Structural Bioinformatics Links
Resource Pages
Cambridge (UK) Crystallography and Bioinformatic servers
Protein/DNA Databases
EMBL
Swiss-prot and TREMBL
TIGR
SRS7 searches at EBI
PIR
Hotworm
Sequence Searches:
NCBI BLAST
NCBI BLASTp
NCBI phi-psi BLAST
TIGR-BLAST
SAM-T02 - Hidden Markov Modelling sequence searching
SUPERFAMILY
Motif Searches:
PFSCAN - Proilfe searches
PSTSAN - Search the PROSITE database with a protin sequence
PatternFind - Search a protein databse with a pattern
PRATT - Pattern Discovery (EBI- Cmbridge, UK)
SAPS
Sequence Alignment Tools:
COMPARER
CLUSTALW
T-COFFEE
LALIGN
Secondary structure prediction:
PSIPRED
PHD PredictProtein
PHD-META - includes secondary struct and homology modelling servers
Secondary Structre Assignment
STRIDE
Coiled-coil prediciton:
COILS
MARCOIL
Disorder prediction:
DISOPRED
Transmembrance prediciton:
TMpred - Prediction of transmembrane regions and orientation
Domain Databases:
PFAM
ProDom
DomPred
BLOCKS
CHOP- ChOPIng proteins into structural domain like fragments
InterPro
Evolutionary Trace method:
TraceSuite II - a fully automoated evolutionary trace server
Fold recognition
GenTHREADER
3D-pssm
FUGUE
UCLA-DOE FOld Server
TOPITS
CPHmodles
Structure Databases
PDB Potein Data Bank
DALI server for 3D protein structure comparision
CATH Protein Structure Classification
SCOP Structural Classification of proteins
Structure based sequence alignment
Sequioa
JOY- Protein structure and alignment analysis
Modelling
Modeller- comparative homology modelling
SWISS-MODEL
RAPPER
Coda - a combined algorithm for prediciting protein loops
Petra - An ab initio protein fragment prediciton method
Predict Nuclear Localization Signal
Predict NLS
Sequence tools
Espript
BOXSHADE
Molecular Graphics
Pymol
