1 enter the following micro-rna sequence into the box run mfold and look at the results mfold using...

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Enter the following Micro-RNA sequence into the box

Run MFold and look at the results

Using MFoldMFold to predict RNA secondary structure

http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form

GGCCAGCUGUGAGUGUUUCUUUGGCAGUGUCUUAGCUGGUUGUUGUGAGCAAUAGUAAGGAAGCAAUCAGCAAGUAUACUGCCCUAGAAGUGCUGCACGUUGUGGGGCCC

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Constraint information

• Force bases 30-35 to be single stranded

• Is the result different?

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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.

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Coil Beta Strand

Helix

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Coil

Beta StrandHelix

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 search2. View the protein with KiNG viewer3. Examine the information and links to

other databases

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Protein visualization with FirstGlance in Jmol http://molvis.sdsc.edu/fgij/

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Secondary Structure Alpha Helices Beta strands Random coils

MMDB

• NCBI's structure database is called MMDB (Molecular Modeling DataBase), and it is a subset of experimentally derived three-dimensional 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.

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• 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.

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Click on the “1” domain to get proteins that consists of a similar structure like the PTPc domain

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

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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)?

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Hemoglobin A and B have a sequence similarity of 40.3 % and a root mean square deviation of 1.49.

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 predictionHMMSTR/Rosetta Web Server