D. Ferguson

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

P. Kollman, T. Fox, I. Gould, 1995 .

New results on protein folding from simulated annealing

D. Ferguson, K. Kastella, D. G. Garrett, 1992 .

A new approach to probing conformational space with molecular mechanics: Random incremental pulse search

D. Ferguson, D. J. Raber, 1989 .

Molecular mechanics conformational analysis of cyclononane using the RIPS method and comparison with quantum‐mechanical calculations

D. Ferguson, D. J. Raber, W. A. Glauser, 1989 .

Molecular mechanics calculations of several lanthanide complexes: An application of the random incremental pulse search

D. Ferguson, D. J. Raber, 1990 .

Transformation of a κ-Opioid Receptor Antagonist to a κ-Agonist by Transfer of a Guanidinium Group from the 5‘- to 6‘-Position of Naltrindole

D. Ferguson, Shiv k. Sharma, P. Portoghese, 2001 .

Transformation of a kappa-opioid receptor antagonist to a kappa-agonist by transfer of a guanidinium group from the 5'- to 6'-position of naltrindole.

R. M. Jones, D. Ferguson, P. Portoghese, 2001, Journal of medicinal chemistry.

Investigation of the selectivity of oxymorphone- and naltrexone-derived ligands via site-directed mutagenesis of opioid receptors: exploring the "address" recognition locus.

D. Ferguson, P. Portoghese, T. Metzger, 2001, Journal of medicinal chemistry.

Potent and selective indolomorphinan antagonists of the kappa-opioid receptor.

R. M. Jones, D. Ferguson, G. Subramanian, 2000, Journal of medicinal chemistry.

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197

P. Kollman, I. Gould, W. Cornell, 1996 .

Triaryl Pyrazoline Compound Inhibits Flavivirus RNA Replication

S. Goebel, D. Ferguson, F. Puig-Basagoiti, 2006, Antimicrobial Agents and Chemotherapy.

4 Molecular Modeling of Opioid Receptor-Ligand Complexes

D. Ferguson, G. Poda, G. Subramanian, 2002 .

Parameterization and Application of the General Amber Force Field to Model Fluoro Substituted Furanose Moieties and Nucleosides

Diego E. Escalante, D. Ferguson, C. Aldrich, 2022, Molecules.

Molecular simulation of dynorphin A-(1-10) binding to extracellular loop 2 of the kappa-opioid receptor. A model for receptor activation.

D. Ferguson, G. Paterlini, P. Portoghese, 1997, Journal of medicinal chemistry.

Structural characteristics of 2'-O-(2-methoxyethyl)-modified nucleic acids from molecular dynamics simulations.

M. Manoharan, D. Ferguson, V. Mohan, 1998, Nucleic acids research.

Effects of C2'-Substitution on arabinonucleic acid structure and conformation

D. Ferguson, D. Venkateswarlu, 1999 .

AMBER: A Program for Simulation of Biological and Organic Molecules

P. Kollman, D. Case, G. Seibel, 2002 .

Polymeric nanoparticles encapsulating novel TLR7/8 agonists as immunostimulatory adjuvants for enhanced cancer immunotherapy.

D. Ferguson, T. Griffith, J. Panyam, 2018, Biomaterials.

Toward a structure-based model of salvinorin A recognition of the kappa-opioid receptor.

D. Ferguson, Brian E Kane, C. McCurdy, 2008, Journal of medicinal chemistry.

Cation-pi interactions: an energy decomposition analysis and its implication in delta-opioid receptor-ligand binding.

D. Ferguson, G. Subramanian, Y. Mo, 2002, Journal of the American Chemical Society.

Analysis of the malondialdehyde-2'-deoxyguanosine adduct pyrimidopurinone in human leukocyte DNA by gas chromatography/electron capture/negative chemical ionization/mass spectrometry.

D. Ferguson, L. Marnett, C. Rouzer, 1997, Chemical research in toxicology.

Acidic pH-responsive polymer nanoparticles as a TLR7/8 agonist delivery platform for cancer immunotherapy.

D. Ferguson, T. Griffith, J. Panyam, 2018, Nanoscale.

QSAR and CoMFA: a perspective on the practical application to drug discovery.

