This page contains links to servers which you will use for the
Tools and Comparative Modelling practical
and for the Mini-Projects.
| Link | Description |
| BLAST | Sequence database search at the NCBI |
| Local BLAST | Sequence database search running locally |
| FASTA | FASTA sequence database search |
| Link | Description |
| InterPro | Integrated resource of secondary databases |
| PRINTS | PRINTS secondary database |
| BLOCKS | BLOCKS secondary database |
| ProSite | ProSite secondary database |
| Pfam | Pfam secondary database (also at Washington University) |
| MOTIF | Integrated motif searching resource |
| Link | Description |
| From manchester... | 6-frame translation software |
| From Expasy | 6-frame translation software |
| From EBI | 6-frame translation software |
| Link | Description |
| NNPredict | Neural network prediction of secondary structure |
| JPRED | Secondary structure prediction |
| GOR | GOR SS Prediction |
| GOR-II/III | GOR-II/III SS Prediction |
| GOR-IV | GOR-IV SS Prediction |
| PSIPred / MemSat | PSIPred SS Prediction - Also MemSat TM prediction |
| Link | Description |
| TSEG | Predict membrane proteins |
| TMHMM-2.0 | TM prediction through Hidden Markov Models |
| TopPred | Predict location and orientation of transmembrane helices through an advanced use of hydrophobicity patterns, and by applying the 'positive-inside' rule |
| DAS | TM Prediction through an advanced use of hydrophobicity patterns |
| PRED-TMR | TM prediction |
| Link | Description |
| NetPhos | NetPhos is a neural network-based method for predicting potential phosphorylation sites at serine, threonine or tyrosine residues in protein sequences. |
| NetOGlyc | The NetOglyc WWW server produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins. |
| big-PI | GPI Modification Site Prediction |
| GPI-anchor | Another tool for GPI cleavage site (GPI-anchor) prediction |
| Link | Description |
| FRSVR | Daniel Fischer's Prediction-based threading, also incorporating purely sequence-based database searches (new server here) |
| SAMt98 | A new HMM based method to find remote homologs. Beta version of SAM-T99 |
| 3D-pssm | Fold recognition |
| Link | Description |
| Swiss-Model | an Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland |
| CPHmodels | A neural net based comparative modelling tool |
| CYSPRED | Disulphide prediction |
| Link | Description |
| ClustalW | Multiple sequence alignment (also at EMBNet). |
| Link | Description |
| Physico- chemical properties | Plot Amino Acid Physico-chemical Properties (hydropathy, predicted accessibility, flexibility, GOR-SS) |
| ProtScale | Plot various sequence-based profiles (hydrophobicity, secondary structure, etc.) |
| Link | Description |
| PSORT | Predict protein sorting signals |
| SignalP | Signal peptides |
| Link | Description |
| PredictProtein | Prediction system from the Columbia University (also available at the EBI) Includes PHD secondary structure prediction, ProSite, domain prediction, threading, solvent accessibility, TM, etc. |