1. Search or Browse

The first step is to find the protein of interest by searching or browsing. You can perform Quick Search and Advanced Search, or browse hierarchical classification trees taken from White's List, TC, or OPM.

Quick Search

You can perform a quick text search using the search box at the top-right corner of each page. See below for search syntax ('Search Tips').

Advanced Search

You can perform advanced search using specific criteria. See below for search syntaxes ('Search Tips').

White's List

The list of membrane protein structures from the Stephen White Laboratory. [Original Website]

TC Tree

Hierarchical classification by the TC (Transporter Classification) system. [Original Website]

OPM Tree

Hierarchical classification by the OPM (Orientations of Proteins in Membranes) database. [Original Website]

2. Select a reference protein

Select a reference protein from the search results or the hierarchical tree by clicking on the title of the protein.

3. Explore conformations

Various graphical views of analysis results are available.

Distance Table

A tables containing distances between all the entries on the page (or the conformational groups).

Tree Diagram

A tree diagram showing relationships between all the entries on the page (or the conformational groups), generated by hierarchical clustering. A red broken line in the tree diagram indicates the RMSD cutoff value.

2D Map

A two-dimensional projection showing relationships between all entries on the page (or the conformational groups), generated by multidimensional scaling (MDS).

View Superimposition

View superimposition of the checked structures using the Jmol plugin.

Download Superimposition

Download an atomic coordinate file (in PDB format) of the superimposed structures. You can visualize the superimposition on your local machine with viewers such as PyMOL.

Protein Cutoff

In the protein clustering process, proteins having a percentage sequence identity greater than or equal to this cutoff value are considered related and clustered together. Their structures will be compared with each other in the next stage. When this cutoff value is decreased, the number of proteins in each first-stage cluster (thus, the number of structures to be compared) will increase.

Conformation Cutoff

In the conformation clustering process, structures with a dissimilarity score (currently measured by the Cα root mean square deviation) greater than this cutoff value are considered distinct conformational groups and clusters separately. When this cutoff value is decreased, the number of distinct conformational groups will increase.

Wildcard search: ∗

Asterisk [ ∗ ] can be used as a wildcard character. The two query terms mechanosensitive and mechano∗ will return identical search results in the current version of the database.

Fuzzy search: ∼

When you are not sure of the correct spelling of a word, you can use fuzzy search with tilde [ ∼ ]. The two query terms "potassium pump" and "potasium~ pump" will return identical search results in the current version of the database.

Boolean operators: AND, OR, +, -

Several examples are shown here: transporter AND symporter, symporter OR antiporter, +calcium pump, rhodopsin -halorhodopsin, and potassium -"related protein".

Grouping: " ", ( )

A phrase can be explicitly grouped with double quotes [ " " ] like "calcium pump". A sub-query can be grouped with parentheses [ ( ) ] like calcium AND (atpase OR pump).

Keyboard shortcuts

Keyboard shortcuts for handling the hierarchical trees.

Expand/Close node

Press Space bar, Enter key, or Cursors [ ← → ].

Select terminal node (PDB ID)

Press Space bar or Enter key.

Move in tree

Press Cursors [ ↑ ↓ ← → ].

Find a specific protein in the whole tree

You can do it in two steps: first, expand all the nodes by clicking "Expand/Close All Nodes" bar at the top, and then use your browser's search function (viz. Mac: Command Key + F, Win: Windows Key + F).

Change representation

Right-click > Style > Structures > select your favorite representation

Change the center of rotation

Right-click > Set picking > Center, then select a center atom to be moved to the center of rotation

Slab (Z-clipping)

Right-click > Console > enter slab on command in the opened console, then Ctrl + Shift, click and drag (slab from front) or Ctrl + Shift, double-click and drag (slab from back). If you are using Mac, click first, then push Ctrl + Shift and drag.

JavaScript

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Jmol

Please check Jmol website for details.

Web Browser

The website has been tested with:

Mac OS X

Safari: 5.0.2, 5.0.3

Firefox: 2.0.0.20, 3.0.19, 3.5.15, 3.5.16, 3.6.8, 3.6.12, 3.6.13

Chrome: 7.0.517.41

Windows

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Firefox: 3.6.8

Chrome: 8.0.552

Safari: 5.0.3