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Exploring 3D Molecular Structures
Summary Objectives Audience Format Outline

   Course Summary

The National Center for Biotechnology Information (NCBI) presents Exploring 3D Molecular Structures, a course including lectures and computer workshops on effectively using the NCBI databases, search services, and analysis tools that focus on 3D macromolecular structure data.

   Scheduled Courses
Upcoming course at NLM - March 5, 2008
Courses in 2008 Previous Courses

   Course Materials
Lecture Slides Workshop I Exercises
Course Handout Workshop II Exercises

   Course Tools
Cn3D 4.1 Alignment Guide
Amino Acid Explorer PSSM Viewer

   Course Objectives

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

  • Understand the origin and organization of 3D structural data and how these data are curated at NCBI (Lecture I)
  • Find structural neighbors using VAST and functional elements within structures using the Conserved Domain Database and RPS-BLAST (Lecture 2)
  • Analyze a 3D structure, highlight features such as bound ligands and active site residues, create customized annotations, and save and export a figure (covered in Workshop I)
  • Find and evaluate a 3D modeling template for a protein by creating multiple sequence alignments using either sequence or structure similarity searches (covered in Workshop II)

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 3D structural data 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 structural data is required. Familiarity with basic computer operation and common Web browsers is assumed.

   Course Formats

In general, the course consists of two sessions, Part I and Part II. Each session requires 2.5 hr, including a 60-minute lecture and a 90-minute computer workshop. In order to accommodate a variety of teaching environments, we currently offer several course formats:

One-day formats

Two-day formats
Participants may choose to attend either Part I or Part II, or both sessions. However, for participants who want to attend only Part II, we recommend that they be familiar with the basic operation of Cn3D 4.1.

The workshops will consist of a 30-minute guided exercise followed by a 60-minute period 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: Structures in Cn3D

Lecture I (60 min)

  • PDB files: content and formatting
  • Structural databases in Entrez
  • Finding structures and related data in Entrez
  • Simple sequence-structure alignments with BLAST

Workshop I (90 min)

  • Searching for structures in Entrez
  • Gathering details from PDB files
  • Viewing NMR ensembles and crystal structures
  • When and how to use molecular rendering and display options
  • Annotating structures and producing figures
  • Saving images and data for use in Powerpoint or other applications

EXERCISE: Analyze a structure and prepare a figure illustrating particular features.

Part II: Alignments in Cn3D

Lecture II (60 min)

  • VAST structural alignments
  • Curated CDD alignments
  • Building a structural template for a protein query
  • Alignment algorithms in Cn3D 4.1

Workshop II (90 min)

  • Finding model structures using pre-computed sequence alignments
  • Finding structural homologs using pre-computed structure alignments
  • Building sequence alignments to a model structure in Cn3D
  • Building structure alignments in Cn3D

EXERCISE: Discover and analyze a structural model for a query protein.

Summary Objectives Audience Format Outline

   NCBI Structure Resources


Analysis Tools

  • Cn3D 4.1: an increasingly powerful tool for viewing molecular structures and creating both structural and sequence alignments
  • Related Structures: a new service for creating sequence-structure alignments
  • CD-Search: Conserved Domain Search, or RPS-BLAST, for finding multiple alignments of conserved, functional domains that match a query protein
  • CDART: the Conserved Domain Architecture Retrieval Tool for finding proteins with similar domain architectures to a query protein
  • VAST: the Vector Alignment Search Tool for creating structural alignments
  • SALTO: the new Structure-based ALignment Tool for assembling structure-linked sequence alignments
  • NCBI Threader: software package for aligning a protein sequence to a 3D structure using associated multiple sequence alignments and chemical potentials, now available in Cn3D 4.1

   About the Instructors

Eric Sayers and Medha Bhagwat are biologists on the User Services staff of the National Center for Biotechnology Information.

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Revised February 28, 2008