Robetta and Rosetta

Category Proteomics>Protein Structure/Modeling Systems/Tools

Abstract Robetta is a full-chain protein structure prediction server. It parses protein chains into putative domains with the Ginzu protocol (see below...), and models those domains either by homology modeling or by ab initio modeling.

Other services of this server, in addition to Domain Parsing and 3-D Modeling, include Fragment Library (see below...) generation and Interface Alanine Scanning (see below...).

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 (see below...) de novo protocol.

Comparative models are built from Parent Protein Data Bases (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.

HHsearch - HHsearch is a program for protein sequence searching that is free for non-commercial use. HHpred is a free protein function and protein structure prediction server based on the HHsearch method.

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.

Domain predictions and molecular coordinates of models spanning the full-length query are given as results. The server can also utilize nuclear magnetic resonance (NMR) constraints data provided by the user to determine protein structures using the RosettaNMR protocol.

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 aid structural genomics efforts by expanding the pool of targets from which structures can be determined.

The Structural Genomics of Pathogenic Protozoa (SGPP) consortium has used an in-house version of Robetta to identify fragments that express and crystallize from ORFs that do Not express as a full chain, and to aid structure refinement.

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.

Fragment Libraries -- Fragment Libraries are the pieces of experimentally determined structures that Rosetta uses to guide the search of conformational space when predicting structures using the ab initio protocol, as well as longer loop conformations in homology models.

Interface Alanine Scanning -- Interface Alanine Scanning attempts to estimate the energetic contribution to the binding free energy provided by each residue at a protein-protein interface.

Briefly, interface Alanine Scanning uses a simple physical model to score a series of protein-protein interfaces (PPIs) in which contact residues are individually replaced with alanine. After each computational alanine mutation, the resulting binding energy is calculated.

The input consists of a three-dimensional structure of a protein-protein complex; output is a list of “hot spots”, or amino acid side chains that are predicted to significantly destabilize the interface when mutated to Alanine, analogous to the results of experimental Alanine-Scanning mutagenesis. 79% of hot spots and 68% of neutral residues were correctly predicted in a test of 233 mutations in 19 protein-protein complexes.

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.

Ginzu -- Ginzu is a protocol that attempts to determine the regions of a protein chain that will fold into globular units, called “domains”.

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.

HMMER- HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called “profile hidden Markov models” (profile HMMs).

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).

Rosetta --

Rosetta is a molecular modeling software package for understanding protein structures, protein design, protein docking, protein-DNA, and protein-protein interactions.

The Rosetta software contains multiple functional modules, including Rosetta ab initio, RosettaNMR, RosettaDesign, RosettaDock, Rosetta Fragment Selection, Rosetta Nucleic Acids, RosettaLigand, and more.

Rosetta Software Functionality Summary --

RosettaAbinitio - Performs de novo protein structure prediction.

RosettaDesign - Identifies low free energy sequences for target protein backbones.

RosettaDesign PyMol plug-in - A user-friendly interface for submitting Protein Design simulations, using RosettaDesign.

RosettaDock - Predicts the structure of a protein-protein complex from the individual structures of the monomer components.

RosettaAntibody - Predicts antibody Fv region structures and performs antibody-antigen docking.

RosettaFragments - Generates fragment libraries for use by Rosetta ab initio in building protein structures.

RosettaNMR - Incorporates NMR data into the basic Rosetta protocol to accelerate the process of NMR structure prediction.

RosettaDNA - For the design of proteins that interacts with specified DNA sequences.

RosettaRNA - Fragment assembly of RNA.

RosettaLigand - For small molecule - protein docking.

RosettaSymmetry - For enforcing symmetry in Rosetta.

RosettaEnzdes - For enzyme design.

RosettaMembrane - For membrane protein ab initio modeling.

RosettaDDG - For estimating the impact of sequence changes on protein stability.

RosettaScripts - An XML-based scripting language for controlling interface design, docking, and interface statistics.

RosettaSnugDock - Enables docking an antibody Fv region to an antigen and allows backbone flexibility in the paratope.

System Requirements

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Manufacturer Web Site Robetta Server

Rosetta Software

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G6G Abstract Number 20726

G6G Manufacturer Number 104296