Protein Analysis
- Posttranslational modifications
- RESID predicts postranslational modifications
- NetPhos at Expasy and CBS predicts phosphorylation sites
- O- glycosylation sites and NetOglyc
- GPI anchor and big-PI Predictor- GPI Modification Site Prediction
- SIGNAL PEPTIDE PREDICTION and Signalp V1.1 and SignalP and PSort
- PredictProtein and TMpred predict transmembrane spanning domains and topology
- Multiple sequence alignment
Ensemble for finding orthologues in genomes
- Protein Domain motif Searches
- Pfam _ HMM Search (St. Louis)
- Expasy has one of the best collection of pattern and profile search tools
- SMART - Simple Modular Architecture Research Tool
- BLOCKS is a protein motif database
- The ProDom protein domain database
- pattern scanner
- Hits at Expasy- Relationships between protein sequences and motifs
- Prosite and PPSEARCH is a database of protein families and domains
- PRINTS is a protein motif fingerprint database
- Frame-ProfileScan -at Expasy Scans a short DNA sequence against protein databases
- DOMO is a protein domain database
- Proteome sites
- Proteome Inc has great annotated database to Yeast and worms
- GadFly and FlyBase have annotated fly database
- Protein Families
- Proweb is one of the best links for protein families
- MEROPS is a protease database
- G-protein coupled receptors
- Protein kinase resource has sequence alignments, structural information, techniques, diseases, and more resources concerning protein kinases.
- Protein families at CMS has more than 25 different protein families
- Protein families at PKR has web pages for more than 15 different protein families
- Protein structure
- RasMol software for viewing 3-dimensional structures
- Swiss-model will model a 3 dimensional structure based on homology to other proteins
- BioMagRsBank is a depository of NMR data
- UCONN-tools for NMR and other tools for protein structure
- MolSurfer is a useful program for looking at surface interactions between two proteins
- WebMol displays and analyzes structural information
- PDB is a structural database
NMR LINKS is a jumpstation for links to NMR resources
- for looking for proteins with similar 3D structures
- Protein sorting signals and specific motifs
- Leucine zippers predicts leucine zippers
- PEST at Expasy and PESTfind- Identification of PEST regions
- PSORT and PSORT2 identifies protein sorting signals
- Protein Physics
- Peptide Mass predicts mass from a nucleotide sequence
- ExPASy - ProtParam tool computes PI, aliphatic index, composition ect.
- ProtScale assigns numerical scale to amino acids in proteins based on physical properties
- hydropathy plots generates a GIF output hydropathy plot
- Keck Facility for mass spec and biophysics
MOTIF SITES
- Yeast two-hybrid screens
- Yeast tools - menu
- False positives in Interaction Trap Table of false positives
- Utilities
- Convert changes sequence formats
- ExPASy - Translate tool for translating DNA sequences
- BoxShade Server make colored format of multiple sequence alignments
- ORF_ DNA Sequence Translation translates nucleotide sequence and finds open reading frames
- Genewise at Expasy will compare a protein sequence to genomic sequence allowing for introns
- Enzyme nomenclature database
- Mass-spec protein resources at Expasy
Hybridoma Bank for cheap antibodies
