Molecular similarity is a key concept in drug discovery. It is based on the assumption that
structurally similar molecules frequently have similar properties. Assessment of similarity …

The superposition of small molecules is a standard technique in molecular modeling and for
some more advanced in silico applications of drug discovery a critical prerequisite. The aims …

A new algorithm for finding a maximum clique in an undirected graph is described. An
approximate coloring algorithm has been improved and used to provide bounds to the size …

ShaEP is a tool for rigid-body superimposition and similarity evaluation of ligand-sized
molecules. Molecular overlay methods traditionally work on either substructures, molecular …

Modern rational drug design not only deals with the search for ligands binding to interesting
and promising validated targets but also aims to identify the function and ligands of yet …

Protein binding sites are the places where molecular interactions occur. Thus, the analysis
of protein binding sites is of crucial importance to understand the biological processes …

Quantitative Structure Activity Relationship (QSAR) is an approach of mapping chemical
structure to properties. A significant development can be observed in the last two decades in …

We have recently announced the largest database of protein–ligand complexes, Binding
MOAD (Mother of All Databases). After the August 2004 update, Binding MOAD contains …

Background The identification of promising drug leads from a large database of compounds
is an important step in the preliminary stages of drug design. Although shape is known to …

Learning machines for pattern recognition, such as neural networks or support vector
machines, are usually conceived to process real–valued vectors with predefined …