Protein analysis and structure prediction

Structure databases PDB: Protein Data Bank World Wide PDB PDBe Europe PDB Japan BIOISIS: Database of SAXS of Biological macromolecules	Expasy: Proteomics tools. ProtParam Translate (DNA=>Prot) Swissprot SRS ScanProsite BLAST at NCBI EBI: Databases SRS Tools: Fasta3 UniProt
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 (T�bingen): HHpred Quick 2D BMERC PSA Server Boston University FFAS03 : Fold & Function Assignment System (Godzik group) Protein Structure Modeling Protein structure clasification CATH DALI server for protein 3D structure searching FSSP database PDBSum Pfam ProDom Protein Domain Database SBASE domain prediction server 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	Effect of mutations, prediction Auto-Mute: predicting functional consequences of mutations in proteins. CUPSAT: Cologne University Protein Stability analysis Tool. DUET server: predicting effects of mutations on protein stability ERIS: protein stability prediction server FoldX: effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. I-Mutant: Prediction of protein stability changes upon mutations. PoPMuSiC: Prediction of protein stability changes upon mutations. Pro-MAYA: Protein Mutant stAbilitY Analyzer. ProSMS: Prediction of protein stability changes due to single amino acid mutations. SMD: Predicting the effect of mutations on protein stability. Temperature sensitive mutations TSpred: server for the rational design of temperature-sensitive mutants.
Homology Modeling (and related) HOMER NIH Center for Molecular Modeling Modeller (Andrej Sali Lab) ModWeb 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 Codon usage RaCC (Rare Codon Calculator) (mirror) Rare Codon Calculator Search of rare codons in nucleotide sequence