Using MFold to predict RNA secondary
structure
http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form
Enter the following Micro-RNA sequence into
the box
GGCCAGCUGUGAGUGUUUCUUUGGCAGUGUCUUAGCUGGUUGUUGUGAGCAAUAGUA
AGGAAGCAAUCAGCAAGUAUACUGCCCUAGAAGUGCUGCACGUUGUGGGGCCC
Run MFold and look at the results
1
Constraint information
• Force bases 30-35 to be
single stranded
• Is the result different?
2
PSIPRED (Protein Structure Prediction Server)
Secondary Structure Prediction
http://bioinf.cs.ucl.ac.uk/psipred/
1. Use the protein NP_360043.
2. Paste the sequence without
the header line.
3. Enter your UH email
address.
4. Click the Predict button.
5. View the results.
3
Helix
Coil
Beta Strand
4
Helix
Beta Strand
Coil
5
3-D structures
Retrieving and displaying a 3-D structure from PDB
http://www.rcsb.org/pdb/
1. Enter the protein's name and click search
2. View the protein with KiNG viewer
3. Examine the information and links to
other databases
8
Protein visualization with FirstGlance in Jmol
http://molvis.sdsc.edu/fgij/
Secondary Structure
Alpha Helices
Beta strands
Random coils
10
MMDB
• NCBI's structure database is called MMDB
(Molecular Modeling DataBase), and it is a
subset of experimentally derived threedimensional structures obtained from the Protein
Data Bank (PDB) (excluding theoretical
predictions)
• http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml
VAST
• NCBI creates and maintains a database of
structure alignments, called VAST, for all
pairs of proteins from MMDB whose
structures have some similar core regions.
They are called “Structural neighbors”.
• http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml
Example
• Type "1D5R" in the query box and hit
"Get." This brings up the MMDB summary
page.
14
• The graphic is saying that the protein is
composed of a single chain (A) that NCBI has
parsed into two domains: the N-terminal domain
1, and C-terminal 2. Clicking on the top bar
marked "Chain A" will bring up VAST neighbors
based on the whole chain, while clicking on the
colored regions marked "1" or "2" will show
neighbors of these individual domains.
16
Click on the “1” domain to get
proteins that consists of a similar
structure like the PTPc domain
17
Lets view the "3D Alignment” of 1D5R:A with
2BZL:A using the CE tool
http://cl.sdsc.edu/ce.html
Crystal Structure Of The Human Protein
Tyrosine Phosphatase N14 At 1.65 A Resolution
19
20
The two sequences have a 20.7% sequence similarity. The root
mean square deviation (RMSD) in terms of structural distance is
2.47. Now lets compare hemoglobin A (4HHB:A) and B
(4HHB:B)?
21
Hemoglobin A and B have a sequence similarity of 40.3 % and a
root mean square deviation of 1.49.
22
Tertiary structure prediction
• From ExPASy http://www.expasy.org/tools/, you
can find links to many prediction servers:
Tertiary structure prediction
• For example the HMMSTR/Rosetta server
predicts protein structure from sequence
(Ab initio).
Protein 3D structure prediction
HMMSTR/Rosetta Web Server