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Papers are grouped by area: in press; most recently in print; most cited; ADME/Tox; biochemistry; biometrics; cheminformatics; QSAR & validation; and synthetic chemistry. Papers bridging multiple areas appear in each section.  Special Journal Issues edited are listed after individual publications. A chronological listing is also available.

Most Recent

Most Cited

  • R.D. CLARK & D.J. WEBSTER-CLARK. Managing bias in ROC curves. J. Comput.-Aided Molec. Design 2008, 22, 141-146.
  • N.J. RICHMOND, C.A. ABRAMS, P.R.N. WOLOHAN, E. ABRAHAMIAN, P. WILLETT & R.D. CLARK. GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D.  J. Comput.-Aided Molec. Design 2006, 20, 567-587.
  • R.D. CLARK & P.C. FOX. Statistical variation in progressive scrambling. J. Comput.-Aided Molec. Design 2004, 18, 563-576.
  • R.D. CLARK, A. STRIZHEV, J. LEONARD, J.F. BLAKE & J.B. MATTHEW. Consensus scoring for ligand/protein interactions.  J. Mol. Graph. Model. 2002, 20, 281-295.
  • R.D. CLARK. OptiSim: An extended dissimilarity selection method for finding diverse representative subsets.  J. Chem. Inf. Comput. Sci. 1997, 37, 1181-1188.
  • R.D. CRAMER, R.D. CLARK, D.E. PATTERSON & A.M. FERGUSON. Bio-isosterism as a molecular diversity descriptor: steric fields of single "topomeric" conformers.  J. Med. Chem. 1996, 39, 3060-3069.
  • D.E. PATTERSON, R.D. CRAMER, A.M. FERGUSON, R.D. CLARK & L.E. WEINBERGER.  Neighborhood behavior: a useful concept for validation of molecular diversity descriptors.   J. Med. Chem. 1996, 39, 3049-3059.
  • R.E. MCDONNELL, R.D. CLARK, W.A. SMITH & M.A. HINCHEE.  A simplified method for the detection of neomycin phosphotransferase II in transformed plant tissues.  Plant Molec. Biol. Report. 1987, 5, 380-386.

ADME & Toxicology

Biochemistry

  • R.D. CLARK.  Through the Looking Glass: Adventures in Kinase Inhibitor Design and Optimization.
    J. Med. Chem.  2013, 56, 1796–1798.
  • U.B. NANDIHALLI, M.V. DUKE, J.W. ASHMORE, V.A. MUSCO, R.D. CLARK & S.O. DUKE.  Enantioselectivity of protoporphyrinogen oxidase-inhibiting herbicides.  Pest. Sci. 1994, 40, 265-277.
  • B.L. ARMBRUSTER, R.D. CLARK, C.R. SHARP & G.M. DILL.  Herbicidal action of nitrophenyl ether MON 12800: Immunolocalization, ultrastructural, and physiological studies. Pest. Biochem. Physiol. 1993, 47, 21-35.
  • T.M. SHERMAN, M.V. DUKE, R.D. CLARK, E.F. SANDERS, H. MATSUMOTO & S.O. DUKE.  Pyrazole phenyl ether herbicides inhibit protoporphyrinogen oxidase.  Pest. Biochem. Physiol. 1991, 40, 236-245.
  • R.E. MCDONNELL, R.D. CLARK, W.A. SMITH & M.A. HINCHEE.  A simplified method for the detection of neomycin phosphotransferase II in transformed plant tissues.  
  • Plant Molec. Biol. Report. 1987, 5, 380-386.
  • R.D. CLARK, G. HIND & J. BENNETT.  Partial purification of a spinach thylakoid protein kinase that can phosphorylate light harvesting chlorophyll a/b proteins.  In: Molecular Biology of the Photosynthetic Apparatus; K.E. Steinbeck, S. Bonitz, C.J. Arntzen & L. Bogorad, Eds.; Cold Spring Harbor Laboratory: Cold Spring Harbor, 1985; pp. 259-267.
  • G. HIND, R.D. CLARK & J.P. HOUCHINS.  Kinetic and spectroscopic studies of cytochrome b563 in isolated cytochrome b/f complex and in thylakoid membranes.  In: Advances in Photosynthesis Research, Vol I; C. Sybesma, Ed.; Martinus Nijhoff/Dr. W. Junk Publishers: Dordrecht, the Netherlands, 1984; pp. 529-536.
  • R.D. CLARK & G. HIND.  Spectrally distinct cytochrome b563 components in a chloroplast cytochrome bf complex: interaction with a hydroxyquinoline N-oxide.  Proc. Natl. Acad. Sci. USA 1983, 80, 6249-6253.
  • R.D. CLARK & G. HIND.  Isolation of a five-polypeptide cytochrome bf complex from spinach chloroplasts.  J. Biol. Chem. 1983, 258, 10348-10354.
  • R.D. CLARK & R.E. MACDONALD.  Photophosphorylation in envelope vesicles from halobacteria.  Biochem. Biophy. Res. Comm. 1981, 102, 545-553.
  • R.D. CLARK & R.E. MACDONALD.  Enzyme crypticity as an indicator of membrane orientation in envelope vesicles from halobacteria.  Biochem. Biophys. Res. Comm. 1980, 97, 1467-1473.
  • R.E. MACDONALD, R.V. GREENE, R.D. CLARK & E.V. LINDLEY.  Characterization of the light-driven sodium pump of Halobacterium halobium.  J. Biol. Chem. 1979, 254, 11831-11838.

