From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library.

Nowadays, computational approaches are an integral part of life science research. Problems related to interpretation of experimental results, data analysis, or visualization tasks highly benefit from the achievements of the digital era. Simulation methods facilitate predictions of physicochemical properties and can assist in understanding macromolecular phenomena.

Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces.

Comparison of three-dimensional interaction patterns in large collections of protein-ligand interfaces is a key element for understanding protein-ligand interactions and supports various steps in the structure-based drug design process. Different methods exist that provide query systems to search for geometrical patterns in protein-ligand complexes. However, these tools do not meet all of the requirements, which are high query variability, an adjustable search set, and high retrieval speed.

UNICON: A Powerful and Easy-to-Use Compound Library Converter.

The accurate handling of different chemical file formats and the consistent conversion between them play important roles for calculations in complex cheminformatics workflows. Working with different cheminformatic tools often makes the conversion between file formats a mandatory step. Such a conversion might become a difficult task in cases where the information content substantially differs.

MONA 2: A Light Cheminformatics Platform for Interactive Compound Library Processing.

Because of the availability of large compound collections on the Web, elementary cheminformatics tasks such as chemical library browsing, analyzing, filtering, or unifying have become widespread in the life science community. Furthermore, the high performance of desktop hardware allows an interactive, problem-driven approach to these tasks, avoiding rigid processing scripts and workflows. Here, we present MONA 2, which is the second major release of our cheminformatics desktop application addressing this need.

Discriminative Chemical Patterns: Automatic and Interactive Design.

The classification of molecules with respect to their inhibiting, activating, or toxicological potential constitutes a central aspect in the field of cheminformatics. Often, a discriminative feature is needed to distinguish two different molecule sets. Besides physicochemical properties, substructures and chemical patterns belong to the descriptors most frequently applied for this purpose.

An integrated approach to knowledge-driven structure-based virtual screening.

In many practical applications of structure-based virtual screening (VS) ligands are already known. This circumstance requires that the obtained hits need to satisfy initial made expectations i.e.

MONA - Interactive manipulation of molecule collections.

: Working with small-molecule datasets is a routine task for cheminformaticians and chemists. The analysis and comparison of vendor catalogues and the compilation of promising candidates as starting points for screening campaigns are but a few very common applications. The workflows applied for this purpose usually consist of multiple basic cheminformatics tasks such as checking for duplicates or filtering by physico-chemical properties.

[Design of an inverse planning system for radiotherapy using linear optimization].

Our approach shows that inverse planning for intensity-modulated beams in radiotherapy can be solved efficiently by the mathematical method of linear optimization. The completeness property of this method guarantees that calculated treatment plans fulfill the dose constraints given by the oncologist. Techniques developed by our group can also avoid the possible infeasibility caused by a physically impossible dose distribution.