D. Ferguson, B. Podlogar, D M Ferguson, 2000, Drug Design and Discovery.

TLR7/8 Agonist Loaded Nanoparticles Augment NK Cell-mediated Antibody-based Cancer Immunotherapy.

D. Ferguson, T. Griffith, J. Panyam, 2020, Molecular pharmaceutics.

Synthesis and evaluation of N-alkyl-9-aminoacridines with antibacterial activity.

John R. Goodell, D. Ferguson, C. Salomon, 2014, Bioorganic & medicinal chemistry letters.

Synthesis and evaluation of acridine- and acridone-based anti-herpes agents with topoisomerase activity.

John R. Goodell, D. Ferguson, H. Hiasa, 2006, Bioorganic & medicinal chemistry.

Isosteric replacement of acidic with neutral residues in extracellular loop-2 of the kappa-opioid receptor does not affect dynorphin A(1-13) affinity and function.

D. Ferguson, P. Law, P. Portoghese, 2000, Journal of medicinal chemistry.

Exploring the unique pharmacology of a novel opioid receptor, ZFOR1, using molecular modeling and the 'message-address' concept.

D. Ferguson, T. Metzger, M. Paterlini, 2001, Protein engineering.

Structural properties of DNA:RNA duplexes containing 2'-O-methyl and 2'-S-methyl substitutions: a molecular dynamics investigation.

M. Manoharan, D. Ferguson, K. Lind, 1999, Nucleic acids research.

Design and Synthesis of N1-Modified Imidazoquinoline Agonists for Selective Activation of Toll-like Receptors 7 and 8.

D. Ferguson, T. Griffith, T. Kucaba, 2017, ACS medicinal chemistry letters.

Structure-activity relationship analysis of imidazoquinolines with Toll-like receptors 7 and 8 selectivity and enhanced cytokine induction.

Michael Olin, Courtney C Aldrich, D. Ferguson, 2014, Journal of medicinal chemistry.

Discovery of Imidazoquinolines with Toll-Like Receptor 7/8 Independent Cytokine Induction.

D. Ferguson, C. Aldrich, J. Ohlfest, 2012, ACS medicinal chemistry letters.

Acridine-based agents with topoisomerase II activity inhibit pancreatic cancer cell proliferation and induce apoptosis.

John R. Goodell, D. Ferguson, A. Ougolkov, 2008, Journal of medicinal chemistry.

4-Amino-2-butyl-7-methoxycarbonylthiazolo[4,5-c]quinoline

D. Ferguson, Peter G. Larson, 2021, Molbank.

Synthesis and cancer cell cytotoxicity of substituted xanthenes.

John R. Goodell, D. Ferguson, H. Hiasa, 2010, Bioorganic & medicinal chemistry.

Novel acridine-based agents with topoisomerase II inhibitor activity suppress mesothelioma cell proliferation and induce apoptosis

D. Ferguson, R. Kratzke, B. Jacobson, 2012, Investigational New Drugs.

Identification of compounds with anti-West Nile Virus activity.

John R. Goodell, D. Ferguson, P. Shi, 2006, Journal of medicinal chemistry.

On the role of topoisomerase I in mediating the cytotoxicity of 9-aminoacridine-based anticancer agents.

D. Ferguson, K. Flatten, S. Kaufmann, 2009, Bioorganic & medicinal chemistry letters.

Spectrophotometric Determination and Computational Evaluation of the Rates of Hydrolysis of 9-Amino-Substituted Acridines

David M. Ferguson, Bengt Svensson, John R. Goodell, 2006, J. Chem. Inf. Model..

AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

Peter A. Kollman, David A. Case, David A. Pearlman, 1995 .

Comparison of ab initio, semiempirical, and molecular mechanics calculations for the conformational analysis of ring systems

P. Kollman, I. Gould, D. Ferguson, 1992 .

Structures of lanthanide shift reagent complexes by molecular mechanics computations

D. Ferguson, D. J. Raber, Douglas J. Brecknell, 1985 .

High-Throughput Assays Using a Luciferase-Expressing Replicon, Virus-Like Particles, and Full-Length Virus for West Nile Virus Drug Discovery

D. Ferguson, P. Shi, Ping Ren, 2005, Antimicrobial Agents and Chemotherapy.

How transferable are hydrogen parameters in molecular mechanics calculations?

