Bioinformatics Applications Note Structural Bioinformatics Openstructure: a Flexible Software Framework for Computational Structural Biology
By Marco Biasini, Valerio Mariani, Jürgen Haas, Stefan Scheuber, A. Schenk, Torsten Schwede, A. Philippsen
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
- Torsten Schwede
- J. Haas
- Lorenza Bordoli
- Marco Biasini
- Stefan Bienert
- Liam J. McGuffin
- Pascal Benkert
- Florian Kiefer
Citations in the corpus
- Toward the estimation of the absolute quality of individual protein structure models (2010, methodology): “The current version of the QMEAN scoring function has been implemented based on the open source molecular modelling and visualization framework OpenStructure (www.openstructure.org) (Biasini et al., 2010).”
- The Protein Model Portal—a comprehensive resource for protein structure and model information (2013, background): “For these reasons, PMP provides an interface to analyze the variability within an ensemble of experimental structures and models for a protein, which is built based on the computational structural biology framework OpenStructure (43).”
- Assessment of ligand binding site predictions in CASP10 (2014, background): “17,23,25,29,32 Some types of this domain use zinc, others use iron or form salt-bridges to create the correct fold, which often does not change conformation upon binding the target.”
- Assessment of template based protein structure predictions in CASP9 (2011, background): “45 For the assessment of close inter-atomic contacts (‘‘van der Waals clashes’’), a list of short distance contacts observed in 1769 high resolution protein structures was derived.”
- OpenStructure: an integrated software framework for computational structural biology (2013, methodology): “Conservation of columns in an alignment may be calculated with a variation of the algorithm from ConSurf (Armon et al., 2001), which considers the pairwise physicochemical similarity of residues in each alignment column (for an example, see Biasini et al., 2010).”
- Assessment of ligand binding residue predictions in CASP9 (2011, background): “29 For targets in which only part of the relevant ligand was present, the binding site definition was extended to include the entire biologically relevant ligand.”