title: RBO Aleph: leveraging novel information sources for protein structure prediction.
abstract: RBO Aleph is a novel protein structure prediction web server for template-based modeling, protein contact prediction and ab initio structure prediction. The server has a strong emphasis on modeling difficult protein targets for which templates cannot be detected. RBO Aleph's unique features are (i) the use of combined evolutionary and physicochemical information to perform residue-residue contact prediction and (ii) leveraging this contact information effectively in conformational space search. RBO Aleph emerged as one of the leading approaches to ab initio protein structure prediction and contact prediction during the most recent Critical Assessment of Protein Structure Prediction experiment (CASP11, 2014). In addition to RBO Aleph's main focus on ab initio modeling, the server also provides state-of-the-art template-based modeling services. Based on template availability, RBO Aleph switches automatically between template-based modeling and ab initio prediction based on the target protein sequence, facilitating use especially for non-expert users. The RBO Aleph web server offers a range of tools for visualization and data analysis, such as the visualization of predicted models, predicted contacts and the estimated prediction error along the model's backbone. The server is accessible at http://compbio.robotics.tu-berlin.de/rbo_aleph/.
authors.affiliation: Robotics and Biology Laboratory, Department of Electrical Engineering and Computer Science, Technische Universität Berlin, Marchstraße 23, 10587 Berlin, Germany.
authors.forename: Mahmoud
authors.initials: M
authors.lastname: Mabrouk
authors.affiliation: Robotics and Biology Laboratory, Department of Electrical Engineering and Computer Science, Technische Universität Berlin, Marchstraße 23, 10587 Berlin, Germany.
authors.forename: Ines
authors.initials: I
authors.lastname: Putz
authors.affiliation: Robotics and Biology Laboratory, Department of Electrical Engineering and Computer Science, Technische Universität Berlin, Marchstraße 23, 10587 Berlin, Germany.
authors.forename: Tim
authors.identifier: http://orcid.org/0000-0002-5055-6686
authors.initials: T
authors.lastname: Werner
authors.affiliation: Robotics and Biology Laboratory, Department of Electrical Engineering and Computer Science, Technische Universität Berlin, Marchstraße 23, 10587 Berlin, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Schneider
authors.affiliation: Robotics and Biology Laboratory, Department of Electrical Engineering and Computer Science, Technische Universität Berlin, Marchstraße 23, 10587 Berlin, Germany.
authors.forename: Moritz
authors.initials: M
authors.lastname: Neeb
authors.affiliation: Robotics and Biology Laboratory, Department of Electrical Engineering and Computer Science, Technische Universität Berlin, Marchstraße 23, 10587 Berlin, Germany.
authors.forename: Philipp
authors.initials: P
authors.lastname: Bartels
authors.affiliation: Robotics and Biology Laboratory, Department of Electrical Engineering and Computer Science, Technische Universität Berlin, Marchstraße 23, 10587 Berlin, Germany oliver.brock@tu-berlin.de.
authors.forename: Oliver
authors.initials: O
authors.lastname: Brock
mesh_terms: D000465:Algorithms; D020407:Internet; D008958:Models, Molecular; D011487:Protein Conformation; D020539:Sequence Analysis, Protein; D012984:Software