During the past few years, pharmacophore modeling has become one of the key components in computer-aided drug design and in modern drug discovery. DrugOn is a fully interactive pipeline designed to exploit the advantages of modern programming and overcome the command line barrier with two friendly environments for the user (either novice or experienced in the field of Computer Aided Drug Design...

In this paper, we explore several extensions to surface pasting. In particular, using the task of modelling a ferret as a driving force, we improved the user interface for cylindrical pasting; we looked at methods for reducing the distortion of pasted features; and we created a method for pasting trimmed features to allow for features that do not have the rectilinear shape of standard pasting.

One of the goals of computational chemistry is the automated de novo design of bioactive molecules. Despite significant progress in computational approaches to ligand design and efficient evaluation of binding energy, novel procedures for ligand design are required. Evolutionary computation provides a new approach to this design issue. A reliable framework for obtaining ligands via evolutionary...

In this article, we discuss what we mean by 'design' and contrast this with the application of computational methods in drug discovery. We suggest that the predictivity of the computational models currently applied in drug discovery is not yet sufficient to permit a true design paradigm, as demonstrated by the large number of compounds that must currently be synthesised and tested to identify a...

often in modeling the engineering optimization design problems, the value of objective function(s) is not clearly defined in terms of design variables. instead it is obtained by some numerical analysis such as fe structural analysis, fluid mechanic analysis, and thermodynamic analysis, etc. yet, the numerical analyses are considerably time consuming to obtain the final value of objective functi...