Custom Coding

Custom Coding from OpenEye

Custom Coding from OpenEye

OpenEye’s modeling applications are all built using the cutting edge cheminformatics and scientific toolkits that OpenEye also offers to our customers; for example, our class-leading shape comparison and scoring tool ROCS is built on the Shape TK. Our toolkits have long provided a solution for users seeking more control over the method and results of a calculation than can be provided in an application. However, we believe that the ultimate value of toolkits lies not in their use separately but in their integration to produce a customized solution, taking a subset of capabilities from multiple toolkits and combining them to solve unique problems. We took this approach when developing the successful lead hopping application EON, which identifies novel compounds by the similarity in shape and electrostatics. EON utilizes a combination of OEChem TK (cheminformatics), Omega TK (conformer sampling), Shape TK (shape scoring) and Zap TK (electrostatic scoring) to achieve this goal.

Having found that the appropriate combination of toolkits is very valuable in solving problems in our own development work we now offer this capability to our customers through the Toolkit Application group. Our customer’s problems are unique to them and as such we aim to develop individual solutions to these unique problems. A few recent examples of collaborations between the custom coding group and our customers have addressed problems at several different scales:

  • Development of a custom fingerprint method.

  • Binding site matching, alignment, and display: using a combination of Shape TK, Spicoli TK and OEChem TK protein binding sites are used to align and score different proteins to one another.

  • Matched molecular pair identification and analysis: using the matched pair output from OEMedChem TK the 2D depiction toolkit OEDepict TK is used to highlight the transformation and display data relevant to it.

  • The design of shape diverse libraries: selecting subsets from large libraries of compounds based on diversification by shape using the OEChem and Shape TKs.

For more detailed information on how Customization might work for you, please contact us at the link below:

 Custom Code Support

Modified FastROCS

The image illustrates how we have modified the FastROCS server for one of our customers. Instead of using only one query molecule to screen a database for similar compounds, we have implemented a workflow where 3D similarity values for each molecule against all the other structures is calculated. This has enabled the user to create a similarity matrix which was used to identify the cluster of highly similar/ dissimilar structures.