David M. Ferguson

Best Publications

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

  Wendy D. Cornell;Piotr Cieplak;Piotr Cieplak;Christopher I. Bayly;Christopher I. Bayly;Ian R. Gould;Ian R. Gould

  16287
  Citations

• 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

  David A. Pearlman;David A. Case;James W. Caldwell;Wilson S. Ross

  3172
  Citations

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

  Wendy D. Cornell;Piotr Cieplak;Christopher I. Bayly;Ian R. Gould

  529
  Citations

• Isothermal-isobaric molecular dynamics simulations with Monte Carlo volume sampling

  Kim Hung Chow;David M. Ferguson

  280
  Citations

• Constant temperature simulations using the Langevin equation with velocity Verlet integration

  M.Germana Paterlini;David M Ferguson

  261
  Citations

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

  David M. Ferguson;Douglas J. Raber

  241
  Citations

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

  Hyunjoon Kim;Lin Niu;Peter Larson;Tamara A. Kucaba

  203
  Citations

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

  John R. Goodell;Avni A. Madhok;Hiroshi Hiasa;David M. Ferguson

  197
  Citations

• Identification of Compounds with Anti-West Nile Virus Activity

  John R. Goodell;Francesc Puig-Basagoiti;Brett M. Forshey;Pei Yong Shi

  185
  Citations

• Parameterization and evaluation of a flexible water model

  David M. Ferguson

  177
  Citations

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

  Yirong Mo;Govindan Subramanian;Jiali Gao;David M. Ferguson

  158
  Citations

• Triaryl Pyrazoline Compound Inhibits Flavivirus RNA Replication

  Francesc Puig-Basagoiti;Mark Tilgner;Brett M. Forshey;Sean M. Philpott;Sean M. Philpott

  148
  Citations

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

  Francesc Puig-Basagoiti;Tia S. Deas;Ping Ren;Mark Tilgner

  140
  Citations

• Synthesis and cancer cell cytotoxicity of substituted xanthenes.

  Rajan Giri;John R. Goodell;Chengguo Xing;Adam Benoit

  129
  Citations

• Potent and Selective Indolomorphinan Antagonists of the Kappa-Opioid Receptor

  William C. Stevens;Robert M. Jones;Govindan Subramanian;Thomas G. Metzger

  129
  Citations

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

  John R. Goodell;Andrei V. Ougolkov;Hiroshi Hiasa;Harneet Kaur

  128
  Citations

• Molecular Docking Reveals a Novel Binding Site Model for Fentanyl at the μ-Opioid Receptor

  G Subramanian;M G Paterlini;P S Portoghese;D M Ferguson

  125
  Citations

• Molecular recognition of opioid receptor ligands.

  Brian E. Kane;Bengt Svensson;David M. Ferguson

  117
  Citations

• Can the Lennard—Jones 6-12 function replace the 10-12 form in molecular mechanics calculations?

  David M. Ferguson;Peter A. Kollman

  117
  Citations

• Determination of the relative binding free energies of peptide inhibitors to the HIV-1 protease.

  David M. Ferguson;Randall J. Radmer;Peter A. Kollman

  113
  Citations