Protein structure prediction and analysis using the Robetta server

Paper

Abstract

The Robetta server (http://robetta.bakerlab.org) provides automated tools for protein structure prediction and analysis. For structure prediction, sequences submitted to the server are parsed into putative domains and structural models are generated using either comparative modeling or de novo structure prediction methods. If a confident match to a protein of known structure is found using BLAST, PSI-BLAST, FFAS03 or 3D-Jury, it is used as a template for comparative modeling. If no match is found, structure predictions are made using the de novo Rosetta fragment insertion method. Experimental nuclear magnetic resonance (NMR) constraints data can also be submitted with a query sequence for RosettaNMR de novo structure determination. Other current capabilities include the prediction of the effects of mutations on protein-protein interactions using computational interface alanine scanning. The Rosetta protein design and protein-protein docking methodologies will soon be available through the server as well.

Analysis

Paper intelligence

Summary

The Robetta server offers automated tools for predicting and analyzing protein structures using comparative modeling or de novo methods, with capabilities for mutation effect prediction and future integration of design and docking.

Key findings

Robetta server automates protein structure prediction and analysis.
It uses comparative modeling or de novo prediction based on sequence similarity.
Experimental NMR constraints can be incorporated for de novo determination.
Predicts mutation effects on protein-protein interactions.

Methods

Comparative modeling using BLAST, PSI-BLAST, FFAS03, or 3D-Jury.
De novo structure prediction using Rosetta fragment insertion.
RosettaNMR for de novo structure determination with NMR constraints.
Computational interface alanine scanning for mutation effect prediction.

Limitations

The paper is from 2004, so methods may be outdated.
Specific accuracy metrics for predictions are not detailed in the abstract.

Applications

Protein structure prediction.
Analysis of protein structures.
Predicting effects of mutations on protein interactions.
Future applications in protein design and docking.

Confidence100%

Discovery

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Source record

Publication metadata

Authors: David E. Kim; Dylan Chivian; David Baker
Published: Jul 1, 2004
Journal or venue: Nucleic Acids Research
DOI: 10.1093/nar/gkh468
Paper type: journal article
Source: Openalex

DOI OpenAlex