Catalyst Tutorials

Catalyst 4.5 Release Notes

1. Simple Tasks to Introduce Catalyst

Window management

Moving a window

Moving a window to a new location

Bringing a window to the front

Resizing a window

Catalyst operating directories

Starting Catalyst

Loading the training data

Catalyst windows

Extended mouse functionality in Catalyst

General Catalyst mouse usage

Opening a workbench

Opening an empty workbench

Closing a workbench

Dragging an object and dropping it onto an instrument

Bringing objects into the workspace

Dropping an object into a workspace

Putting another object onto the workbench

Moving objects

Moving one object in the workspace

Scrolling the workspace

Zooming the view of molecules

Zooming molecules in and out

Making all displayed objects fit in the workspace

Rotating an object

Rotating an object in one plane

Rotating an object in 3D

Changing views and styles

Changing views

Changing 3D styles

Changing layout and styles for workbenches

Changing the workspace layout for an open workbench

Setting styles and layout for new workbenches

Leaving a workbench

Iconifying, reopening, and closing a workbench

Help in Catalyst

Using the context-sensitive help system

Using the online help system

Getting help

Using the index for the online help system

Printing pages from the online help system

Leaving the online help system

Summary

2. Introduction to Hypotheses

Examining two ready-made hypotheses

Displaying a substructure hypothesis

Displaying a hypothesis that has chemical functions

Using hypotheses

Using a hypothesis to search a database

Fitting a molecule to a hypothesis

Using a hypothesis to estimate the activity of compounds

Summary

3. Building Molecules

Using the view compound workbench

Opening the workbench

General rules for building molecules

Selecting atoms and groups in the periodic table

Placing atoms and groups in the workspaces

Selecting and changing bond types and styles

Adding a bond between two atoms

Practicing molecule-building skills

Placing the first atom

Adding atoms in the 2D workspace

Changing the element of an existing atom

Deselecting everything

Adding atoms in the 3D workspace

Keyboard shortcuts for element selection

Building molecules summary

Changing bond styles and adding bonds

Adding some groups

Using the erase tool to correct mistakes

Keyboard shortcuts for bond selection

Selecting and deselecting in the workspace

Selecting a single item

Selecting multiple atoms and bonds (extend-select)

Selecting multiple atoms and bonds that are grouped together (region-select)

Selecting everything

Deselecting all selected items

Deselecting some, but not all selected atoms and bonds (extend-deselect)

Building a sample molecule

Building baclofen

Tidying up the structures in both 2d and 3d workspaces

Saving the molecule to the shelf

Using the tools in the view compound workbench

Minimizing the 3D structure

Flipping the 2D molecule

Orienting the 3D molecule to the 2D molecule

Changing stereochemistry

Changing the chirality of a chiral atom

Changing the stereochemistry at a double bond

Aromatizing and de-aromatizing rings

Protonating atoms and converting ions to neutral atoms

Oxidation and reduction

Dynamic modeling

Moving atoms and bonds in the 2D workspace

Moving groups in the 2D workspace

Measuring atomic distances, angles, and dihedral angles

Building a peptide

Building a glu-ala-pro peptide

Summary

4. Building Hypotheses and Searching Databases

Different methods for building hypotheses

Building a substructure hypothesis and searching a database with it

Building the substructure hypothesis

Searching a database with the hypothesis

Saving a compound to the shelf

Sorting the entries in the report by name or molecular weight

Reports

Building a hypothesis with the feature dictionary

Building a beta-adrenergic agonist hypothesis

Using the feature dictionary to add functions and fragments to a hypothesis

Linking functions with a distance constraint

Adding a fragment to the hypothesis

Linking the parts of the hypothesis together

Finishing the hypothesis

Searching the database for beta-adrenergic agonists

Building a sophisticated hypothesis for D2 agonists

Placing the basic amine, the acceptor, and an aromatic ring

Joining the features with distance constraints

Making a least-squares plane around the phenyl and adding an acceptor vector to the amine

Constraining the angle of the amine lone pair to the plane of the ring

Adding a torsion constraint between the acceptor vectors

Using the Find command

Summary

5. Organizing Your Data

Using labs

Creating labs

Moving objects to a lab

Tidying a lab or shelf and displaying the icons in different ways

Changing the name of an object

Getting data into and out of Catalyst

Saving your data (StockroomDB)

Determining which databases appear in the stockroom

Exporting objects

Disposing of objects

Importing objects

Printing data from Catalyst

Printing the contents of a workspace

Managing 1D data in Catalyst

The stockroom property dictionary

Entering 1D data using the View Database workbench

Sorting and selectively viewing your data using 1D constraints

Summary

6. Generating Conformational Models

Fast and best-quality conformer generation

Fast conformer generation

Best conformer generation

Generating conformational models interactively or in the background

Generating and displaying conformational models

Generating conformers interactively

Examining the conformers

Displaying, registering, unregistering, and deleting individual conformers

Generating a conformational model in the background

Monitoring the background process

Retrieving the conformers

Cleaning up the background process

Summary

7. Generating a Hypothesis

Introduction

Background on the data used in this example

Generating a hypothesis

Entering the training set molecules

Checking structures

Checking function mapping

Generating conformational exercise models, if needed

Using the Generate Hypothesis workbench

Adding activity data to your training set spreadsheet

Setting up to run hypothesis generation

Using control parameters

Running hypothesis generation

Monitoring and managing data for a background task

Using the hypothesis generation log file

Running hypothesis generation from a UNIX shell

Evaluating the quality of a hypothesis

Using the hypothesis to fit and estimate the activity of training set compounds

Comparing multiple molecules to a hypothesis simultaneously

Using the hypothesis to fit and estimate the activity of compounds from outside the training set

Clustering hypotheses

Merging hypotheses

Summary

8. Generating Common Features Hypotheses

Experiment

Analysis

Summary

9. Shape-Based Search

Solving the problem

Nature of the experiment

Creating a hypothesis from a bound conformation

Creating a shape query

Creating a shape/hypothesis query

Searching the sample database

Review

10. Building Databases

Before you start building databases

Building a multiconformer database

Testing the database

Summary

11. The Exclude/OR QuickTool

Catalyst's default POS IONIZABLE feature

Constructing a heteroaromatic hypothesis

Modifying the default POSITIVE IONIZABLE feature

Summary

12. Customizing Functions

Customizing a function

Creating a vectorized function

Creating a NOT function

Working with peptides

Creating fragments

Using the customized functions/fragments

13. Understanding HypoGen output

HypoGen output

Summary

FIGURES

Figure 1. Molecules for Lesson 8

TABLES

Table 1. Mouse button functionality

Table 2. Color coding key for spheres

Table 3. Keybord shortcuts for periodic table selections

Table 4. Training set for ACE inhibitors

Table 5. Inter-centroid distances

Table 6. HypoGen and HipHop files