How To and Tips Archive

How To - Docking

How to dock a ligand to an electron density map. The ICM X-Ray AutoFit is an automated method to fit a ligand into electron density. The tool combines the powerful ICM docking algorithm with an electron density fitting function. Click here for step by step instructions.

How to dock a focused Markush library. A Markush library can be generated on the fly and docked using ICM. In this example we use the roscovitine ligand bound to CDK5 to identify scaffolds which may improve ligand-receptor interaction.

NOTE: Tutorials and Frequently Asked Questions can also be found in the ICM Graphical User Interface Manual. If there is a key tutorial that you really would like to see then please post your request on the ICM Forum.

ICM Tips

This section is a log of all the latest tips from ICM developers and experienced users. Use the web browser (Edit/Find) to find keywords.

by Ruben Abagyan Oct 18, 9:11 am

Dear ICMers,

Ability to select atoms of interest is important in scripts. The selection language and functions returning selections are extensive, Here I wanted to describe some new functions. First, the three functions that EXPAND the source selection with different kind of terminal atoms.

- Adding terminal hydrogens to a selection, For example you graphically selected just the heavy atoms of a side chain, but you really want the attached hydrogens as well. This function will do exactly that:

Select(  <mySel>  hydrogen ) 

#example
build string "ASD"
aa = a_//cb,cg
Select(aa hydrogen)  # will return a new selection to which hydrogens are added.

- Adding ANY terminal atom (not only the hydrogens) is achieved with this function:

Select( <mySel> smooth )

It sort of patches 'holes' in the selection and makes it smooth. Example:

Select(a_/2/c smooth )  # adds the carbonyl oxygen

- Adding only the polar hydrogens potentially involved in hydrogen bonds is another variation. This may be achieved with this function:

Select( <mySel> hbond ) 

The previous three expanded the selection, the next function will return a SUBSET with a fixed number of neighbors.

Select( <sourceSelection> bond  1 ) #for atoms with one covalent bond
Select(<selectSelection> bond 2 ) #with two atoms attached
.. etc.

Use it or loose it :-)

Ruben

by Ruben Abagyan Oct 17, 10:16 am

Problem. Frequently a protein sequence from a PDB file contains N- or C- terminal expression tags and can not be recognize its SWISSPROT origin (e.g. IL2_HUMAN) if you search for near identity (>98%). The near identity search is necessary however to separate from close species.

The new array S_proteinTags contains regular expressions for the majority of expression tags (e.g. {"^.{1,10}HHHHH",..}. You can edit or replace this set with your own.

The new function:

Trim( <sequence> <S_tags> ) #returns a sequence from which all the mentioned
tags are removed.

#example

a=Sequence("ADGSHHHHHHQWRTEYQWRTEYQWRTEY")

Trim(a,S_proteinTags)  # returns sequence QWRTEYQWRTEYQWRTEY

(this is a random, but potentially useful message, just to test if and how this group is working)

Ruben