Open Source Programs
Using OpenEye Toolkits
Clearly, the OpenEye
toolkits are not themselves open
source. However, the programs below use them and are available
for download under a BSD open-source license. To compile
and run them, you will need to obtain
licenses for the relevant toolkits.
open-source, under a BSD license. As well as contributing to
the core code itself, notably the 2D drawing functionality,
David has published the following programs that use the
SDFs are a convenient format for passing structures and data
around, for example between 2 organisations using different
database systems for their cheminformatics. Most such systems
can export and import in SDF format. They are less convenient
if one wants to perform a quick inspection of the tabulated
data with the associated structures. Normally this would
require firing up a piece of commercial software which seems
this. It is a simple completely self-contained web page that
reads an SDF, tabulates the tagged data and displays the
structures in either 2D or 3D form as appropriate.
Molecular Shape Comparison Using Spectral Geometry: The
Framework. M.P. Seddon, D.A. Cosgrove, M.J. Packer and
V.J. Gillet. J. Chem. Inf. Model., ASAP (2018).
Quantitative Approach to Predicting Rate Constants for
Aqueous Racemization Allows Pointless Stereoselective
Syntheses to be Avoided. A. Ballard, H.O. Ahmad,
S. Narduolo, L. Rosa, N. Chand, D.A. Cosgrove,
P. Varkonyi, N. Asaad, S. Tomasi, N.J. Buurma and
A.G. Leach, Angewandte Chemie, Accepted Articles (2017)
and Evaluation of Anti-Fibrinolytic Plasmin Inhibitors
Derived from 5-(4-Piperidyl)isoxazol-3-ol (4-PIOL).
T.C. Schmidt, P.-O. Eriksson, D. Gustafsson,
D.A. Cosgrove, B. Frolund, J. Bostrom,
J. Chem. Inf. Model., 57, 1703-1714 (2017)
Investigation of the Use of Spectral Clustering for the Analysis of Molecular Data. S. Gan, D.A. Cosgrove, E.J. Gardiner, V.J. Gillet. J. Chem. Inf. Model., 54, 3302-3319 (2014).
An Extensive and Diverse Set of Molecular Overlays for the Validation of Pharmacophore Porgrams, I. Giangreco, D.A. Cosgrove, M.J. Packer, J. Chem. Inf. Model., 53, 852-866 (2013).
A System for Encoding and Searching Markush Structures. D.A. Cosgrove, K.M. Green, A.G. Leach, A. Poirrette, J. Winter. J. Chem. Inf. Model., 52, 1936-1947 (2012).
Development and Validation of an Improved Algorithm for Overlaying Flexible Molecules. R. Taylor, J.C. Cole, D.A. Cosgrove, E.J. Gardiner, V.J. Gillet, O. Korb. JCAMD, 26, 451-472 (2012).
Design of Compound Libraries for Fragment Screening. N. Blomberg, D.A.Cosgrove, P.W.Kenny and K. Kolmodin. JCAMD, 23, 513-525 (2009).
Multiobjective Optimization of Pharmacophore Hypotheses: Bias Toward Low-Energy Conformations, E.J. Gardiner, D.A. Cosgrove, R. Taylor, V.J. Gillet, J. Chem. Inf. Mod., 49, 2761-2773, (2009).
Representing Clusters Using a Maximum Common Edge Substructure Algorithm applied to Reduced Graphs and Molecular Graphs. E.J. Gardiner, V.J. Gillet, P. Willett, D.A.Cosgrove. J. Chem. Inf. Mod., 47, 354-366 (2007).
Scaffold Hopping Using Clique Detection Applied to Reduced Graphs. E.J. Barker, D. Buttar, D.A. Cosgrove, E.J. Gardiner, P. Kitts, P. Willett, V.J. Gillet, J. Chem. Inf. Mod., 46, 503-511 (2006).
Matched Molecular Pairs as a Guide in the Optimization of Pharmaceutical Properties; a Study of Aqueous Solubility, Plasma Protein Binding and Oral Exposure. A.G. Leach, H.D. Jones, D.A. Cosgrove, P.W. Kenny, L. Ruston, P. MacFaul, J. Wood, N. Colclough, B. Law. J. Med. Chem., 49, 6672-6682 (2006).
Scaffold Hopping Using Clique Detection Applied to Reduced Graphs. E.J. Barker, D. Buttar, D.A. Cosgrove, E.J. Gardiner, P. Kitts, P. Willett, and V.J. Gillet. J. Chem. Inf. Mod., 46, 503-511 (2006).
Lead Hopping Using SVM and 3D Pharmacophore Fingerprints. J.C. Saeh, P.D. Lyne, B.K. Takasaki and D.A. Cosgrove. J. Chem. Inf. Mod., 45, 1122-1133 (2005).
Identification of Compounds with Nanomolar Binding Affinity for Checkpoint Kinase-1 Using Knowledge-Based Virtual Screening. P.D. Lyne, P.W. Kenny, D.A. Cosgrove, C. Deng, S. Zabludoff, J.J. Wendoloski and S. Ashwell. J. Med. Chem., 47, 1962-1968 (2004).
A novel method of aligning molecules by local surface shape similarity. D.A. Cosgrove, D. Bayada and A.P. Johnson. JCAMD, 14, 573-591 (2000).
SLASH: A program for analysing the functional groups in molecules. D.A. Cosgrove and P. Willett. J. Mol. Graph. and Mod., 16, 19-32 (1998).
BOOMSLANG: A program for combinatorial structure generation. D.A. Cosgrove and P.W. Kenny. J. Mol. Graph., 14, 1-5 (1996).