Biometrics

  • R.D. CLARK. Synthesis and QSAR of herbicidal 3-pyrazolyl α,α,α-trifluorotolyl ethers.  J. Agricult. Food Chem. 1996, 44, 3643-3652.
  • J.J. PARLOW & R.D. CLARK. Synthesis and herbicidal activity of phenylproparginols.  J. Agricult. Food Chem. 1994, 42, 2600-2609.
  • R.D. CLARK, J.J. PARLOW, L.H. BRANNIGAN, D.M. SCHNUR & D.L. DUEWER. Applications of scaled rank-sum statistics in herbicide QSAR.  In: Classical and Three-Dimensional QSAR in Agrochemistry, ACS Symposium Series No. 606; C. Hansch and T. Fujita, Eds.; American Chemical Society: Washington, DC, 1995; pp. 264-281.
  • D.L. DUEWER & R.D. CLARK.  Rank-order analysis for robust evaluation of multi-response, multi-block comparisons.  J. Chemometrics 1991, 5, 503-521.

Cheminformatics

  • R.D. CLARK, D.N. MORRIS, G. CHINIGO, M.S. LAWLESS, J. PRUDHOMME, K.G. LE ROCH, M.J. LAFUENTE, S. FERRER, F.J. GAMO, R. GADWOOD & W.S. WOLTOSZ. Design and tests of prospective property predictions for novel antimalarial 2-aminopropylaminoquinolones. J. Comput. -Aided Molec. Design 2020, 34, 1117-1132.
  • M.S. LAWLESS, M. WALDMAN, R. FRACZKIEWICZ & R.D. CLARK. Using Cheminformatics in Drug Discovery. In: Handbook of Experimental Pharmacology; Springer International, Berlin, 2015 (doi: 10.1007/164_2015_23)
  • M. WALDMAN, R. FRACZKIEWICZ & R.D. CLARK. Tales from the War on Error: The Art and Science of Curating QSAR Data. J. Comput.-Aided Molec. Design 2015, 29, 897-910,
  • R. FRACZKIEWICZ,  M. LOBELL, A.H. GÖLLER, U. , R. SCHOENNEIS, R.D. CLARK & A. HILLISCH.  Best of Both Worlds: Combining Pharma Data and State of the Art Modeling Technology To Improve in silico pKa Prediction.  J. Chem. Inf. Model. 2015, 55, 389–397.
  • R.D. CLARK, W. LIANG, A.C. LEE, M.S. LAWLESS, R. FRACZKIEWICZ & M. WALDMAN. Using beta binomials to estimate classification uncertainty for ensemble models.  J. Cheminfo. 2014, 6, 34 (doi: 10.1186/1758-2946-6-34).
  • R.D. CLARK & M. WALDMAN.  Lions and tigers and bears, oh my! Three barriers to progress
    in computer-aided molecular design.      J. Comput.-Aided Molec. Design 2012, 26, 29-34
  • R.D. CLARK & D.C. ROE. Ligand- and structure-based virtual screening. In: Handbook of Chemoinformatics Algorithms; A. Bender & J.-L. Faulon, Eds.; CRC Press, Boca Raton FL, 2010; pp. 145-171.
  • R.D. CLARK.  Prospective ligand- and target-based 3D QSAR: State of the art 2008. Curr. Topics Med. Chem. 2009, 9, 791-810.
  • R.D. CLARK, J. K. SHEPPHIRD & J. HOLLIDAY.  The effect of structural redundancy in validation sets on virtual screening performance.  J. Chemometrics 2009, 23, 471-478.
  • R.W. HOMER, J. SWANSON, R.J. JILEK, T. HURST & R.D. CLARK.  SYBYL line notation (SLN): A single notation to represent chemical structures, queries, reactions, and virtual libraries.  J. Chem. Inf. Model. 2008, 48, 2294-2307.
  • R.J. DORFMAN, K.M. SMITH, B.B. MASEK & R.D. CLARK.   A knowledge-based ap¬proach to generating diverse but energetically representative ensembles of ligand conformers.  J. Comput.-Aided Molec. Design 2008, 22, 681-691.
  • R.D. CLARK & D.J. WEBSTER-CLARK. Managing bias in ROC curves.  J. Comput.-Aided Molec. Design 2008, 22, 141-146.
  • A. STRIZHEV, E.J. ABRAHAMIAN, S. CHOI, J.M. LEONARD, P.R.N. WOLOHAN & R.D. CLARK.  The effects of biasing torsional mutations in a conformational GA.  J. Chem. Inf. Model. 2006, 46, 1862 -1870.
  • P.R.N. WOLOHAN, L.B. AKELLA, R.J. DORFMAN, P.G. NELL, S.M. MUNDT & R.D. CLARK.  Structural Unit Analysis identifies lead series and facilitates scaffold hopping in combinatorial chemistry.  J. Chem. Inf. Model. 2006, 46, 1188-1193.
  • R.D. CLARK, P.C. FOX & E. ABRAHAMIAN. Using pharmacophore multiplet fingerprints for virtual HTS.  In: Virtual Screening in Drug Discovery; J. Alvarez & B. Shoichet, Eds.; CRC Press, Taylor & Francis: Boca Raton, 2005; pp.207-225.
