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 from OpenEye licenses for the relevant toolkits.

• Various fingerprint-related programs
• Tautomer-independent molecule representation
• Virtual screening by pharmacphore similarity
• Enumeration of tautomers likely to be present at physiological pH
• SMILES and SMARTS viewer
• 2D Pharmacophore fingerprints

Using RDKit

The RDKit is fully 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 toolkits:

• An RDKit-based SMILES and SMARTS viewer similar to SmiV.
• The code and test data for the Spectral Clustering paper

In 2020, David overhauled the 2D drawing code, in particular to improve the positioning of atomic symbols and other text. This was presented at the RDKit 2020 Virtual UGM. As an example of the improvement, it went from to and if you want to irritate your colleagues you can use different fonts, such as the XKCD font

Miscellaneous

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 somewhat of overkill. The HTML/Javascript app HSV (https://github.com/DavidACosgrove/HTML-SDF-Viewer) addresses 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.

Papers

• Racemisation in Chemistry and Biology. A. Ballard, S. Narduolo, H.O. Ahmed, N.I. Keymer, N. Asaad, D.A. Cosgrove, N.J. Buurma and A.G. Leach. Chemistry, 2019.
• The problem of racemization in drug discovery and tools to predict it. A. Ballard, S. Narduolo, H.O. Ahmad, D.A. Cosgrove, A.G. Leach and N.J. Buurma. Expert Opinion on Drug Discovery, 14, 527-539 (2019).
• Alignment-Free 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).
• A 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)
• Discovery 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).