Structural Analysis

The determination of a protein's 2D/3D structure is crucial in the study of its function. The user will find here access to various services explicitly designed to help in this complex process such as DALI.

The following are links to the various structural analysis tools we have available at the EBI.

Tool	Description
DaliLite	This is a program for pairwise structure comparison. Compare your structure(first structure) to a reference structure(second structure).
EMsearch	A search tool for electron microscopy depositions.
MaxSprout	Reconstruction of 3D coordinates from C(alpha) trace.
MSDfold	Secondary structure matching - Compare protein chains/structures and look for similar ones in the whole PDB archive or among SCOP domains.
MSDpro	A java applet tool that allows you to construct complex relational queries on the PDBe, without needing to know the arrangement of the data within the database, or the language in which such queries are usually written, SQL.
PDBeSite	This tool allows the ability to search the active site database based on ligand (eg ATP) or active site (eg CYS CYS CYS CYS) information.
NMR Representatives	Search for NMR elucidated structures in the PDB.
PDBe Services	A complete list and summary of all the tools and services the Protein Databank in Europe (PDBe) group have to offer.
PQS	Protein quaternary structure query.
PQS-Quick	Quickly retrive protein quaternary structure information from PDB ID code.
PROCOGNATE	PROCOGNATE is a database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam.
Tempura New	Tempura is a function prediction tool and local structural comparison service. It uses the "reverse template" approach published as part of the ProFunc server but has been modified to allow the user to specify the amino acids to be used in the template generation process.

Please Note

The DALI service at the EBI will be phased out of use on the 26th Jan 2008. This is an effect of new hardware and technical changes at the EBI. DALI no longer offers the service that was unique in 1996 when it started. An alternative system is available through SSM. This is an interactive procedure and is available on URL http://www.ebi.ac.uk/msd-srv/ssm/.

http://biotech.ebi.ac.uk/ has been phased out since 26th Jan 2008.

The EBI ReLiBase mirror (http://relibase.ebi.ac.uk/) was phased out in January, 2008. However, the up-to-date version of this service is still available from the Cambridge Crystallographic Data Centre (CCDC) at http://relibase.ccdc.cam.ac.uk/.

http://www.ebi.ac.uk/msd-srv/msdtarget/status.html has been phased out since 26th Jan 2008.

The Macromolecular Structure Database (MSD) group has moved to http://www.ebi.ac.uk/pdbe/ and changed its name to the Protein Databank in Europe (PDBe) as of Jan 2009.