DIMACS Short Course: Exploring 3D Molecular Structures Using NCBI Tools
May 16 - 17, 2006
DIMACS Center, CoRE Building, Rutgers University
- Organizers:
- Tamar Barkay, Department of Biochemistry and Microbiology, barkay@AESOP.Rutgers.edu
- Nicholas Beckloff, UMDNJ, beckloni@umdnj.edu
- Paul Ehrlich, BioMaPS Institute, pehrlich@lutece.rutgers.edu
- Mel Janowitz, DIMACS, melj@dimacs.rutgers.edu
- Tara Matise, Department of Genetics, matise@biology.rutgers.edu
Presented by The National Center for Biotechnology Information,
the DIMACS/BioMaPS/MB Special Focus on Information Processing in Biology,
the Department of Biochemistry and Microbiology of Rutgers University,
the University of Medicine and Dentistry of New Jersey (UMDNJ), BioMaPS Institute for Quantitative Biology,
and the Department of Genetics at Rutgers University.
Course Summary
The National Center for Biotechnology Information (NCBI) presents
Exploring 3D Molecular Structures Using NCBI Tools, a
course including lectures and computer workshops on effectively using the NCBI databases, search services,
analysis tools that focus on 3D macromolecular structure data.
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)
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.
People who have attended The Field Guide course will find this an interesting followup.
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.
NCBI Structure Resources
Databases:
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
- SA LTO: 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
Next: Call for Participation
Workshop Index
DIMACS Homepage
Contacting the Center
Document last modified on January 9, 2006.