisms from structure and function analysis of HIV-1 reverse transcriptase.

A. D. Clark, Jianping Ding, R. Raag, 1995, Biochemistry.

Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution.

A. D. Clark, Jianping Ding, S. Sarafianos, 1998, Journal of molecular biology.

Structure of HIV-1 reverse transcriptase in a complex with the non-nucleoside inhibitor α-APA R 95845 at 2.8 å resolution

A. D. Clark, R. Pauwels, E. Arnold, 1995 .

Concentration and pH dependent aggregation of hydrophobic drug molecules and relevance to oral bioavailability.

Paul J Lewi, Eddy Arnold, A. D. Clark, 2005, Journal of medicinal chemistry.

Recent results and new hardware developments for protein crystal growth in microgravity

A. D. Clark, A. Sacco, K. Moore, 1994 .

Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistance.

A. D. Clark, Jianping Ding, S. Hughes, 1998, Journal of molecular biology.

Correlations between Factors Determining the Pharmacokinetics and Antiviral Activity of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors of the Diaryltriazine and Diarylpyrimidine Classes of Compounds

A. D. Clark, E. Arnold, F. Daeyaert, 2004, Drugs in R&D.

On the detection of multiple-binding modes of ligands to proteins, from biological, structural, and modeling data

Eddy Arnold, Paul J. Lewi, Kalyan Das, 2003, J. Comput. Aided Mol. Des..