  • R.D. CLARK. Compound selection. In: The Encyclopedia of Computational Chemistry (online edition); P. von Ragué Schleyer, H.F. Schaefer III, P.R. Schreiner, W.L. Jorgensen, W. Thiel & R.C. Glen, Eds.; JohnWiley & Sons, Ltd.: Chichester UK, 2005;  available online at: http://dx.doi.org/10.1002/0470845015.cu0052.
  • R.D. CLARK, P.C. FOX & E. ABRAHAMIAN. Using pharmacophore multiplet fingerprints for virtual HTS.  In: Virtual Screening in Drug Discovery; J. Alvarez & B. Shoichet, Eds.; CRC Press, Taylor & Francis: Boca Raton FL, 2005; pp.207-225.
  • R.D. CRAMER, R.J. JILEK, S. GUESSREGEN, S.J. CLARK, B. WENDT & R.D. CLARK.  “Lead-Hopping”. Validation of topomer similarity as a superior predictor of similar biological activities.  J. Med. Chem. 2004, 47, 6777-6791.
  • D.G. SPROUS, D.R. LOWIS, J.M. LEONARD, T. HERITAGE, S.N. BURKETT, D.S. BAKER & R.D. CLARK. OptiDock: Virtual HTS of combinatorial libraries by efficient sampling of binding modes in product space.  J. Comb. Chem. 2004, 6, 530-539.
  • L. XING, R.C. GLEN & R.D. CLARK. Predicting pKa by molecular tree structured fingerprints and PLS.  J. Chem. Inf. Comput. Sci. 2003, 43, 870-879.
  • R.D. CLARK, J. KAR, L. AKELLA & F. SOLTANSHAHI. OptDesign: Extending optimizable k-dissimilarity selection to combinatorial library design.  J. Chem. Inf. Comput. Sci. 2003, 43, 829-836.
  • R.D. CLARK. Getting past diversity in assessing virtual library designs.  J. Brazilian Chem. Soc. 2002, 13, 788-794.
  • R.D. CLARK, A. STRIZHEV, J. LEONARD, J.F. BLAKE & J.B. MATTHEW. Consensus scoring for ligand/protein interactions.  J. Mol. Graph. Model. 2002, 20, 281-295.
  • R.D. CLARK. Relative and absolute diversity analysis of combinatorial libraries.  In: Combinatorial Library Design and Evaluation for Drug Discovery: Principles, Software Tools and Applications in Drug Discovery; A.K. Ghose & V.N. Viswanadhan, Eds.; Marcel Dekker: New York, NY, 2001; pp 337-362.
  • R.D. CLARK, D.E. PATTERSON, F. SOLTANSHAHI, J.F. BLAKE & J.B. MATTHEW. Visualizing substructural fingerprints.  J. Mol. Graph. Model. 2000, 18, 404-411.
  • R.D. CLARK, M. BRUSATI, R. JILEK, T. HERITAGE & R.D. CRAMER. Validating novel QSAR descriptors for use in diversity analysis.  In: Molecular Modeling and Prediction of Bioactivity; K. Gundertofte & F.S. Jørgensen, Eds.; Kluwer Academic/Plenum Publishers, New York, NY, 2000; pp. 95-100.
  • R.D. CLARK & W.J. LANGTON. Balancing representativeness against diversity using optimizable K-dissimilarity and hierarchical clustering.  J. Chem. Inf. Comput. Sci. 1998, 38, 1079-1086.
  • R.D. CRAMER, D.E. PATTERSON, R.D. CLARK, F. SOLTANSHAHI & M.S. LAWLESS.  Virtual compound libraries: A new approach to decision making in molecular discovery research.  J. Chem. Inf. Comput. Sci. 1998, 38, 1010-1023.
  • R.D. CLARK, A.M. FERGUSON & R.D. CRAMER. Bioisosterism and molecular diversity.  In: 3D QSAR in Drug Design, Vol  2;  H. Kubinyi, Y.C. Martin & G. Folkers, Eds.; Kluwer Academic Publishers: Dordrecht, the Netherlands, 1998; pp 211-224.
  • R.D. CLARK. OptiSim: An extended dissimilarity selection method for finding diverse representative subsets. J. Chem. Inf. Comput. Sci. 1997, 37, 1181-1188.
  • R.D. CLARK & R.D. CRAMER. Taming the combinatorial centipede. CHEMTECH 1997, 27, 24-31.
  • R.D. CRAMER, R.D. CLARK, D.E. PATTERSON & A.M. FERGUSON. Bio-isosterism as a molecular diversity descriptor: steric fields of single "topomeric" conformers.  J. Med. Chem. 1996, 39, 3060-3069.
  • D.E. PATTERSON, R.D. CRAMER, A.M. FERGUSON, R.D. CLARK & L.E. WEINBERGER.  Neighborhood behavior: a useful concept for validation of molecular diversity descriptors.   J. Med. Chem. 1996, 39, 3049-3059.

