Relibase manual

All entries have been derived from the PDB. ReLiBase was developed as a tool for studying binding preferences and binding geometries of protein ligands and as a practical help in modelling. The PDB has several severe deficiencies regarding the handling of non-protein molecules. First, in contrast to ReLiBase, the PDB does not include information about bond and atom types of non-protein molecules.

The ability to discriminate between e. Secondly, ReLiBase implements query tools for identifying ligands and analysing receptor—ligand complexes which are not available in the PDB. In the PDB ligands can only be identified by searching for chemical names and keywords. Taking into account the complexity of chemical naming conventions this is highly ineffective e.

ReLiBase provides similar search tools as the Cambridge Structure Database but optimized for protein—ligand complexes. The main search tools and their applications are summarized in Table 1. Table 1 Summary of query tools in ReLiBase. Using the PDB to analyse such questions is, in principle, possible but inefficient and time consuming. With ReLiBase such an analysis can be performed within minutes. Substructures and distance restraints can be specified graphically with a JAVA-based molecule editor Fig.

ReLiBase tests all ligands for the presence of a quaternary N atom and checks all hits for aromatic side chains within the specified distance range.

In two other complexes in both cases phosphatidylcholine lipids the N atom points towards the solvent and makes no interaction with the protein. The search time for this particular query was ReLiBase is, therefore, an extremely efficient tool for analysing structures of receptor—ligand complexes.

Depending on the complexity of the query search times are normally in the range of several seconds for substructure searches to several minutes for complex three-dimensional queries.

Interactions due to crystal contacts cannot be identified. Queries regarding the packing of side chains in proteins and protein—protein contacts are in principle possible but slow and, therefore, not available on the WWW. ReLiBase is still very much in development and driven by the acute needs of users. Several new enhancements are currently under development and will be made available within the next few months.

This includes new components for analysing conformational flexibility in binding sites and tools for studying water structures in binding sites. An updated version of ReLiBase with improved performance and a new user interface as shown in Fig. The recent explosion of experimental data about protein—ligand complexes will continue in the near future. New and improved experimental techniques will even accelerate the output of data. To exploit this rich body of data for studying and modelling of receptor—ligand complexes, databases are indispensable.

Driven by this acute need for freely available data many highly specialized databases have been developed and made available on the WWW. Only registered users can comment on this article. Sign in Register. More Review. Subscribe Advertise Topics Issues Contributors. Abstract Knowledge discovery from the exponentially growing body of structurally characterised protein-ligand complexes as a source of information in structure-based drug design is a major challenge in contemporary drug research.

Publication types Research Support, Non-U. Since we are continuously optimizing our plug-ins for current operating systems, technical support is only available for the newest product versions with their respective system requirements. Skip to content. Facebook page opens in new window Twitter page opens in new window YouTube page opens in new window SoundCloud page opens in new window. My Relab Account Top Bar menu. Download Our Newest Product Installers. Select product.

Sessions using the LX Complete are only compatible as far back as V2. LX Complete Mac changelog. LX Complete — Version 3. LX Complete Win changelog. Sessions using the LX RHall are fully backwards compatible. LX RHall Mac changelog. LX RHall — Version 3. LX RHall Win changelog. RHall — Ver 3.