Web-based tools for Bioinformatics; A (free) introduction to (freely available) NCBI, MUSC and World-wide.

When and Where---Wednesdays 1pm-2pm Room 438 Library Admin Building Beginning September 10, 2003.

Overview Tools for Protein Analysis Wednesday, October 1, 2003

After battling the vagaries of the genetic code and suffering with the gene and intron-exon boundaries you will ultimately have a protein sequence in hand. At this point you have at your fingertips a plethora of diagnostic tools. You can use your similarity search skills to find orthologous and possible paralogous protein sequences, structural homologs if they exist, conserved domains, basic statistics such as molecular weight, a host of potential secondary modification sites,pI, and predicted antigenic regions and much, much more.

Introduction/Scope

By the way did you notice the new ENTREZ Global Database Portal. It went Live about one week ago.

As with the analysis of nucleic acids, the bioinformatic analysis of proteins is well
represented on the Web. All commercial software suites contain standard proteolytic enzyme
mapping tools, molecular weight predictions, various composition tools and many metrics to find
transmembrane regions and a host of antigenic, hydrophobic index and secondary modification predictors.

A worked Example

  >NP_203126 LOCUS NP_203126 253 aa linear PRI 07-SEP-2003 
  MADDQGCIEEQGVEDSANEDSVDAKPDRSSFVPSLFSKKKKNVTMRSIKTTRDRVPTYQY 
  NMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQ
  DLLKKASEEDHTNAACFACILLSHGEENMESCSVTQAGVQRRDLGRLQPPPPRLAEGPSL 
  MMASRPTRGPSMTQMLILDTRSQWKLTSSSPIPRFQAITRGGAQEEAPGLCKPSAPSWRS
  TEKTWKSCRSSPG 

The SWISSPROT reference ids for this sequence are: locus ICE7_HUMAN, accession P55210. The NCBI G.I. number is 15718702.

Here are some peptide fragment masses for CNBr digestion of the protein.

 
149.2      
1128.3     
2129.4     
2527.0      
3874.4       
4148.7       
4803.2    
15642.5 
 
  

>gi|1723217|sp|Q10142|AUR1_SCHPO Aureobasidin A resistance protein homolog
MSALSTLKKRLAACNRASQYKLETSLNPMPTFRLLRNTKWSWTHLQYVFLAGNLIFACIVIESPGFWGKF
GIACLLAIALTVPLTRQIFFPAIVIITWAILFYSCRFIPERWRPPIWVRVLPTLENILYGSNLSSLLSKT
THSILDILAWVPYGVMHYSAPFIISFILFIFAPPGTLPVWARTFGYMNLFGVLIQMAFPCSPPWYENMYG
LEPATYAVRGSPGGLARIDALFGTSIYTDGFSNSPVVFGAFPSLHAGWAMLEALFLSHVFPRYRFCFYGY
VLWLCWCTMYLTHHYFVDLVGGMCLAIICFVFAQKLRLPQLQTGKILRWEYEFVIHGHGLSEKTSNSLAR
TGSPYLLGRDSFTQNPNAVAFMSGLNNMELANTDHEWSVGSSSPEPLPSPAADLIDRPASTTSSIFDASH
LP

Basic statistics GCG PepSort with NoCUT enzyme.

The SeqLab Editor

The SeqWeb BLASTViewer Annotation Feature

MacVector Protein Tools

VectorNTI Protein Tools

A MetaServer at Columbia U

Expert Protein Analysis System (EXPASY). A Long List of Tools at EXPASY Proteomics

Swiss 2D Page Tools

Reproducibility of 2D PAGE gels and the tools to analyze them as well as the searchable databases for such analyses have improved dramatically over the last few years. Commercial software for 2D gel work is rather expensive. Consult a local expert before, during and after launching any project utilizing these methods.

BCR Molecular Modeling Page

Launching a molecular modeling project should be an interim solution for anyone seeking actual experimental structure data. In most cases a modeling effort can give you a heuristic tool much sooner than experimental methods are able to. As a guiding principle remind yourself that a model is a means to insight, and not generally a tool that provides answers.

BCR Protein Domains Page

BCR Mass Spectroscopy Links Page

Most Web services for Mass Spectral Analysis are designed to accept data formats as produced by various commercial spectrometers and/or various mass/intensity formats. The sophistication of these programs is rapidly evolving and you need to consult the MS experts here at MUSC before during and after you start a project.

These next links are also on the BCR web site see: Relational Databases

Protein Information Resource (PIR) Georgetown University Web PagePIR

United Protein Databases Georgetown University Web PageUNIPROT

InterPro Database EMBL-EBI Web PageINTERPRO

Biology WorkBench Proteins Section, Result for Transmembrane Region Search

Biomolecular Interaction Network Database. BIND

Database of Interacting Proteins DIP

Protein Function and Biochemical Pathways PFMP/aMAZE

Danish Centre for Human Genome ResearchCancer Proteomics

TinyGRAP- A SEARCHABLE Mutant Database for G-Protein Coupled Receptors
TinyGRAP Home. AND TinyGRAP Search Form.

Sample Questions/Data

• What proteins interact with rhodopsin?.
• Caspase 7 is an important enzyme in apoptosis. In the area of proteomics you need to get a broad picture of the enzyme?
• Which enzymes need metals like manganese, selenium or cobalt as co-factors?
• Enzymes are sorted into Enzyme classes, and a 4 field EC number is assigned (1.2.3.4 represent the enzyme class, subclass, sub-subclass and entry number, respectively). What kind of Enzymes have the number (3. 2. any. any)?
• Searching 2D Gels for nucleolar proteins from Human HeLa cells.
• In order to study diabetes, you are investigating the proteome of Pancreatic tissue in mice under different experimental conditions. The proteins from pancreas of treated animals were separated by 2D gel electrophoresis. How can you calibrate your gels?