QSAR and Validation

  • CLARK, R.D. Putting deep learning in perspective for pest management scientists. Pest Manage. Sci. 2020, 76, 2267-2275.
  • CLARK, R.D. A path to next-generation reproducibility in cheminformatics. J. Cheminform. 2019, 11, 62.
  • R.D. CLARK & P.R. DAGA. Building a Quantitative Structure-Property Relationship (QSPR) Model. In: Bioinformatics and Drug Discovery,  Humana Press, 2019, pp. 139-159.
  • M.S. LAWLESS, M. WALDMAN, R. FRACZKIEWICZ & R.D. CLARK. Using Cheminformatics in Drug Discovery. In: Handbook of Experimental Pharmacology; Springer International, Switzerland, 2015; in press.
  • M. WALDMAN, R. FRACZKIEWICZ & R.D. CLARK. Tales from the War on Error: The Art and Science of Curating QSAR Data. J. Comput.-Aided Molec. Design 2015, in press.
  • R.D. CLARK, W. LIANG, A.C. LEE, M.S. LAWLESS, R. FRACZKIEWICZ & M. WALDMAN. Using beta binomials to estimate classification uncertainty for ensemble models.  J. Cheminfo. 2014, 6, 34 (doi: 10.1186/1758-2946-6-34).
  • R.D. CLARK.  A perspective on the role of quantitative structure–activity and structure–property relationships in herbicide discovery.  Pest Manage. Sci.  2012, 68, 513–518.
  • R.D. CLARK & M. WALDMAN.  Lions and tigers and bears, oh my! Three barriers to progress
    in computer-aided molecular design.      J. Comput.-Aided Molec. Design 2012, 26, 29-34
    (doi: 10.1007/s10822-011-9504-3) 
  • R.D. CLARK & U. NORINDER. Two personal perspectives on a key issue in contemporary
    3D QSAR.       WIREs Comput. Mol. Sci. 2012, 2, 108–113 (doi: 10.1002/wcms.69).
  • R.D. CLARK.  Prospective ligand- and target-based 3D QSAR: State of the art 2008. Curr. Topics Med. Chem. 2009, 9, 791-810.
  • R.D. CLARK & E. ABRAHAMIAN. Using a staged multi-objective optimization approach to finding selective pharmacophore models.  J. Comput.-Aided Molec. Des. , 23, 765-771.
  • P.C. FOX, P.R.N. WOLOHAN, E. ABRAHAMIAN & R.D. CLARK. Parameterization and conformational sampling effects in pharmacophore multiplet searching. J. Chem. Inf. Model. 2008, 48, 2326-2334.
  • R.J. DORFMAN, K.M. SMITH, B.B. MASEK & R.D. CLARK.  A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers.  J. Comput.-Aided Molec. Design 2008, 22, 681-691.
  • R.D. CLARK. Worlds in collision: A ligand’s-eye view of protein binding.  J. Comput.-Aided Molec. Design 2008, 22, 507-521.
