Pharm 207/Bio 207

Using Internet Resources in Molecular Biology - Fall 2003
Course Instructors:

Prof. Philip E. Bourne PhD

Location: San Diego Supercomputer Center Room 116 [map]
Graduate Student Course, 2 Credits
Last Update October 14, 2003

Students with laptops and wireless Internet connections are encouraged to bring them to class

Course Outline | External Internet Resources | Assignment

Synopsis

Increasingly the Internet is a source both of data and analysis tools in the field of molecular biology. Knowing what is available, being able to use these resources, and to interpret results returned by these resources is important to principal investigators, fellows, and students alike.

A hands-on series of instructional lectures is presented with emphasis on working through real problems.

Assessment: Graduate students taking this course select their "pet protein" based on their research projects and solve these problems using that protein. Assessment is based upon a student's protein annotation developed during the course which describes features of their protein deciphered using a variety of Internet resources. Course assignments are written using Bioeditor.

Prerequisites: None

Pharm/Bio207 is a companion course to Bioinformatics I (Pharm201). The latter provides a more in-depth and theoretical study of the material presented here and teaches the student how to build a useful database of biological data.

Course Outline

***Follow links for all on-line course materials***
Date	Topics
Lecture 1 (Bourne) 09/30 3-5PM	Overview Characterizing data resources (by currency, content, cross-linking etc.) Major data resources (e.g. Genbank, PIR, Swiss-Prot, Prosite, GDB, PDB) Composite searching (e.g. ExPASy, Entrez) Technical issues - plug-ins, helper applications
Lecture 2 (Bourne)10/07 3-5PM	DNA/Protein Sequence Comparison ( Backup Notes as a PDF) Similarity and homology Sequence alignments Database searches
Lecture 3 (Bourne)10/14 3-5PM	Protein Domains and Motifs & Using BioEditor BioEditor basics including rasmol and chime commands Definition of domains and motifs Resources providing domain and motif annotation Defining your own domains and motifs
Lecture 4 (TBN) 10/21 3-5PM	Problem Solving with Entrez Basic Sequence/Structure/Bibliographic Searching Entrez field specifiers Using neighbors Advanced boolean searches
Lecture 5 (Bourne) 10/28 3-5PM	Protein Secondary Structure Prediction Methods (Statistical, Multisequence, Neural Net) Comparisons with known structure Techniques
Lecture 6 (Shindyalov) 11/04 3-5PM	Phylogenetic trees Principle of maximum parsimony Distance methods: UPGMA, neighbor-joining Multiple sequence alignment using ClustalW Building tree using Biology WorkBench
Lecture 7 (Smith) 11/18 3-5PM	Protein Physico-Chemical Data Analysis Analytical tools for physico-chemical empirical data Theoretical calculation of physico-chemical features Compendiums of analytical tools
Lecture 8 (Bourne) 11/25 3-5PM	Protein Structure Classification Domains Structural motifs Folds
Lecture 9 (Shindyalov/Bourne) 12/02 3-5PM	Protein Tertiary Structure Prediction Comparative modelling. Fold recognition (threading). Molecular mechanics (ab initio methods).

Internet Resources

Portals (i.e., entry points to a number of useful data, tool and information resources)

CMS Molecular Biology Resource - Large collection of relevant links
DNASYSTEM - An alternative to CMS MBR
ExPaSy - Entry point to databases and tools of the (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB).
Macromolecular Structure Related Resources - Provided by the Protein Data Bank (PDB)

Access Points to Multiple Databases

Sequence Retreival System (SRS)
Entrez - Access to the literature, protein and DNA sequence databases, structure database, taxonomy, and genomes

Important Databases

[See Nucleic Acids Research 2001 29(1) and the first issue of previous years for discussions of relevant biological databases]

Sequence

GenBank - An annotated collection of all publicly available DNA sequences
SwissProt - Curated protein sequences
PIR - the Protein Information Resource - Curated protein sequences
Prosite - Database of protein families and domains
InterPro - Inetegrated resource of domains and functional sites
BLOCKS - Multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins
Pfam - Collection of multiple sequence alignments and hidden Markov models covering many common protein domains
PRINTS - Compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family
ProDom - Automatic compilation of homologous domains

Structure

Protein Data Bank
Nucleic Acid Database
SCOP - Structural Classification of Proteins
CATH - Class, architecture, topology and homologous superfamily
FSSP - Fold classification based on Structure-Striucture alignment of Proteins using the DALI algorithm
CE - Structure homology based on the CE algorithm

Genomes

Genomes at NCBI

Miscellaneous

ENZYME - Enzyme nomenclature
WWW Virtual Library: Chemistry
WWW Virtual Library: Crystallography
WWW Virtual Library: Biosciences
Molecular Viewers - Rasmol Chime Others...

Other Relevant Courses

Bioinformatics I - Particularly lecture 1 - "What is Bioinformatics"
Biocomputing Course Resource List : Course Syllabi A list maintained by Georg Fuellen as part of the VSNS BioComputing Division
Birkbeck College's Principles of Protein Structure online course