Table of Contents

  1. Browsing proteins
  2. Editing proteins
  3. Protein identity check

Editing proteins

You may work with protein text in either of the PLN, UniProt or GPMAW formats. Proteax will automatically recognize the format of the protein text that you enter or copy/paste into the text field in the middle.

To the right you will see the sequence of the protein visualized along with information about the total number of residues and the protein structure's average molecular weight.

Projects

Each protein entry is asscoiated with a project in order to group related entries. The total list of projects is displayed to the left and the project that the current entry belongs to will be highlighted. You may move the protein entry to a different project by simply clicking that project. Clicking a project name also allows you to rename the project - but only if the project is not locked. Locked projects are displayed with a blue background while open projects have a white background.

You can add and delete projects by using the small buttons below the project list.

A quick PLN primer

The easiest way to enter protein entries by hand is via PLN: Protein Line Notaton. This section will give you a quick introduction to building a protein structure using PLN.

A basic two-chain protein

Let's start by entering a simple two-chain protein. Chains consist in their simplest form of a string of one-letter residue codes. Chains are separated by periods and must be terminated properly.

H-GIVEQCCTSICSLYQN-OH.H-FVNQHLCGSHLFYTPKT-OH

This protein is really two separate fragments so we should add disulfide bonds to link them together. Cysteines that form disulifde bonds are linked by adding a unique number in parenthesis after the cysteine. The unique number identifies the particular disulfide bond. After adding two disulfide bonds, the PLN becomes the following.

H-GIVEQC(1)C(2)TSIC(1)SLYQN-OH.H-FVNQHLC(2)GSHLFYTPKT-OH

Finally, we can add a modified residue and a terminal modification. Glu-4 is changed into "Gla" aka. "4-carboxyglutamate" and the second chain is terminated with an amide residue.

H-GIV[Gla]QC(1)C(2)TSIC(1)SLYQN-OH.H-FVNQHLC(2)GSHLFYTPKT-[NH2]