The Robetta server provides automated tools for protein structure prediction and analysis. Current capabilities include the prediction of the effects of mutations on protein–protein interactions using computational interface alanine scanning.
Features include an interactive submission interface that allows custom sequence alignments for homology modeling, constraints, local fragments, and more. It can model multi-chain complexes and provides the option for large scale sampling. It uses the PDB100 template database, which is updated weekly, a co-evolution based model database (MDB), and also provides the option for custom templates. Robetta provides both ab initio and comparative models of protein domains. It uses the Rosetta fragment insertion method. Domains without a detectable PDB homolog are modeled with the Rosetta de novo protocol.
Comparative models are built from Parent Protein DataBases (PDBs) detected by UW-PDB-BLAST or HHsearch and aligned by various methods which include HHsearch, Compass, and Promals. Loop regions are assembled from fragments and optimized to fit the aligned template structure. The procedure is fully automated. Robetta also provides automated structure prediction and analysis tools that can be used to infer protein structural information from genomic data.
The server uses one of the first fully automated structure prediction procedures that produce a model for an entire protein sequence, in the presence or absence of sequence homology to protein(s) of known structure.
Robetta parses input sequences into domains and builds models for domains with sequence homology to proteins of known structure using comparative modeling, and models for domains lacking such homology, using the Rosetta de novo structure prediction method.
These tools can be used in conjunction with current structural genomics initiatives to help accelerate structure determination and gain structural insight for targeted open reading frames (ORFs).
Additionally, since multi-domain proteins are often difficult to crystallize and many are too large for NMR structure determination, domain prediction using Robetta can help structural genomics efforts by expanding the pool of targets from which structures can be determined.
Robetta also provides the ability to identify energetically important side-chains involved in the interface of protein-protein complexes using ‘computational interface Alanine Scanning’.
The ultimate goal for Robetta is to provide structural information of sufficient quality to aid research, infer function and assist drug design. Comparative models are currently being used to infer function and guide experimental efforts.
A single interface can be analyzed in minutes. The computational methodology has been validated by the successful design of protein interfaces with new specificity and activity and has yielded new insights into the mechanisms of receptor specificity and promiscuity in biological systems.
It scans the protein chain sequence with successively less confident methods of detection to determine any homologs with experimentally determined structures, starting with PDB-BLAST, and followed by the more remote fold-detection method HHsearch. After any homologs are identified, a search of remaining regions is done with HMMER against the PFAM-A protein family database. Lastly, the PSI-BLAST multiple sequence alignment is used to assign regions of increased likelihood of possessing a contiguous domain based on sequence clusters.
The final step consists of selecting cut-points between the domains (and possibly defining new domains based on the strongest cut-points for any remaining long stretches of the sequence that have Not already matched a homolog with a structure or PFAM-A) using the Position Specific Iterated-Basic Local Alignment Search Tool Multiple Sequence Alignment (PSI-BLAST MSA).