BibliographyΒΆ

[Bostrom-2001]
Jonas Bostrom,
Reproducing the Conformations of Protein-Bound Ligands: A Critical Evaluation of Several Popular Conformational Searching Tools,
Journal of Computer-Aided Molecular Design, Vol. 15, pp. 1137, 2001
[Bostrom-2003]
J. Bostrom, 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
[Coutsias-2016]
E. A. Coutsias, K. W. Lexa, M. J. Wester, S. N. Pollock, M. P. Jacobson,
Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics,
J. Chem. Theory Comput., Vol. 12, pp. 4674–4687, 2016
[Crippen-1988]
G. M. Crippen, T. F. Havel,
Distance Geometry and Molecular Conformation,
Chemometric Series, Vol. 15, Research Studies Press: Taunton, UK, 1988
[Gasteiger-1990]
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
[Gasteiger-1993]
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
[Grant-2001]
J. Andrew Grant, Anthony Nicholls, A. Geoffrey Skillman, and Matthew T. Stahl,
Dude, where are my conformers?,
222nd National ACS Meeting, 2001
[Grant-2007]
J.A. Grant, B.T. Pickup, M.J. Sykes, C.A. Kitchen and A. Nicholls,
A Simple Formula for Dielectric Polarization Energies: The Sheffield Solvation Model,
Chem. Phys. Letters, Vol. 441, pp. 163-166, 2007
[Guba-2016]
W. Guba, A. Meyder, M. Rarey and J. Hert,
Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules,
Journal of Chemical Information and Modeling, Vol. 56, pp. 1-5, 2016
[Halgren-1996-1]
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
[Halgren-1996-2]
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
[Halgren-1996-3]
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
[Halgren-1996-4]
T.A. Halgren,
Merck Molecular Force Field: IV. Conformational Energies amd Geometries for MMFF94,
Journal of Computational Chemistry, Vol. 17, No. 5, pp. 587-615, 1996
[Halgren-1996-5]
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
[Hawkins-2010]
P.C.D. Hawkins, A.G. Skillman, G.L. Warren, B.A. Ellingson and M.T. Stahl,
Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database,
Journal of Chemical Information and Modeling, Vol. 50, No. 4, pp 572-584, 2010
[Labute-2010]
P. Labute,
LowModeMD - Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops,
Journal of Chemical Information and Modeling, Vol. 50, pp 792–800, 2010
[Sadowski-1994]
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, Vol. 34, pp. 1000-1008, 1994
[Spellmeyer-1997]
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
[Stahl-2000]
Matthew T. Stahl,
Rapid 3D Database Searching,
IIR: Computational Drug Design, 2000
[Stahl-2001]
Matthew T. Stahl,
You want conformers? I’ll give you conformers!,
2nd Annual OpenEye Customers, Users, and Programmers Meeting, 2001
[Stahl-2002]
Matthew T. Stahl,
Omega, AESOP, and other cautionary tales of naming programs.,
3rd Annual OpenEye Customers, Users, and Programmers Meeting, 2002
[Watts-2014]
K.S. Watts, P. Dalal, A.J. Tebben, D.L. Cheney, and J.C. Shelley,
Macrocycle Conformational Sampling with MacroModel,
Journal of Chemical Information and Modeling, Vol. 54, pp 2680–2696, 2014