Software & Server
Auf dieser Seite finden Sie die vom ZBH angebotenen Bioinformatik-Server. Details zur Verwendung der Server finden Sie auf den entsprechenden Webpages (nur in englisch). Sie finden außerdem eine vollständige Liste mit allen Webressourcen unter den jeweiligen Arbeitsgruppen (Datensätze, Softwarepakete, Server).
Computational Molecular Design Group (AMD, Prof. Rarey)
AMD Software Server
The AMD Software Server is the central download plattform for all our tools. After registration you get access to several programs related to cheminformatics and structure-based design. The software is for free for academic use and evaluation purposes.
The ProteinsPlus server offers a rich functionality related to protein structures. After uploading or selecting a PDB file, you can visualize the protein using the brand new NGL viewer, get an overview of small molecules bound and calculate various protein-related content. Protoss adds hydrogen atoms and optimizes the hydrogen bond network for you. Furthermore, it determines the tautomeric and protomeric states of the protein as well as small molecules contained. The DoGSiteScorer detects binding sites and estimates their druggability to name just two widely used services.
The SMARTSviewer provides a visualization for SMARTS strings. The depiction is based on structure diagrams as known from standard molecule visualization. Complex SMARTS pattern are splitted in more simple parts by extracting the recursive parts in separate structure diagrams. A legend explains the new graphic symbols as well as the meaning of the SMARTS in words.
Biomolecular Modeling Group (BM, Prof. Torda)
This takes a protein structure (PDB format) or asks for the name of a PDB file. This is then compared against structures from the PDB. After about 20 minutes, you will receive a set of structural alignments, completely independent of sequence identity. The service is similar to that provided by dali.
This is a version of our protein superposition code. If you have two proteins and want a structural superposition and alignment, use this.
Applied Cheminformatics and Molecular Design Group (ACM, Prof. Kirchmair)
New e-Resource for Drug Discovery (NERDD)
NERDD is the ACM group’s new web platform providing free access to most models and tools developed in this lab. NERDD is designed to be maintainable and scalable. The platform meets modern security standards and supports encrypted communication via HTTPS. The web service is linked to an in-house high-performance computing facility that can handle large numbers of concurrent requests. Currently, NERDD features the following modules:
- FAME 3, a predictor the site of metabolism for phase 1 and phase 2 metabolic enzymes
- GLORY, a predictor of the likely metabolites of small molecules
- Hit Dexter, a set of models for predicting compounds likely to cause false readouts in biological assays
- NP-Scout, a machine learning model for identifying natural products and natural product analogs in large molecular libraries
- Skin Doctor, a set of machine learning models for predicting skin sensitizers
Former Server (replaced or out of service)
DoGSiteScorer is an automated pocket detection and analysis tool. Size, shape and physico-chemical features of automatically predicted pockets are annotated and incorporated into a support vector machine for druggability estimations. The DoGSiteScorer became part of the ProteinsPlus Server (see above).
PoseViewWeb automatically creates two-dimensional diagrams of complexes with known complex structure according to chemical standards. A diagram contains the ligand, the amino acids of the receptor which interact with the ligand, and the hydrophilic interactions schematized as dashed lines between the corresponding atoms. The PoseViewWeb Server became part of the ProteinsPlus Server (see above).
PPI Prediction Server classifies a protein-protein complex concerning its interaction type into permanent, transient or crystal artifact. The discrimination is performed using two characteristics of the protein-protein complex, the hydrophobicity of the interface and the quotient of interface area ratios. The PPI server became part of the ProteinsPlus Server (see above).
Protoss is a fully automated hydrogen prediction tool for protein-ligand complexes. It adds missing hydrogen atoms to protein structures (PDB-format) and detects reasonable protonation states, tautomers, and hydrogen coordinates of both protein and ligand molecules. The Protoss Server became part of the ProteinsPlus Server (see above).
It takes a protein sequence, aligns it to a library of structures and mails structure predictions back to you (protein threading).
The ChemBioNavigator allows the user to visualize the chemical and biological space of a set of molecules in a chemically-aware manner. The physicochemical properties of sets of molecules can be plotted against each other and each individual data point investigated further via direct links to original data sources. The ChemBioNavigator allows searching for structurally related molecules via a substructure pattern or general similarity search. Note that the ChemBioNavigator is currently switched off due to compatibility issues with the OpenPHACTS API.