  • J.K. SHEPPHIRD & R.D. CLARK.  A marriage made in torsional space: Using GALAHAD models to drive pharmacophore multiplet searches.  J. Comput.-Aided Molec. Design 2006, 20, 763-771.
  • N.J. RICHMOND, C.A. ABRAMS, P.R.N. WOLOHAN, E. ABRAHAMIAN, P. WILLETT & R.D. CLARK. GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D.  J. Comput.-Aided Molec. Design 2006, 20, 567-587.
  • F. SOLTANSHAHI, T.E. MANSLEY, S. CHOI & R.D. CLARK. Balancing focused combinatorial libraries based on multiple GPCR ligands.  J. Comput.-Aided Molec. Design 2006, 20, 529-538.
  • R.D. CLARK, P.C. FOX & E. ABRAHAMIAN. Using pharmacophore multiplet fingerprints for virtual HTS.  In: Virtual Screening in Drug Discovery; J. Alvarez & B. Shoichet, Eds.; CRC Press, Taylor & Francis: Boca Raton, 2005; pp.207-225.
  • R.D. CLARK & P.C. FOX. Statistical variation in progressive scrambling.  J. Comput.-Aided Molec. Design 2004, 18, 563-576.
  • R.D. CLARK, P.R.N. WOLOHAN, E.E. HODGKIN, J.H. KELLY & N.L. SUSSMAN.  Modelling in vitro hepatotoxicity using molecular interaction fields and SIMCA.  J. Mol. Graph. Model. 2004, 22, 487-497.
  • N.J. RICHMOND, P. WILLETT & R.D. CLARK. Alignment of three-dimensional molecules using an image recognition algorithm.   J. Mol. Graph. Model. 2004, 23, 199-209.
  • R.D. CLARK. Boosted leave-many-out cross-validation: the effect of training and test set diversity on PLS statistics.  J. Comput.-Aided Molec. Design 2003, 17, 265-275.
  • P.R.N. WOLOHAN & R.D. CLARK. Predicting drug pharmacokinetic properties using molecular interaction fields and SIMCA.  J. Comput.-Aided Molec. Design 2003, 17, 65-76.
  • E. ABRAHAMIAN, P.C. FOX, L. NÆRUM, I.T. CHRISTENSEN, H. THØGERSEN & R.D. CLARK. Efficient generation, storage and manipulation of fully flexible pharmacophore multiplets and their use in 3-D similarity searching. J. Chem. Inf. Comput. Sci. 2003, 43, 458-468.
  • R.D. CLARK, D.G. SPROUS & J.M. LEONARD. Validating models based on large data sets.  In:  Rational Approaches to Drug Design; H.-D. Höltje & W. Sippl, Eds.; Prous Science: Barcelona, Spain, 2001; pp 475-485.
  • R.D. CLARK, J.M. LEONARD & A. STRIZHEV.  Pharmacophore models and comparative molecular field analysis (CoMFA).  In: Pharmacophore Perception, Development, and Use in Drug Design; O. Güner, Ed.; International University Line: La Jolla, CA, 1999; pp. 151-169.R.D.
  • CLARK. Synthesis and QSAR of herbicidal 3-pyrazolyl α,α,α-trifluorotolyl ethers.  J. Agricult. Food Chem. 1996, 44, 3643-3652.  

