Scaffold-based Enumeration

With the rapid development of the cheminformatics discipline, scaffold-based enumeration methods have become a simple and powerful method for establishing virtual compound libraries. Scientists can combine the results of R-group analysis to design and synthesize a virtual library representing a family of potential lead compounds.

BOC Sciences scaffold-based enumeration allows for the generation of virtual libraries via substituent variation, thus generating molecules with scaffolds of interest. Attachment point can indicate which part of the fragment can be directly connected to the core structure. We therefore provide accurate fragment definitions for each R-group on the scaffold.

Figure 1. Simplified workflow diagram of PKS Enumerator system. (Kyaw, P. P.; et al. 2018)

Scaffold-based Enumeration Process

BOC Sciences can provide structures that are derived from the same scaffold but with different substituents using our well-designed method. Our enumeration process is listed as following:

• Preparation of a scaffold-based enumeration

1. Creating the scaffold

We create the scaffolds that must contain one or more R-atoms that can be replaced.

2. Addition of the R-group definitions

We offer three different ways to create definitions for R-groups:

1) Loading R-groups from a collection: Building Blocks library is the most important source for R-groups.

2) Loading R groups from files: R-group definitions can be obtained from some common chemical file formats that support R group attachment points.

3) Plotting R-groups

We analyze the fragments before they are added to the R-group.

• Enumerating Markush structures

We apply the Markush structure which contains both scaffold and R-group definition.

• Enumeration type settings

1. Random enumeration

We conduct random selection to replace the R-atoms.

2. Sequential enumeration

The R-atoms are replace with other groups systematically.

3. Maximum number of structures

Our clients can determine the number of generated compounds.

4. Enumeration of homologous groups
5. Duplicate filtering of results

We ensure that only unique molecules are saved from the results.

6. Filter valence errors

Our experts filter out faulty result structures.

7. Filter geometrically infeasible rings

• Compound library preview

Our customers can preview of molecules generated.

• Enumeration implementation

BOC Sciences provides professional, rapid and high-quality services of Scaffold-based Enumeration at competitive prices for global customers. Personalized and customized services of Scaffold-based Enumeration can satisfy any innovative scientific study demands. Our clients have direct access to our staff and prompt feedback to their inquiries. If you are interested in our services, please contact us immediately!