Peter A. Kollman, David M. Ferguson, D. L. Veenstra, 1992 .

Molecular recognition of opioid receptor ligands

David M. Ferguson, Bengt Svensson, D. Ferguson, 2006, The AAPS Journal.

Parameterization and evaluation of a flexible water model

DAVID M. FERGUSON, D. Ferguson, 1995, J. Comput. Chem..

Parameterization and Application of the General Amber Force Field to Model Fluro Substituted Furanose Moieties and Nucleosides

Diego E. Escalante, D. Ferguson, C. Aldrich, 2022, bioRxiv.

Novel TLR 7/8 agonists for improving NK cell mediated antibody-dependent cellular cytotoxicity (ADCC)

D. Ferguson, T. Griffith, J. Panyam, 2021, Scientific Reports.

Stereochemical requirements for receptor recognition of the mu-opioid peptide endomorphin-1.

D. Ferguson, P. Portoghese, M. Paterlini, 2000, Biophysical Journal.

Investigation of ( S)-(-)-Acidomycin: A Selective Antimycobacterial Natural Product That Inhibits Biotin Synthase.

N. Mishra, D. Ferguson, D. Schnappinger, 2019, ACS infectious diseases.

Chapter 17 Simulated annealing-optimal histogram applications to the protein folding problem

D. Ferguson, D. G. Garrett, 1995 .

9-Amino acridine pharmacokinetics, brain distribution, and in vitro/in vivo efficacy against malignant glioma

D. Ferguson, J. Ohlfest, R. Remmel, 2012, Cancer Chemotherapy and Pharmacology.

Conformational analysis of the endogenous μ‐opioid agonist endomorphin‐1 using NMR spectroscopy and molecular modeling

D. Ferguson, B. Podlogar, F. Brown, 1998, FEBS letters.

Application of the message-address concept to the docking of naltrexone and selective naltrexone-derived opioid antagonists into opioid receptor models

Philip S. Portoghese, Thomas G. Metzger, David M. Ferguson, 1996, Neurochemical Research.

Conformational searches for the global minimum of protein models

Thomas G. Metzger, David M. Ferguson, Keith Kastella, 1994, J. Glob. Optim..

Free energy perturbation calculations involving potential function changes

P. Kollman, W. C. Swope, D. Ferguson, 1992 .

Novel acridine-based compounds that exhibit an anti-pancreatic cancer activity are catalytic inhibitors of human topoisomerase II.

John R. Goodell, D. Ferguson, A. Ougolkov, 2009, European journal of pharmacology.

Combination of Sunitinib and PD-L1 Blockade Enhances Anticancer Efficacy of TLR7/8 Agonist-Based Nanovaccine.

D. Ferguson, T. Griffith, J. Panyam, 2019, Molecular pharmaceutics.

A computational analysis of interaction energies in methane and neopentane dimer systems

D. Ferguson, W. A. Glauser, T. Metzger, 1997, J. Comput. Chem..

Can the Lennard–Jones 6‐12 function replace the 10‐12 form in molecular mechanics calculations?

Peter A. Kollman, David M. Ferguson, P. Kollman, 1991 .

Synthesis and Evaluation of Acridone and Xanthone Epoxides with Anti-MRSA and Anti-MSSA Activity

D. Ferguson, Junshu Yang, Yinduo Ji, 2021, bioRxiv.

Synthesis and evaluation of xanomeline analogs--probing the wash-resistant phenomenon at the M1 muscarinic acetylcholine receptor.

D. Ferguson, Brian E Kane, E. El-Fakahany, 2008, Bioorganic & medicinal chemistry.

Structure and Stability of Human Telomeric G-Quadruplex with Preclinical 9-Amino Acridines

D. Ferguson, R. Gargallo, R. Eritja, 2013, PloS one.

A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist

David M. Ferguson, Christopher R. McCurdy, Nidhi Singh, 2006, J. Comput. Aided Mol. Des..

