Protein structure
From BITS wiki
The structure of a protein is generally the 3-dimensional space is occupies. In a bioinformatics sense, the structure can be divided in the primary structure (i.e. the amino acid sequence), the secondary structure (the structural components of which the protein is made up, e.g. alpha-helices, beta-turns, beta-stands), the tertiary structure (the three-dimensional structure formed by integrating the secondary structure components in space) and a quarternary structure (the interaction between several proteins forming a larger complex).
Contents
Databases
- PDB (protein data bank) is the major database holding protein structure information, obtained from XRAY and NMR. The data is retrievable in PDB-formatted flat files. More info can be found here.
- PDBsum, very nice entry to explore your structure of interest. PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.
Structure Prediction
secondary structure prediction
- Links to secondary protein prediction
- PSI-PRED
- JPRED
- Phobius, transmembrane topology and signal peptide for secretion prediction.
- Octopus, OCTOPUS predicts the transmembrane helices and signal peptides (SOctopus) with high sensitivity.
tertiary structure prediction
To be filled...
Visualising protein structure
- PDBviewer - a basic protein structure viewer - Win / Mac / Linux
- RasMol - a free proteins structure viewer - Win / Mac / Linux
- Cn3D - a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service - Win / Mac / Linux
- JMol - open-source protein structure viewer - Win / Mac / Linux
- UTOPIA - more advanced software for protein visualisation - Win / Mac / -
- Yasara - a very powerful and extensible suite for both beginners as advanced users. The basic version is free. Extensible. - Win / Mac / Linux
- PyMOL - PyMOL is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation. Also extensible.
- UCSF Chimera - a highly extensible program for interactive visualization and analysis of molecular structures - chimera tutorials
- HyperProtein1.0 - Stand-alone - Win / Mac / Linux
Comparing protein structures
Note: Many of above tools can superimpose structures
- MatchMaker - Superimposes protein or nucleic acid structures -tut
Database search on protein structure
- 3D-Fun
Given a PDB file, this tool searches homologuous structures and reports the enzymes. Ideal for predicting protein function from structure. - DALI
DALI compares the submitted coordinates of a query protein structure against the Protein Data Bank entries. - VAST
VAST Search is NCBI's structure-structure similarity search service. - CATH search
BLAST your protein sequence against the entries in PDB and CATH (a manually curated classification of protein domain structures)
Wise concluding remarks
"We should be quite remiss not to emphasize that despite the popularity of secondary structural prediction schemes, and the almost ritual performance of these calculations, the information available from this is of limited reliability. This is true even of the best methods now known, and much more so of the less successful methods commonly available in sequence analysis packages. Running a secondary structure prediction on a newly-determined sequence just because everyone else does so, is to be deplored, and the fact that the results of such predictions are generally ignored is insufficient justification for doing and publishing them." Arthur Lesk, 1988.
