ARIA: automated NOE assignment and NMR structure calculation

By J. Linge, M. Habeck, W. Rieping, M. Nilges. 2003

392 citations recorded by the source corpus.

Subfields: Molecular Biology, Spectroscopy

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Alexandre M. J. J. Bonvin
2. M. V. van Dijk
3. Debora Marks
4. Oliver F. Lange
5. Christopher Sander
6. João P. G. L. M. Rodrigues
7. Thomas A. Hopf
8. Woonghee Lee

In Spectroscopy

1. Oliver F. Lange
2. Alexandre M. J. J. Bonvin
3. João P. G. L. M. Rodrigues
4. M. V. van Dijk
5. Oliver Kohlbacher
6. Christopher Sander
7. Sjoerd Jacob de Vries
8. John L. Markley

Citations in the corpus

• Sequence co-evolution gives 3D contacts and structures of protein complexes (2014, methodology): “, 2003), a widely used docking program based on ARIA (Linge et al., 2003) and the CNS software (Brunger, 2007) (Crystallography and NMR System), to”
• Automatic NOESY assignment in CS-RASREC-Rosetta (2014, methodology): “For iterative refinement of NOE assignments usually all assigned distances that are significantly violated by the preliminary models are removed (Nilges 1993; Herrmann et al. 2002; Huang et al. 2003; Linge et al. 2003).”
• Information-driven structural modelling of protein-protein interactions. (2015, methodology): “HADDOCK is an information-driven docking software [7] that was originally adapted from the NMR automated structure determination approach ARIA [8].”
• The HADDOCK web server for data-driven biomolecular docking (2010, methodology): “This drives the docking in a similar manner as ambiguous distance restraints based on NOE data drive the structural calculation of an NMR structure (see e.g., Linge et al. 38 ).”
• Refinement of protein structures in explicit solvent (2003, methodology): “2.(11) The simulated annealing protocol consisted of four stages: a high-temperature torsion angle simulated annealing phase(24,25) at 10,000 K (1100 steps), a first torsion angle dynamics cooling phase from 10,000 K to 2000 K (550 steps), a second Cartesian dynamics cooling phase from 2000 K to 100”
• PONDEROSA-C/S: client–server based software package for automated protein 3D structure determination (2014, methodology): “Alternatively, water bath refinement, as inspired by the RECOORD and ARIA projects (Nederveen et al. 2005; Linge et al. 2003) can be generated and executed by use of CNS (Bru¨nger et al. 1998).”