Cation−π Interactions: An Energy Decomposition Analysis and Its Implication in δ-Opioid Receptor−Ligand Binding

Jiali Gao, David M. Ferguson, Yirong Mo, 2002 .

On the role of extracellular loops of opioid receptors in conferring ligand selectivity

D. Ferguson, T. Metzger, 1995, FEBS letters.

A computational analysis of interaction energies in methane and neopentane dimer systems

Thomas G. Metzger, David M. Ferguson, William A. Glauser, 1997, Journal of Computational Chemistry.

Simulated Annealing—Optimal Histogram Methods

D. Ferguson, D. G. Garrett, 1999 .

Constant temperature simulations using the Langevin equation with velocity Verlet integration

David M. Ferguson, M. Germana Paterlini, D. Ferguson, 1998 .

A Cinchona Alkaloid Antibiotic That Appears To Target ATP Synthase in Streptococcus pneumoniae.

D. Ferguson, C. Aldrich, Xu Wang, 2019, Journal of medicinal chemistry.

Isothermal-isobaric molecular dynamics simulations with Monte Carlo volume sampling

D. Ferguson, K. Chow, 1995 .

A unique binding epitope for salvinorin A, a non‐nitrogenous kappa opioid receptor agonist

Christopher R McCurdy, D. Ferguson, Brian E Kane, 2006, The FEBS journal.

Molecular docking reveals a novel binding site model for fentanyl at the mu-opioid receptor.

D. Ferguson, G. Subramanian, P. Portoghese, 2000, Journal of medicinal chemistry.

Parameterization and Simulation of the Physical Properties of Phosphorothioate Nucleic Acids

R. Griffey, D. Ferguson, V. Mohan, 1998 .

Covalently induced activation of the delta opioid receptor by a fluorogenic affinity label, 7'-(phthalaldehydecarboxamido)naltrindole (PNTI).

D. Ferguson, G. Poda, H. Loh, 2001, Journal of Medicinal Chemistry.

Quantitative three dimensional structure linear interaction energy model of 5'-O-[N-(salicyl)sulfamoyl]adenosine and the aryl acid adenylating enzyme MbtA.

D. Ferguson, C. Aldrich, E. Bennett, 2008, Journal of medicinal chemistry.

On the use of acceptance ratio methods in free energy calculations

David M. Ferguson, D. Ferguson, 1993 .

Knowledge‐based modeling of a bacterial dichloromethane dehalogenase

D. Ferguson, Amanda Marsh and, 1997, Proteins.

Structural Modeling of the TMPRSS Subfamily of Host Cell Proteases Reveals Potential Binding Sites

Diego E. Escalante, D. Ferguson, Austin Wang, 2021, bioRxiv.

Structural modeling and analysis of the SARS-CoV-2 cell entry inhibitor camostat bound to the trypsin-like protease TMPRSS2

Diego E. Escalante, D. Ferguson, 2021, Medicinal Chemistry Research.

Proteasomal Stimulation by MK886 and Its Derivatives Can Rescue Tau-Induced Neurite Pathology

D. Ferguson, J. Sachs, Anthony R Braun, 2023, Molecular Neurobiology.

Conformational analysis and automated receptor docking of selective arylacetamide-based kappa-opioid agonists.

D. L. Larson, D. Ferguson, G. Subramanian, 1998, Journal of medicinal chemistry.

Polymeric nanoparticles encapsulating novel TLR7/8 agonists as immunostimulatory adjuvants for enhanced cancer immunotherapy.

D. Ferguson, T. Griffith, J. Panyam, 2018, Biomaterials.

A second generation force field for the simulation of proteins

P. Kollman, T. Fox, I. Gould, 1995 .

Zafirlukast Is a Promising Scaffold for Selectively Inhibiting TNFR1 Signaling

D. Ferguson, J. Sachs, William D. Fiers, 2023, ACS bio & med chem Au.

Toward a structure-based model of salvinorin A recognition of the kappa-opioid receptor.

D. Ferguson, Brian E Kane, C. McCurdy, 2008, Journal of medicinal chemistry.