Retrieval of Crystallographically-Derived Molecular Geometry Information

By Ian J. Bruno, Jason C. Cole, M. Kessler, Jie Luo, W. Motherwell, L. H. Purkis, Barry R. Smith, Robin Taylor, Richard I. Cooper, S. E. Harris and 1 more. Journal of Chemical Information and Modeling, 2004

848 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/b37f2a66b5a6e59bc1c61613a53793fca9451481

How researchers see this paper

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

In Computational Theory and Mathematics

1. Paul D. Adams
2. Nigel W. Moriarty
3. Randy J. Read
4. T. C. Terwilliger
5. Nathaniel Echols
6. B. Lohkamp
7. G. Murshudov
8. Jane S. Richardson

In Materials Chemistry

1. Paul D. Adams
2. Randy J. Read
3. T. C. Terwilliger
4. Pavel V. Afonine
5. Nigel W. Moriarty
6. G. Murshudov
7. Nathaniel Echols
8. Jane S. Richardson

In Spectroscopy

1. Paul D. Adams
2. T. C. Terwilliger
3. Anastassis Perrakis
4. G. Murshudov
5. Nathaniel Echols
6. Robbie P. Joosten
7. F. Long
8. Jane S. Richardson

Citations in the corpus

• A New Generation of Crystallographic Validation Tools for the Protein Data Bank (2011, methodology): “As part of the agreement, wwPDB will have access to Mogul, which will be integrated into the wwPDB validation pipeline, and to the experimental coordinates of ligands that are or have been deposited in the PDB and that also occur in the CSD.”
• DASH: a program for crystal structure determination from powder diffraction data (2006, methodology): “Mogul (Bruno et al., 2004), a library of intramolecular geometries obtained from the analysis of organic crystal structures within the Cambridge Structural Database (CSD; Allen, 2002), provides quick and easy access to ‘probability distributions’ for bond lengths, bond angles and torsion angles.”
• Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data (2019, methodology): “However, this tool has not been widely adopted by the community, perhaps because of its dependency on CCDC's Mogul validation program.(43) Consequently, the validation feedback has been reworked so that it is based on a dictionary rather than using Mogul and so that the module has no external depend”
• Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes (2016, methodology): “The geometry of didemnin B model was analyzed using Mogul, a molecular-geometry library derived from the Cambridge Structural Database (CSD) (Bruno et al., 2004).”
• The Cambridge Structural Database (2016, methodology): “As well as these services there are a number of other avenues to explore and exploit the data ranging from free lookup tools such as CellCheckCSD (Wood, 2011) to advanced search, analysis and validation tools in the CSD-System (Bruno et al., 1997, 2002, 2004; Macrae et al., 2008).”
• Mercury: visualization and analysis of crystal structures (2006, methodology): “Since several of the file formats do not carry bond-type information, an algorithm has been implemented for deducing bond types from three-dimensional atomic coordinate information (Bruno et al., 2004).”
• Implementing an X-ray validation pipeline for the Protein Data Bank (2012, methodology): “Finally, the geometrical quality of ligand molecules will be assessed using the program Mogul (Bruno et al., 2004), which will be provided by the Cambridge Crystallographic Data Centre (CCDC; http://www.ccdc.cam.ac.uk/products/csd_system/mogul).”
• Ligand placement based on prior structures: the guided ligand-replacement method (2013, methodology): “These newer tools often use the Cambridge Structural Database/Mogul (Bruno et al., 2004) and quantummechanical calculations to provide robust parameterization with only the chemical structure as input.”
• AceDRG: a stereochemical description generator for ligands (2017, methodology): “- elbow (Moriarty et al. , 2009) from the PHENIX software suite (Adams et al. , 2010), grade (Smart et al. , 2011) from Global Phasing and pyrogen from Coot (Emsley et al. , 2010) use Mogul to generate accurate ligand descriptions.”
• Mercury 4.0: from visualization to analysis, design and prediction (2020, methodology): “The recently added ‘CSD-System’ menu in Mercury collects together links to the full set of CSD-System components, including WebCSD, ConQuest, Data Analysis, Mogul and IsoStar.”
• Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures (2008, background): “Mogul A facility to check easily the intramolecular geometry of a molecule is now available.”