Part5SecondaryStructures-weblinks.pdf

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Useful Web Sites for Part 5
Secondary Structures
Chapter 11:
Obtaining Secondary Structure from Sequence
Chapter 12: Predicting Secondary Structures
Useful information:
Until 2002, secondary structure prediction methods were included in the Critical Assessment of techniques For Protein Structure
Prediction (until
CASP5)
and Critical Assessment of Fully Automated Structure Prediction (until
CAFASP3).
Databases and other useful sites of information:
PDB_SELECT
is a non-redundant collection of protein structures.
Many hydrophobicity scales are available in the
AAINDEX
database.
Programs
For secondary structure assignment:
PROCHECK
DSSP
PALSSE
STRIDE
For secondary structure prediction:
COILS
HMMTOP
MEMSAT
PHDhtm, PHDsec and PHDtopology are part of the
PredictProtein
program
PREDATOR
PROF
PSIPRED
SSpro
TMHMM
Web servers
The following web sites provide on-line access to secondary structure prediction:
GOR-V
Jnet
NNSSP
PHD
PREDATOR
PROF
PSIPRED
SIMPA96
Sspro
The following web site provides on-line access to structure assignment:
PALLSE
The following web sites provide on-line access to transmembrane prediction
DAS
HMMTOP
MEMSAT
PHDhtm
SOSUI
TMAP
TMHMM
TMPred
The following web sites provide on-line access to prediction of coiled-coils:
COILS
MARCOIL
MULTICOIL
PAIRCOIL
The following web site provides on-line access to prediction of leucine zipper structures:
2ZIP
The following web sites provide on-line access to prediction of RNA secondary structure:
GeneBee
MFOLD
RNAfold
Datafiles used for Chapter 11 examples
Structural coordinates from the RCSB Protein Databank (PDB) for protein structures of:
parvalbumin (1B8C)
translation initiation factor 5A (1BKB)
serotonin N-acetyltransferase (1CJW)
yeast hypothetical protein YBL036C (1CT5)
bovine rhodopsin (1F88)
the complex of human RhoA and the effector domain of the protein kinase PKN/PRK1 (1CXZ)
GCN4 leucine zipper (GCN4)
B1 immunoglobulin-binding domain of streptococcal protein G (1PGA)
B2 immunoglobulin-binding domain of streptococcal protein G (1PGX)
viral hemagglutinin in two alternative conformations (3HMG and
1HTM)
Note that there are links to the protein sequence in FASTA format on the left-hand side of the above link pages.
Sequence files will be found in the archive ‘Part 5 Secondary Structures datafiles.zip’.
parvalbumin
translation initiation factor 5A
serotonin N-acetyltransferase
yeast hypothetical protein YBL036C
effector domain of the protein kinase PKN/PRK1 (used in coiled coil prediction)
GCN4 leucine zipper (used in coiled coil prediction)
tRNA sequence used RNA structure predictions
1b8c.seq
1bkb.seq
1cjw.seq
1ct5.seq
PKN.seq
GCN4.seq
tRNA.seq

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