Pipeline Pilot Cheminformatics

Modules

1. Cheminformatics Introduction

   An introduction to Pipeline Pilot’s Chemistry collection of components and their general uses. You’ll also be instructed on chemistry data manipulator components that alter data records in a variety of ways, including cleaning, structural altering, and standardizing.

   • Exploring the Chemistry Collection
   • Reviewing Common Chemistry Manipulators

2. Calculate Molecular Properties

   Learn to use property calculators, calculable properties, and molecular fingerprints.

   • Working with Property Calculators
   • Utilizing the Molecular Fingerprints Component

3. Filter Molecules

   Instruction on filters that act on molecular data, allowing customization of workflows to incorporate processing according to the chemical and structural features of a molecule on a data record.

   • Reviewing the Filters
   • Modeling Data
   • Accessing and Manipulating Data
   • Similarity

4. Perform Molecule Searches and Identify Similarities

   Learn to utilize various components to perform database-style searching of molecules, and to identify similarities among them. Note that to execute the tasks in this course, you must have the Data Modeling component collection installed on your Pipeline Pilot server.

   • Reviewing the Search and Similarity Components
   • Checking Molecules for Query Substructures
   • Finding Molecules Similar to the Query Structure
   • Constructing a Query
   • Generating Maximal Common Substructure
   • Calculating Similarity Values

5. Estimate and Visualize

   Learn how to use components that analyze research data and present the results in a meaningful manner. Note that to execute the tasks in this module, you must have the Data Modeling component collection installed on your Pipeline Pilot server.

   • Generating SAR Information
   • Clustering
   • Estimating logD and pKa

6. Enumerate Tautomers and Stereochemistry

   Provides descriptions of tautomers and stereochemistry are, and instructs you on how to use Pipeline Pilot components with these types of structures.

   • Enumerating Tautomers
   • Enumerating Stereoisomers

7. Perform Reactions

   Instruction on how to use reactions with a protocol on individual molecules, on a set of starting materials, and on using a core structure. You’ll also receive instruction on the enumeration methods for each of these types of reactions.

   • Reviewing Reaction Components
   • Working with Reaction-Based Enumeration
   • Working with Scaffold-Based Enumeration

8. Explore and Work with Bioisosteres

   Provides descriptions of bioisosteres, how they are used in chemistry research, and the main components Pipeline Pilot offers for discovering and working with bioisosteres.

   • Reviewing Bioisosteres Components
   • Identifying and Enumerating Bioisosteres
   • Reviewing Similarity Bioisosteres
   • Utilizing the Similarity Components