PROTEIN ANALYSIS / STRUCTURE / PREDICTION LINKS

Structure databases PDB (mirror sites Cambridge / EBI ) 3DB Browser ( Cambridge / EBI ) World Wide PDB MSD: Macromolecular Structure Database at EBI PDB Japan BIOISIS: Database of SAXS of Biological macromolecules Metalloprotein database	Expasy: Proteomics tools. ProtParam. Swissprot - SRS. ScanProsite. BLAST at NCBI. EBI: Databases SRS Tools: Fasta3. UniProt BCM Search Launcher
Secondary Structure Prediction Jpred (Barton group) nnPredict Cohen et al. PredictProtein Server (PHD), secondary strucure prediction: At the EBI At predictprotein.org PHYRE: Protein Homology/analogY Recognition Engine. PORTER(University College Dublin). PREDATOR Frishman & Argos. PSIPRED. SABLE: prediction of relative Solvent AccessiBiLitiEs, secondary structures and transmembrane domains. Self Optomised Prediction method Deleage (IBCP, France) SSP (Nearest-neighbor segment method) Solovyev and Salamov SSPRED Argos et al. ZPRED server Zvelebil et al. Coiled coils prediction COILS A.Lupas PAIRCOIL P.Kim et al. PAIRCOIL2 MULTICOIL P.Kim et al.	Structure prediction and related Bioinformatics Toolkit (Tübingen): HHpred Quick 2D BMERC PSA Server Boston University FFAS03 : Fold & Function Assignment System (Godzik group) Protein structure clasification CATH DALI server for protein 3D structure searching FSSP database PDBSum Pfam (Cambridge / St Louis / Stockholm ). ProDom Protein Domain Database SBASE domain sequence server (Trieste) SCOP: Structural Classification of Proteins SMART (Bork group).
Post-translational modification Prediction Phosphorylation sites Phospho ELM database (not a prediction server). NetPhos (phosphorylation in eukariotic proteins). NetPhosK (kinase specific phosphorylation in eukariotic proteins). GPS (Group-based Prediction System). Motif Scan Kinase Phos
Homology Modeling (and related) HOMER NIH Center for Molecular Modeling Modeller (Andrej Sali Lab) Swiss Model: automatic modeller What If Web Interface	Mass Spectrometry ProteinProspector: MS-Digest Circular Dichroism CCA+ DichroWeb. Contains a very complete list of links. K2D2 CDPro CD practical guide Codon usage RaCC (Rare Codon Calculator) (mirror) Rare Codon Calculator Search of rare codons in nucleotide sequence

Last update: 5th October 2011