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Papers are listed
chronologically; a list grouped
by area is also available.
- 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.
- D.A. SILVA, D.W. PATE, R.D. CLARK, N.M. DAVIES, A.O.
EL-KADI, & R. LÖBENBERG. Phytocannabinoid
drug-drug interactions and their clinical
implications. Pharmacology &
Therapeutics 2020, 215, 107621.
- 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.
- H. MASAMITSU, A.
KITAZAWA, A. CAYLEY, R.V. WILLIAMS, R.V. RICHARDS,
C. BARBER, T. HANSER, R. SAIAKHOV, S. CHAKRAVARTI,
G.J. MYATT, K.P.CROSS, E. BENFENATI, E. RAITANO, O.
MEKENYAN, P. PETKOV, C. BOSSA, B. ROMUALDO, C.L.
BATTISTELLI, A. GIULIANI, O. TCHEREMENSKAIA, C.
DEMEO, U. NORINDER, H. KOGA, C. JOSE, N. JELIAZKOVA,
N. KOCHEV, V. PASKALA, C. YANG, P.R. DAGA, R.D.CLARK
& J. RATHMAN. Improvement
of quantitative structure–activity relationship
(QSAR) tools for predicting Ames mutagenicity:
outcomes of the Ames/QSAR International Challenge
Project. Mutagenesis 2019,
34, 3-16.
- R.D.
CLARK. Predicting mammalian metabolism and toxicity
of pesticides in silico. Pest
Manage. Sci. 2018, 4,
1992-2003.
- P.R. DAGA M.B. BOLGER,
I.S. HAWORTH, R.D. CLARK & E.J. MARTIN. Physiologically
based pharmacokinetic modeling in lead
optimization. 1. Evaluation and adaptation of
GastroPlus to predict bioavailability of medchem
series. Mol. Pharmaceutics 2018,
15, 821-30.
- P.R. DAGA, M.B. BOLGER,
I.S. HAWORTH, R.D. CLARK & Eric J. Martin. Physiologically
Based Pharmacokinetic Modeling in Lead
Optimization. 2. Rational Bioavailability Design
by Global Sensitivity Analysis To Identify
Properties Affecting Bioavailability. Mol.
Pharmaceutics 2018, 15,
831-839.
- T.H. GRASELA, V. LUKACOVA, D.N. MORRIS, R.D. CLARK,
K.A. ANDREWS & M.B. Bolger. Human
PK Prediction and Modeling. In: Reference
Module in Chemistry, Molecular Sciences and Chemical
Engineering, Elsevier, 2016 (doi:
10.1016/B978-0-12-409547-2.12373-X)
- M.S. LAWLESS, M.
WALDMAN, R. FRACZKIEWICZ & R.D. CLARK. Using
Cheminformatics in Drug Discovery. In: Handbook of
Experimental Pharmacology; U. Nielsch, U.
Fuhrmann & S. Jaroch, Eds.; 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.
- R.D. CLARK. Through
the Looking Glass: Adventures in Kinase Inhibitor
Design and Optimization. J. Med. Chem.
2013,
56,
1796-1798.
- 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
- R.D. CLARK & U. NORINDER. Two
personal perspectives on a key issue in contemporary
3D QSAR. WIREs Comput. Mol. Sci. 2012, 2, 108–113.
- R.D. CLARK & D.C. ROE. Similarity searching for
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 & E.
ABRAHAMIAN. Using
a staged multi-objective optimization approach to
find selective pharmacophore models. J. Comput.-Aided Molec.
Des. 2009,
23, 765-771.
- 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. DPRESS:
Localizing
estimates of predictive uncertainty. J. Cheminformatics 2009, 1, 11.
- 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.
- 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.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 approach to generating diverse but
energetically representative ensembles of ligand
conformers. J.
Comput.-Aided Molec. Design 2008, 22, 681-691.
- R.D. CLARK. A
ligand’s-eye view of protein binding. J. Comput.-Aided Molec.
Design 2008,
22, 507-521.
- R.D. CLARK & D.J. WEBSTER-CLARK. Managing
bias
in ROC curves. J. Comput.-Aided Molec. Design 2008, 22, 141-146.
- 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.
- 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.
- 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. 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.
- 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.
- 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.
- 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. 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.
- 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.
- 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.
- R.D. CLARK & P.R.N. WOLOHAN. Molecular
design and bioavailability. Curr. Topics Med. Chem.
2003, 3,
1269-1288.
- 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, 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. 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, 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.
- 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.
- R.D. CLARK. Synthesis and QSAR of herbicidal
3-pyrazolyl α,α,α-trifluorotolyl ethers. J. Agricult. Food Chem.
1996, 44, 3643-3652.
- 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.
- 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.
- 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.
- D.L. DUEWER & R.D. CLARK. Rank-order
analysis for robust evaluation of multi-response,
multi-block comparisons. J. Chemometrics 1991, 5, 503-521.
- 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, M.J. Hawkesford, S.J. Coughlan, J.
Bennett & G. Hind
- 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 orien¬tation 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.
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.
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