(PS)2 Protein Structure Prediction Server performs automated homology modeling by combining PSI-BLAST, IMPALA, and T-Coffee for template selection and target-template alignment. The final three-dimensional (3D) structure is built using RAMP or MODELLER.
This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).
The Berkeley Phylogenomics Group provides a series of
web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.
BIND SOAP is a web service providing end users with the ability to access functionality offered by the BIND Search Service through a remote Application Programming Interface (API).
Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
The Blocks WWW server provides tools to search DNA and protein queries against the Blocks database of multiple alignments, which represent conserved protein regions.
botXminer is a literature searching tool that allows you to search BotDB. BotDB citations contain only those articles with either \'botulinum\' or \'tetanus\' anywhere in their text. botXminer is an interface to this subset of complete medline xml files loaded into an Oracle XMLDB.
Cascade PSI-BLAST detects distant protein similarities using a cascade search protocol where PSI-BLAST searches are carried out on each hit, until no new hits are found in the selected database (SwissProt, SCOP, or Pfam).
