Protein structure prediction and analysis using the Robetta server

TLDR

The Robetta server provides automated tools for protein structure prediction and analysis. The server parses submitted sequences into domains and builds structural models using comparative modeling when a suitable template is found via BLAST/PSI‑BLAST/FFAS03/3D‑Jury, otherwise it employs Rosetta fragment‑insertion de novo prediction, with optional NMR constraints and mutation‑effect analysis, and will soon support Rosetta design and docking.

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.