Protein Sequence & Structure

Protein Sequence & Structure

Physiochemical Properties

• ProtParam (Calculate aa comp, MW, pI, extinction coefficient at ExPASy, CH)

• ProTherm (Thermodynamic Database for Proteins and Mutants, Jp)

Analyse Primary Sequence

• ProtColourer (Make colour-coded representation of an amino acid sequence at EBI)
• ProtScale (Hydrophobicity, other conformational parameters, etc. at ExPASy)
• SignalP (Prediction of peptide signal sequence at CBS, Denmark)
• TargetP (Prediction of subcellular localization at CBS, Denmark)
• NetOGlyc (Prediction of O-glycosylation sites in mammalian proteins at CBS, Denmark)
• NetPhos (Prediction of phosphorylation sites in eukaryotic proteins)
• Helical Wheel (Representation of alpha-helical peptides)
• Hydropathy plots (At Pensylvania State University, Department of Biochemistry and Molecular Biology)
• SAPS (Statistical Analysis for charge clusters, repeats, hydrophobic regions, compositional domains etc. at ISREC, CH)
• PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
• DGPI (Prediction of GPI-anchor and cleavage sites, University of Geneva, CH)
• Scansite (Prediction of protein signaling sequence motifs at HIM, Boston, USA)
• Other primary sequence analysis tools at ExPaSy

Alignment

• Pairwise

• Blast 2 Sequences (Alignment of two protein sequences using BLAST at NCBI, USA)

• SIM (Alignment of 2 protein sequences at ExPASy, Switzerland)

• Pairwise sequence alignment (at Baylor College of Medecine, USA)

• Align (Pairwise sequence alignment with GAP, SIM (DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)

• Multiple

• ClustalW (at EBI, UK)

• ClustalW (at the Baylor College of Medicine, USA)

• MAP (Multiple alignment of (long) sequences without penalizing large gaps)

• Multiple sequence alignment (at Baylor College of Medecine, USA)

• Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)

• AMAS (Analyze multiple aligned sequences at Oxford University, UK)

• Editors

• CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)

• BOXSHADE (Software for visual information on aligned regions at ISREC, Switzerland)

Predict Secondary Structure

• TMpred (Prediction of membrane-spanning regions and their orientation at ISREC)
• SOSUI (Prediction of Transmembrane Regions, JP)
• DAS (Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method, Stockholm University)
• TopPred2 (Topology prediction of membrane proteins at the Institut Pasteur, Paris, France)
• JPred (Protein secondary structure prediction at EBI)
• HNN (Hierarchical Neural Network secondary structure prediction at NPS, Lyon, France)
• nnPredict (Protein secondary structure prediction at UCSF, CA, USA)
• BTPRED (Prediction of beta-turns at UCL, UK)
• PairCoil (Prediction of coiled Coil regions, Bergers method)
• TOPS (Protein topology cartoon generation at EBI, UK)
• TMHMM (Prediction of transmembrane helices in proteins at CBS, Denmark)
• PSort (Prediction of signal sequence, transmembrane regions and protein localization, IMCB, Jp)
• HMMTOP (Prediction of transmembrane helices and topology of proteins at Hungarian Academy of Sciences)
• PredictProtein (Protein secondary structure prediction at EMBL)
• Predator (Secondary structure prediction from single or multiple sequences at EMBL, Heidelberg)
• PSIpred (Protein secondary structure prediction at Brunel University, UK)
• Other secondary structure prediction tools at ExPASy
• Coils (Prediction of coiled Coil regions Lupas' method at EMBnet-CH)
• MultiCoil (Prediction of coiled coil regions as dimeric or trimeric assemblies at WI , USA)
• TOPS (Protein topology cartoon generation at University of Leeds, UK)