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 (NAOMI ChemBio Suite)
The AMD Software Server is the central download platform for all our tools that are part of the NAOMI ChemBio Suite. After registration, you get access to several programs related to cheminformatics and structure-based design. The software is available free of charge for academic use and evaluation purposes.

ProteinsPlus
The ProteinsPlus web server offers numerous functionalities related to protein structures. After uploading or selecting a PDB entry, an AlphaFold2 structure, or uploading your own PDB file, you can visualize the protein using the NGL Viewer, get an overview of small molecules bound, and calculate various protein-related content.

Several tools are integrated into ProteinsPlus. Protoss adds hydrogen atoms and optimizes the hydrogen bond network for you. Furthermore, it determines the tautomeric and protomeric states of the protein and bound small molecules. WarPP predicts the position of water molecules, while METALizer assists in analyzing metal coordination geometries. The DoGSite method detects binding sites and estimates their druggability. The detected pockets can immediately be used for molecular docking with the online tool JAMDA. 2D protein-ligand interaction diagrams of the predicted poses can be generated with PoseView, while PoseEdit helps to further improve the quality and style of the diagrams. The method LifeSoaks detects solvent channels in protein crystals. Structure quality can be estimated using EDIAscorer or StructureProfiler. Similarity searches in the PDB can be performed with SIENA and GeoMine, while MicroMiner searches the PDB for single-residue substitutions with respect to a given protein structure.

SMARTSplus
SMARTSplus is the ultimate visualization and analysis platform for SMARTS patterns in cheminformatics. It provides access to five tools. SMARTSview revolutionizes the way chemical patterns are interpreted by transforming complex SMARTS expressions into intuitive, visual representations. SMARTScreate extends the power of SMARTSview with an interactive graphical editor and a graph mining component. It generates discriminative SMARTS patterns automatically based on molecule sets. SMARTScompare and SMARTSsearch enable pattern analysis and similarity searches. SMARTSexplore is a specialized tool designed to visualize and analyze numerous collections of SMARTS expressions and their similarity relationships.

SmartChemist
The SmartChemist server shall enable anyone to discuss the chemistry of molecules competently and adequately. It matches common substructures and highlights them, providing their (trivial) names. The substructures highlighted are common functional groups, small (hetero-)cycles, and some biologically relevant molecules.

FastGrow
FastGrow is a fast fragment-growing approach using a shape-based algorithm. It also features pharmacophore-like constraints, geometry optimization, and built-in ensemble flexibility. Beginning with a fragment in the active site and an exit vector, FastGrow scans through thousands of possible fragment extensions in seconds.

Biomolecular Modeling Group (BM, Prof. Torda)

SALAMI
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.

WURSTL
This is a version of our protein superposition code. If you have two proteins and want a structural superposition and alignment, use this.

Former Server (replaced or out of service)

DoGSiteScorer
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
PoseViewWeb automatically creates two-dimensional diagrams of complexes with known complex structure according to chemical standards. A diagram contains the ligand, the receptor residues interacting 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 Server
PPI Prediction Server classifies a protein-protein complex according to its interaction type as 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
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).

WURST
It takes a protein sequence, aligns it to a library of structures and mails structure predictions back to you (protein threading).

ChemBioNavigator
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.