Sep 13 2018 Feedback.
Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
Learn and Predict
Docking
Virtual Screening
MolScreen
3D Ligand Editor
 Setup Ligand and Receptor
 Preferences
 Display Options
 Score and Strain
 Edit Ligand
 Screen Replacement Group
 Scan
 Bioisostere Scan
 Dock or Minimize
 Dock Table
 Fragment Linking
 Restraints
 Docking Templates
 Flexible Groups
 Refinement
 Multiple Receptor Docking
 Covalent Docking
 Dock to APF
 Save Docked Complex
 Export Docking Project
 Close Project
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index
PrevICM User's Guide
15.11 Fragment Linking
Next

Available in the following product(s): ICM-Pro | ICM-VLS | ICM-Chemist-Pro

This feature finds the best scaffold replacement or linker fragment from a database. It lets you interactively select two or more points of connection or replacement and search for possible fragments in the 3D database (SDF or Molsoft local database MOLT). The cutting bonds used to define scaffold are matched against a 3D database with a certain RMSD cutoff (usually very small). The best superposition is taken for the original compound and the chemical is minimized. The result is returned as a standard Ligand Editor hit list where results can be easily browsed, sorted and compared. Linker prediction can be made in the presence or absence of the receptor. Filters such as energy strain, maximum number of rotatable bonds and contact distance to the receptor can be used.

Step 1: Setup the ligand and/or the receptor in the 3D ligand editor. If you have fragments already made you should select the fragments and then choose "Selection" in the drop down menu in the ligand setup step. If you do not wish for the receptor to be considered when sampling linkers then just setup the ligand only. Once the ligand and/or receptor are setup it is generally a good idea to minimize the ligand to remove any clashes and optimize the geometry.

Step 2: Once the ligand and/or the receptor has been setup click on the edit tools button. A panel of editing tools will be displayed, click on the scissors button. Mark two or more bonds using the scissors tool. The first click on the bond will assign some direction (which should point the part you want to preserve), second click inverts the direction, third click clears the mark. For bonds to the hydrogen or bonds to the terminal heavy atom only one possible direction is available.

Step 3: Select the Advanced button and choose the option Find Linker. A dialog window will be displayed as shown above. You can choose to screen one ore more SDF files containing 3D coordinates or a molt file that is stored locally on your machine or on MolCart.
  • Provide a path to the 3D SDF or Molt file. We have provided some examples of 3D conformer databases here ftp://ftp.molsoft.com/molcartdb/3D
  • Strain Cutoff - any ligand exceeding this Strain value will not be placed in the results table. If you are using a ligand directly from the PDB it is a good idea to minimize the ligand and check the initial strain or increase this cutoff.
  • Max Rot Bonds in the Core - any ligand exceeding this number of rotatable bond value will not be placed in the results table.
  • Contact with Receptor CutOff - any ligand exceeding this distance will not be placed in the results table. This value is significant if the receptor is included in setup.
  • The use pharmacophore filter allows you to match linkers with a pharmacophore object. Learn how to make a 3D pharmacophore object here.

Step 4: Once the fragment fitting has completed a table of results will be displayed. The table is ranked by strain with the top hit in row 1. You can browse the hits using the toggle buttons in the "L" column.

  • Strain is the energy strain of the ligand.
  • Score2 is the same value as strain (possible place holder for future release).
  • RMSD - is the RMSD to the original fragment before linker connection.

Three Point Core Replacement Three cores can be linked by selecting them with the scissors button as shown in Step 1 above. Number of hits will be significantly lower then in 2 point replacement because the extra anchor adds some restraint. We recommend to use larger database for the search (e.g. chembridge100K.molt ) and make sure that ligand is minimized before searching.


Prev
Covalent Docking
Home
Up
Next
Restraints

Copyright© 1989-2018, Molsoft,LLC - All Rights Reserved.
This document contains proprietary and confidential information of Molsoft, LLC.
The content of this document may not be disclosed to third parties, copied or duplicated in any form,
in whole or in part, without the prior written permission from Molsoft, LLC.