Combinatorial chemical libraries produced on solid support offer fast and 
cost-effective access to a large number of unique compounds. If such libraries 
are screened directly on-bead, the speed at which chemical space can be explored 
by chemists is much greater than that addressable using solution based synthesis 
and screening methods. Solution based screening has a large supporting body of 
software such as structure-based virtual screening tools which enable the 
prediction of protein-ligand complexes. Use of these techniques to predict the 
protein bound complexes of compounds synthesized on solid support neglects to 
take into account the conjugation site on the small molecule ligand. This may 
invalidate predicted binding modes, the linker may be clashing with protein 
atoms. We present CSBB-ConeExclusion, a methodology and computer program which 
provides a measure of the applicability of solution dockings to solid support. 
Output is given in the form of statistics for each docking pose, a unique 2D 
visualization method which can be used to determine applicability at a glance, 
and automatically generated PyMol scripts allowing visualization of protein atom 
incursion into a defined exclusion volume. CSBB-ConeExclusion is then 
exemplarically used to determine the optimum attachment point for a purine 
library targeting cyclin-dependent kinase 2 CDK2.