Protein Databases:
- UniProt
- the central repository of protein sequence and function data, created
by combining the information contained in Swiss-Prot, TrEMBL, and PIR
- DSSP
- Database of Secondary Structure
- SCOP
-
Structural Classification Of Protein
- PDB - Protein
structure Data Bank [Molecules
R Us | PDBsum]
Specialized Viral Protein
Databases:
- VOG -
Viral
Clusters of Orthologous Groups of proteins at NCBI.
- dbMHC
- Major Histocompatibility Complex database at NCBI
- MEROPS -
Peptidase database.
- HIV Drug
Resistance
Database - All published drug-related variations in Protease and
Reverse Transcriptase
Motif and Transcription Factors
Databases:
- Pfam
-
Protein Family classification
- ProDom
- Protein Domain database
- MOTIF -
Dictionary
of Protein Sites and Patterns
- PROSITE
- Protein Motif Fingerprint Database
|
Proteomics site map, with external links to main databases and
tools.
|
Protein
sequence
similarity searches:
- BLAST
(HIV, SIV, HCV and HBV) - Protein sequence comparison tool that
implements a Heuristic algorithm - BioAfrica
- PSI-BLAST
- Position Specific Iterated BLAST - NCBI
- MPsrch
- Protein sequence comparison tool that implements true Smith &
Waterman exhaustive algorithm
Protein sequence alignment:
- ClustalW
-
Produces multiple sequence alignments
- TCoffee -
More accurate than ClustalW for sequences with <30% identity
- MultAlin
- Global
similarity multiple sequence alignment using hierarchical clustering
- Dotlet
- Dot Matrix sequence comparison
Protein sequence prediction tools:
- PA-IBM
- Protein annotation tool, searches SwissProt/TrEMBL for similar
proteins, and provides predicted functional regions
- N-Glycosite
- Predict potential N-glycosylation sites in an aligned set of protein
sequences
- NetPhos
- Prediction of Ser, Thr and Tyr phosphorylation sites
- PeptideCutter
- Predicts potential cleavage sites
Protein sequence
analysis/manipulation:
- GENIO/logo
- Colour sequences based on specified characteristics and analyze amino
acid replacement and distribution
- ProtParam
- Calculate physico-chemical parameters of a protein sequence
- Backtranslation
- Translates a protein sequence back to a nucleotide sequence
- ReadSeq
-
Convert between sequence file formats
|
Protein structure analysis:
- SWISS-MODEL
- Automated knowledge-based protein structure prediction server
- PredictProtein
- Gateway to multiple prediction servers (secondary structure, membrane
regions, homology modelling and threading)
- SMART
-
Simple Modular Architecture Research Tool
- PINTS
-
Patterns In Non-homologous Tertiary Structures (finds clusters
of functionally relevant amino acids)
Molecular Modelling tools:
- DOCK
- Characterization of binding site.
- AutoDock
- Docking of flexible ligands into receptor binding sites.
- DOT - Rigid body protein-protein
docking
Tutorials:
Downloads:
- Cn3D
(Linux, PC, Mac, Unix) - NCBI - Simultaneously displays structure,
sequence, annotation and alignment data
- SwissPDB Viewer
(Linux, PC, Mac, Unix) - Expasy - Analyze proteins structures,
with the ability to deduce structural alignments, mutate amino acids,
and perform molecular surface calculations, homology modelling and
energy minimization calculations.
|
