tree example
GPCR Browser Home How to use About LMC Home

HOW TO USE


In this web server, full sequence and binding site classifications are stored and a web interface enabling users to find the related information for a query receptor. Using as input the uniprot protein code or the fasta sequence of a GPCR, the web application displays detailed information about it and produces several tables and analysis graphs. The information is intended to be displayed on a highly user-friendly interface.


GPCR-browser


Once the input is introduced, the server generates four different sections:

i) TM sequence classification: It shows the closest resembling branch of protein according to our pre-calculated phylogenetic tree. This is very useful to observe the closest similar proteins to users’ input. The phylogenetic tree is browsable, adjusting the number of branches the user wants to see. Users can zoom in and out of tree branches, adjusting the number of nodes they want to observe. Branches of receptors with known crystal structure are shown in orange.

TM_tree

ii) Ligand-binding site representation: This figure shows the binding site of the users’ query and their relative position in Ballesteros-Numbering scheme numeration.

BS_draw

iii) Ligand-binding site classification: Most similar receptors’ binding sites are listed, in order of similarity. A link to IUPHAR web page of their known ligand in is provided.

BS_list

iv) Crystal structure template research: a phylogenetic tree is generated using the input receptor and receptors with known 3D structure. This tool is intended to assist in the template selection for homology modelling. A graph is generated showing phylogenetic distances between crystallized GPCR and the user’s query. The closest crystal in the tree is the best suited to build an homology model of the query receptor.