Out-of-the-box Solutions

Hazard and Risk Assessment

Computational methods for hazard and risk assessment and evaluation of toxicity of chemicals have become of increasing interest. In particular, the REACH (Registration, Evaluation, Authorization and Restriction of Chemicals) initiative has put heavy emphasis on non-testing methods to improve the protection of human health and the environment through the better and earlier identification of the intrinsic properties of chemical substances.

• CRAFT for modeling and evaluating the chemical reactivity, persistence and bio-degradation of chemicals (including their degradation products) in the environment

Drug Design and Property Prediction

During the past decades, in silico methodologies have become standard technology to support the drug discovery and design process. Ligand-based virtual screening, similarity searching, scaffhold hopping, predictive QSAR and QSPR, such as modeling and prediction of ADME-Tox properties and biological activities, are some of the methods that are used routinely to identify and optimize new lead structures for a certain biological target. Robust statistical and machine learning methods and proper numerical representations of chemical structures, called molecular descriptors, play a crucial role for all these techniques.

• CORINA for generating 3D molecular models
• ROTATE for exploring conformational spaces
• ADRIANA.Code for calculating physicochemical, 2D, 3D and surface-based molecular descriptors and properties
• SONNIA for analyzing and modeling chemical data

Synthesis Design and Reaction Prediction

The synthesis of new chemical entities is a difficult task that requires the expert knowledge of a well-trained chemist. Over the last decade, the increasing demand for novel chemical compounds is challenging chemists to increase their productivity. Therefore, computer-assisted synthesis design and reaction prediction can provide a valuable support to experts in order to identify fast and reliable suggestions on synthesis pathways and prioritize compounds according to their synthetic feasibility.

• THERESA for planning organic syntheses based on reaction databases
• SYLVIA for estimating the ease of synthesis of organic compounds

Metabolic Engineering and White Biotechnology

White Biotechnology or Green Chemistry, the production of bulk or fine chemicals and of biofuels by biotechnological processes, is gaining increasing importance. It allows the synthesis of chemicals in a more sustainable way with less environmental impact. Furthermore, these processes can lead to substantial manufacturing cost savings for compounds traditionally synthesized chemically. These processes also allow the switching from petrochemical starting materials to renewable biological feedstocks.

• BioPath.Design for planning of biosyntheses based on enzyme-catalyzed biochemical reactions

Analysis and Prediction of Metabolism

Endogenous Metabolism

The study of biochemical pathways, i.e., the endogenous metabolism, in living species is of central importance in many disciplines of modern life sciences. The systematic analysis of the intracellular transformations and pathways of metabolic, enzyme-catalyzed reactions can contribute an enormous value to address challenges in the areas of metabolomics, drug discovery, modeling of biological systems or "green chemistry" and metabolic engineering.

• BioPath and BioPath.Explore a database and a retrieval system for the analysis of molecules, reactions and pathways involved in the endogenous metabolism

Metabolism of Xenobiotics

In silico prediction of ADMET (absorption, distribution, metabolism, excretion, toxicity) properties is of special interest in the drug discovery and design process in order to detect and eliminate compounds with inappropriate pharmacokinetic properties at an early stage. A central step in the ADMET profiling of potential drug candidates is the evaluation of drug metabolism. Some enzymes involved in the detoxification process show polymorphism and have multimodal binding sites. The majority of the oxidation reactions in phase I metabolism are catalyzed by cytochrome P450 enzymes.

• isoCYP for predicting the predominant isoform of human CYP P450 substrates
• MetaboGen for generating and evaluating human metabolites of xenobiotics

Building and Enriching Chemical Databases

Chemical databases are one of the core technologies and of central importance in any computationally-based research and development effort in life sciences and chemistry. Building and maintaining databases requires robust and reliable powerful tools when chemical compounds from different sources and origin have to be converted into normalized, high-quality structural data. Enriching a database with additional data, such as 3D structures and multiple conformations, stereoisomeric and tautomeric forms or physicochemical properties, drastically increases its value as well as the likelihood of the R&D project's success.

• ADRIANA.Code for calculating physicochemical, 2D, 3D and surface-based molecular descriptors and properties
• CORINA for generating 3D molecular models
• ROTATE for exploring conformational spaces
• MN.2DCOOR generates 2D depiction-like atomic coordinates
• MN.CHECK performs structure validation and normalization of molecular structures
• MN.CONVERT inter-converts 40 different structure and reaction file formats
• MN.IMAGE converts structure files into raster or vector images
• MN.JOIN concatenates a series of SDFiles into one single SDFile
• MN.MERGE generates an SDFile by merging separated structure and data files
• MN.PAGE converts chemical files into printable documents
• MN.SPLIT splits an SDFile containing n structures into n single SDFiles
• MN.STERGEN enumerates all possible combinations of stereoisomers
• MN.TABLE converts SDFiles containing structures and data into spreadsheets
• MN.TAUTOMER enumerates all tautomeric forms