Sequence Analysis Training

NCBI Workshop
April 10-11, 2007  


 DAY 1:
  "Exploring 3D Molecular Structures Using NCBI Tools"
DAY 2:
  "Principles of PubChem"




 Overview:
Three dimensional (3D) Structures are now an important part of nearly all areas of biological and biomedical research. The National Center for Biotechnology Information (NCBI) at the National Library of Medicine builds and maintains the largest collection of 3D macromolecular structure information in the world and develops software tools to access these data. The National Center for Biotechnology Information (NCBI) presents Exploring 3D Molecular Structures Using NCBI Tools, a course that we will host to effectively use the NCBI integrated system: a collection of databases, search services, and analysis tools that focus on 3D structures and related resources. The course consists of two parts, each including a one-hour orientation lecture followed by two-hour hands-on practice session in the computer classroom featuring practical examples using the new features, services and databases including the following recent improvements and additions.

Topics Covered:

  • Understand the origin and organization of 3D structural data and how these data are curated at NCBI (morning lecture)
  • 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 morning computer hands-on session)
  • Find structural neighbors using VAST and functional elements within structures using the Conserved Domain Database and RPS-BLAST (afternoon lecture)
  • Find and evaluate a 3D modeling template for a protein by creating multiple sequence alignments using either sequence or structure similarity searches (covered in afternoon computer hands-on session)

Click here to download the handout

Click below to download the slides
Slides-Part 1
Slides-Part 2

"Principles of PubChem"
Click here to download flyer.

Overview:
The National Center for Biotechnology Information (NCBI) will present a new course Principles of PubChem. This course will show you how to effectively use the NCBI PubChem system: a collection of databases, search services, and analysis tools that focus on small chemicals and their biological activities. The course consists of a one-hour orientation lecture followed by a two-hour hands-on practice session in the computer classroom featuring practical examples using the new features, services and databases including the following recent improvements and additions.

Topics Covered:

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 Power Tools
  • 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




Attendance by Cancer Center Members:
Cancer Center Attendees
CB 8
DCT 9
HM 3
CCPS 1
CI 1
TOTAL 22

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