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Protein sequence & Structure
Protein sequence & Structure
Physiochemcial Properties |
- ProtParam (Calculate aa comp, MW, pI, extinction coefficient at ExPASy, CH)
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- ProTherm (Thermodynamic Database for Proteins and Mutants, Jp)
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- 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)
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- 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
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- Blast 2 Sequences (Alignment of two protein sequences using BLAST at NCBI, USA)
- ClustalW (Multiple sequence alignement at WUSTL, USA)
- Align (Pairwise sequence alignment with GAP, SIM (DNA or protein alignment), NAP, LAP2 (DNA-protein alignment) or GAP2 (DNA-cDNA alignment)
- AMAS (Analyze multiple aligned sequences at Oxford University, UK)
- CINEMA (Colour INteractive Editor for Multiple Alignments at BCM group, UK)
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- SIM (Alignment of 2 protein sequences at ExPASy, Switzerland)
- ClustalW (at EBI, UK)
- ClustalW (at the Baylor College of Medicine, USA)
- MAP (Multiple alignment of (long) sequences without penalizing large gaps
- Launcher: multiple alignment (Choose from different alignment applications at Bailor College of Medecine, Houston, Tx, USA)
- BOXSHADE (Software for visual information on aligned regions at ISREC, Switzerland)
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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)
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- 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)
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