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Principles of PubChem
Summary Objectives Audience Format Outline

   Course Summary

The National Center for Biotechnology Information (NCBI) presents Principles of PubChem, a course including lectures and computer workshops on effectively using the NCBI PubChem system: a collection of databases, search services, and analysis tools that focus on small chemicals and their biological activities.

   Scheduled Courses
Courses in 2008 Previous Courses

   Course Materials
Lecture Slides Essentials Exercises
Course Handout PowerTools Exercises
PubChem Fact Sheet Amino Acid Explorer

   Course Objectives

After attending the course, participants should be able to do the following:

PubChem Essentials

  • Understand the content and organization of the PubChem databases and how these data are submitted to and curated by NCBI
  • Find links from a given compound to related data including bioactivity studies, literature abstracts, protein sequences, protein structures, genes, and diseases
PubChem Powertools
  • Find structurally similar chemicals to a given compound based on bonding, stereochemistry, molecular parameters, and the presence or absence of substructures or isotopes
  • Find sets of compounds with defined bioactivity profiles, and use these sets to guide further searching for related compounds

Summary Objectives Audience Format Outline

   Intended Audience

The course is intended for principal investigators, postdoctoral fellows, graduate students, advanced undergraduates, and other scientific staff who either work with chemical databases or are interested in understanding how to incorporate such data into their research. Participants do not need to have taken any other NCBI course to attend, and no prior experience with chemical databases is required. Familiarity with basic computer operation and common Web browsers is assumed.

   Course Formats

The course consists of two sessions, PubChem Essentials and PubChem PowerTools. Each session requires 3 hours, including a 1-hour lecture and a 2-hour computer workshop. In order to accommodate a variety of teaching environments, we currently offer both a one- and two-day format:

One-day format

Two-day format
Participants may choose to attend either session or both sessions. However, for participants who want to attend only PubChem Powertools, we recommend that they already be familiar with basic PubChem operations.

The workshops will consist of a mix of guided exercises and periods during which the participants will work independently on one or more exercises chosen from a provided set. Participants are welcome to bring their own projects or questions to the workshops as well.

Summary Objectives Audience Format Outline

   Course Outline

Part I: PubChem Essentials

Lecture (60 min)

  • PubChem databases in Entrez
  • Finding compounds and related data in Entrez
  • Simple structure searching

Workshop (105 min)

  • Searching for compounds in Entrez
  • Using Entrez links in PubChem
  • Finding and viewing 3D structures containing compounds
  • Finding basic bioactivity data

Part II: PubChem PowerTools

Lecture (60 min)

  • Advanced structure search service
  • Clustering compounds by structural similarity
  • Summarizing bioactivity data for sets of compounds
  • Using Entrez links and history to filter and combine bioactivity data

Workshop (105 min)

  • Finding bioactivity data for structurally related compounds
  • Viewing bioactivity data from multiple assay datasets
  • Creating sets of compounds with defined activity profiles

Summary Objectives Audience Format Outline

   NCBI PubChem Resources


PubChem Resources and Tools

   About the Instructors

Medha Bhagwat, Emir Khatipov, Rana Morris and Eric Sayers are biologists on the User Services staff of the National Center for Biotechnology Information.

Help Desk NCBI NLM NIH Credits

Revised February 28, 2008