1985 …2023
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Research Output 1985 2019

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Article
1997
72 Citations (Scopus)
Dynorphins
Chemical activation
Opioid Analgesics
Opioid Receptors
Ligands
1996
14 Citations (Scopus)
G-Protein-Coupled Receptors
Proteins
Bacteriorhodopsins
Proline
Mutagenesis
81 Citations (Scopus)
Naltrexone
Narcotic Antagonists
Opioid Receptors
Ligands
naltrindole
1995
2324 Citations (Scopus)

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

Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., DeBolt, S., Ferguson, D., Seibel, G. & Kollman, P., Sep 2 1995, In : Computer Physics Communications. 91, 1-3, p. 1-41 41 p.

Research output: Contribution to journalArticle

Computational chemistry
Molecular mechanics
Free energy
Molecular dynamics
Computer program listings
10340 Citations (Scopus)

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

Bayly, C. I., Merz, K. M., Ferguson, D. M., Cornell, W. D., Fox, T., Caldwell, J. W., Kollman, P. A., Cieplak, P., Gould, I. R. & Spellmeyer, D. C., May 1995, In : Journal of the American Chemical Society. 117, 19, p. 5179-5197 19 p.

Research output: Contribution to journalArticle

Nucleic acids
Static Electricity
Nucleic Acids
Electrostatics
Proteins
28 Citations (Scopus)

Isothermal-isobaric molecular dynamics simulations with Monte Carlo volume sampling

Chow, K. H. & Ferguson, D. M., Sep 2 1995, In : Computer Physics Communications. 91, 1-3, p. 283-289 7 p.

Research output: Contribution to journalArticle

Molecular dynamics
sampling
molecular dynamics
Sampling
Computer simulation
70 Citations (Scopus)

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

Metzger, T. G. & Ferguson, D. M., Nov 13 1995, In : FEBS Letters. 375, 1-2, p. 1-4 4 p.

Research output: Contribution to journalArticle

Opioid Receptors
Opioid Analgesics
Ligands
Mutagenesis
Site-Directed Mutagenesis
115 Citations (Scopus)

Parameterization and evaluation of a flexible water model

Ferguson, D. M., Apr 1995, In : Journal of Computational Chemistry. 16, 4, p. 501-511 11 p.

Research output: Contribution to journalArticle

Parameterization
Water
Evaluation
Water Potential
Dielectric Properties
1 Citation (Scopus)

Simulated annealing-optimal histogram applications to the protein folding problem

Ferguson, D. M. & Garrett, D. G., Jan 1 1995, In : Data Handling in Science and Technology. 15, C, p. 369-394 26 p.

Research output: Contribution to journalArticle

Protein folding
Protein Folding
Simulated annealing
Simulated Annealing
Histogram
1994
7 Citations (Scopus)

Conformational searches for the global minimum of protein models

Ferguson, D. M., Marsh, A., Metzger, T., Garrett, D. G. & Kastella, K., Mar 1 1994, In : Journal of Global Optimization. 4, 2, p. 209-227 19 p.

Research output: Contribution to journalArticle

Global Minimum
Conformation
Conformations
Search Methods
Proteins
1992
13 Citations (Scopus)

Alternative expressions for energies and forces due to angle bending and torsional energy

Swope, W. C. & Ferguson, D. M., Jun 1992, In : Journal of Computational Chemistry. 13, 5, p. 585-594 10 p.

Research output: Contribution to journalArticle

Molecular mechanics
Torsional stress
Molecular dynamics
Computer program listings
Derivatives
55 Citations (Scopus)

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

Ferguson, D. M., Gould, I. R., Glauser, W. A., Schroeder, S. & Kollman, P. A., May 1992, In : Journal of Computational Chemistry. 13, 4, p. 525-532 8 p.

Research output: Contribution to journalArticle

Molecular Mechanics
Molecular mechanics
Alkanes
Ring
Paraffins
27 Citations (Scopus)

Free energy perturbation calculations involving potential function changes

Ferguson, D. M., Pearlman, D. A., Swope, W. C. & Kollman, P. A., Apr 1992, In : Journal of Computational Chemistry. 13, 3, p. 362-370 9 p.

Research output: Contribution to journalArticle

Potential Function
Free energy
Free Energy
Perturbation
Solvation
31 Citations (Scopus)

How transferable are hydrogen parameters in molecular mechanics calculations?

Veenstra, D. L., Ferguson, D. M. & Kollman, P. A., Oct 1992, In : Journal of Computational Chemistry. 13, 8, p. 971-978 8 p.

Research output: Contribution to journalArticle

Molecular Mechanics
Molecular mechanics
Hydrogen
Van Der Waals
Quantum theory
17 Citations (Scopus)

New Results on Protein Folding from Simulated Annealing

Garrett, D. G., Kastella, K. & Ferguson, D. M., Jul 1 1992, In : Journal of the American Chemical Society. 114, 16, p. 6555-6556 2 p.

Research output: Contribution to journalArticle

Protein folding
Protein Folding
Simulated annealing
1991
14 Citations (Scopus)
Oligodeoxyribonucleotides
Free energy
Decomposition
Organophosphonates
Single-Stranded DNA
91 Citations (Scopus)

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

Ferguson, D. M. & Kollman, P. A., Jun 1991, In : Journal of Computational Chemistry. 12, 5, p. 620-626 7 p.

Research output: Contribution to journalArticle

Molecular Mechanics
Molecular mechanics
Hydrogen Bonds
Hydrogen bonds
Force Field
86 Citations (Scopus)

Determination of the Relative Binding Free Energies of Peptide Inhibitors to the HIV-1 Protease

Ferguson, D. M., Radmer, R. J. & Kollman, P. A., Aug 1 1991, In : Journal of Medicinal Chemistry. 34, 8, p. 2654-2659 6 p.

Research output: Contribution to journalArticle

1990
28 Citations (Scopus)
Molecular Mechanics
Lanthanoid Series Elements
Molecular mechanics
Coordination Complexes
Metal complexes
1989
178 Citations (Scopus)

A New Approach to Probing Conformational Space with Molecular Mechanics: Random Incremental Pulse Search

Ferguson, D. M. & Raber, D. J., Jun 1989, In : Journal of the American Chemical Society. 111, 12, p. 4371-4378 8 p.

Research output: Contribution to journalArticle

Molecular mechanics
Mechanics
Cycloparaffins
Potential energy surfaces
Computational methods
38 Citations (Scopus)

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

Ferguson, D. M., Glauser, W. A. & Raber, D. J., Jan 1 1989, In : Journal of Computational Chemistry. 10, 7, p. 903-910 8 p.

Research output: Contribution to journalArticle

Molecular Mechanics
Molecular mechanics
Conformation
Search Methods
Conformations
1985
30 Citations (Scopus)

Structures of lanthanide shift reagent complexes by molecular mechanics computations

Brecknell, D. J., Raber, D. J. & Ferguson, D. M., Oct 1985, In : Journal of Molecular Structure: THEOCHEM. 124, 3-4, p. 343-351 9 p.

Research output: Contribution to journalArticle

Molecular Computers
Lanthanoid Series Elements
Molecular mechanics
Mechanics
reagents