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- 1
- Jonas Boström, ``Reproducing the Conformations of
Protein-Bound Ligands: A Critical Evaluation of Several Popular
Conformational Searching Tools'', Journal of Computer-Aided Molecular
Design (JCAMD), Vol. 15, pp. 1137, 2002.
- 2
- J. Boström, J. R. Greenwood, and J. Gottfries,
``Assessing the Performance of OMEGA with Respect to Retrieving Bioactive
Conformations'', Journal of Molecular Graphics and Modeling, Vol.
21, pp. 449-462, 2003.
- 3
- Mongoose
- 4
- Wizard
- 5
- J. Gasteiger, C. Rudolph and J. Sadowski, ``Automatic Generation of
3D Atomic Coordinates for Organic Molecules'', Tetrahedron Comp.
Method., Vol 3., pp. 537-547, 1990.
- 6
- J. Sadowski and J. Gasteiger, ``From Atoms and Bonds to
Three-dimensional Atomic Coordinates: Automatic Model Builders'', Chemical Reviews, Vol. 93, pp. 2567-2581, 1993.
- 7
- J. Sadowski, J. Gasteiger and G. Klebe, ``Comparison of Automatic
Three-dimensional Model Builders using 639 X-Ray Structures'', Journal
of Chemical Information and Computer Science (JCICS), Vol. 34, pp.
1000-1008, 1994.
- 8
- Concord
- 9
- David C. Spellmeyer, A.K. Wong, M.J. Bower and J.M. Blaney,
``Conformational Analysis using Distance Geometry Methods'', Journal
of Molecular Graphics and Modeling, Vol. 15, No. 1, pp. 18-36 1997.
- 10
- Matthew T. Stahl, ``Rapid 3D Database Searching'', IIR:
Computational Drug Design, circa 2000.
- 11
- Matthew T. Stahl, ``You want conformers? I'll give you
conformers!'', 2nd Annual OpenEye Customers, Users, and Programmers
Meeting, March 2001.
- 12
- J. Andrew Grant, Anthony Nicholls, A. Geoffrey Skillman, and Matthew
T. Stahl, ``Dude, where are my conformers?'', 222nd National ACS
Meeting, August 25th, 2001.
- 13
- Matthew T. Stahl, ``Omega, AESOP, and other cautionary tales of
naming programs.'', 3rd Annual OpenEye Customers, Users, and Programmers
Meeting, March 2002.
- 14
- T.A. Halgren, ``Merck Molecular Force Field: I. Basis, Form,
Scope, Parameterization and Performance of MMFF94'', Journal
of Computational Chemistry, Vol. 17, No. 5, pp. 490-519, 1996.
- 15
- T.A. Halgren, ``Merck Molecular Force Field: II. MMFF94 van
der Waals and Electrostatic Parameters for Intermolecular Interactions'',
Journal of Computational Chemistry, Vol. 17, No. 5, pp. 520-552,
1996.
- 16
- T.A. Halgren, ``Merck Molecular Force Field: III. Molecular
Geometries and Vibrational Frequencies'', Journal of Computational
Chemistry, Vol. 17, No. 5, pp. 553-586, 1996.
- 17
- T.A. Halgren and R.B. Nachbar, ``Merck Molecular Force Field:
IV. Conformational Energies amd Geometries for MMFF94'', Journal
of Computational Chemistry, Vol. 17, No. 5, pp. 687-615, 1996.
- 18
- T.A. Halgren, ``Merck Molecular Force Field: V. Extension of
MMFF94 using Experimental Data, Additional Computational Data and
Empirical Rules'', Journal of Computational Chemistry, Vol. 17,
No. 5, pp. 616-641, 1996.
- 19
- T.A. Halgren, ``MMFF VI. MMFF94s Option for Energy Minimization
Studies'', Journal of Computational Chemistry, Vol. 20, pp.
720-729, 1999.
- 20
- T.A. Halgren, ``MMFF VII. Characterization of MMFF94, MMFF94s
and Other Widely Available Force Fields for Conformational Energies
and for Intermolecular Interaction Energies and Geometries'', Journal of Computational Chemistry, Vol. 20, pp. 730-748, 1999.
- 21
- M. Sykes, B. Pickup, J.A. Grant, ``The Sheffield Solvation
Model'', In preparation.