Synthetic Chemistry

  • R.D. CLARK.  Through the Looking Glass: Adventures in Kinase Inhibitor Design and Optimization.
    J. Med. Chem.  2013, 56, 1796–1798 (doi: 10.1021/jm400243u).
  • J.J. PARLOW & R.D. CLARK. Synthesis and herbicidal activity of phenylproparginols.  J. Agricult. Food Chem. 1994, 42, 2600-2609.
  • R.D. CLARK.  Synthesis of protoporphyrinogen oxidase inhibitors.  In: Porphyric Pesticides, ACS Symposium Series No. 559; S.O. Duke and C.A. Rebeiz, Eds.; American Chemical Society: Washington, DC, 1994; pp. 34-47.
  • K. MOEDRITZER, S.G. ALLGOOD, P. CHARUMILIND, R.D. CLARK, B.J. GAEDE, M.L. KURTZWEIL, D.A. MISCHKE, J.J. PARLOW, M.D. ROGERS, R.K. SINGH, G.L. STIKES & R.K. WEBBER (1992).  Novel pyrazole phenyl ether herbicides.  In: Synthesis and Chemistry of Agrochemicals III, ACS Symposium Series No. 504;  D.R. Baker, J.G. Feynes & J.J. Steffens, Eds.; American Chemical Society: Washington, DC, 1994; pp 147-160.

SPECIAL JOURNAL ISSUES EDITED

  • R.D. CLARK, ED. Dr. Philip S. Magee Memorial Issue.  J. Comput.-Aided Molec. Design 2008, 22(6-7).
  • R.D. CLARK, ED. Special Section: QSAR in vivo. J. Mol. Graph. Model. 2002, 20, 257-309.