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Protein Structure Prediction Using Rosetta
This chapter elaborates protein structure prediction using Rosetta, where short fragments of known proteins are assembled by a Monte Carlo strategy to yield native-like protein conformations. Expand
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.
The effects of multiple sequence information and different types of conformational constraints on the overall performance of the method are investigated, and the ability of a variety of recently developed scoring functions to recognize the native-like conformations in the ensembles of simulated structures are investigated. Expand
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.
This chapter describes the requirements for the ROSETTA molecular modeling program's new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform. Expand
Protein structure prediction and analysis using the Robetta server
The Robetta server provides automated tools for protein structure prediction and analysis and current capabilities include the prediction of the effects of mutations on protein-protein interactions using computational interface alanine scanning. Expand
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.
A new method to predict protein-protein complexes from the coordinates of the unbound monomer components using a low-resolution, rigid-body, Monte Carlo search followed by simultaneous optimization of backbone displacement and side-chain conformations using Monte Carlo minimization is presented. Expand
Contact order, transition state placement and the refolding rates of single domain proteins.
Investigations have revealed statistically significant correlations between the average sequence separation between contacting residues in the native state and the rate and transition state placement of folding for a non-homologous set of simple, single domain proteins, indicating that proteins featuring primarily sequence-local contacts tend to fold more rapidly and exhibit less compact folding transition states than those characterized by more non-local interactions. Expand
A simple physical model for binding energy hot spots in protein–protein complexes
  • T. Kortemme, D. Baker
  • Chemistry, Medicine
  • Proceedings of the National Academy of Sciences…
  • 15 October 2002
The results test the understanding of the dominant contributions to the free energy of protein–protein interactions, can guide experiments aimed at the design of protein interaction inhibitors, and provide a stepping-stone to important applications such as interface redesign. Expand
Toward High-Resolution de Novo Structure Prediction for Small Proteins
The prediction of protein structure from amino acid sequence is a grand challenge of computational molecular biology and the primary bottleneck to consistent high-resolution prediction appears to be conformational sampling. Expand
Predicting protein structures with a multiplayer online game
Foldit is described, a multiplayer online game that engages non-scientists in solving hard prediction problems and shows that top-ranked Foldit players excel at solving challenging structure refinement problems in which substantial backbone rearrangements are necessary to achieve the burial of hydrophobic residues. Expand
Macromolecular modeling with rosetta.
  • Rhiju Das, D. Baker
  • Computer Science, Medicine
  • Annual review of biochemistry
  • 2 June 2008
A unified energetic and kinematic framework in the Rosetta program allows a wide range of molecular modeling problems, from fibril structure prediction to RNA folding to the design of new protein interfaces, to be readily investigated and highlights areas for improvement. Expand