Proteins

By James J. L'ltalien. 1987

Subfields: Computational Biology & Bioinformatics

How researchers see this paper

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

In Computational Biology & Bioinformatics

Citations in the corpus

Towards automated crystallographic structure refinement with phenix.refine (2012, background): “Other structures, 2elg (Ohishi et al. , 2007), 1g2y (Rose et al. , 2000) and 2ppn (Szep et al. , 2009), were also selected on the basis of unusually high R factors.”
Features and development of Coot (2010, neutral): “The background of the plot shows frequency data for Ramachandran angles using the Richardsons’ data (Lovell et al. , 2003).”
Overview of the CCP4 suite and current developments (2011, methodology): “The supplementary program Sloop (Cowtan, unpublished program) builds missing loops using fragments taken from the Richardson’s Top500 library of structures (Lovell et al. , 2003) to ﬁll gaps in the chain.”
Phaser crystallographic software (2007, background): “Bahar et al. (1997) and Hinsen (1998) have shown that it is possible to find the lowest frequency normal modes of proteins in the elastic network model by considering amino acid C atoms only.”
Structure of a rabbit muscle fructose-1,6-bisphosphate aldolase A dimer variant (2008, positive): “The difference in the relative orientations of the monomers within the D128V aldolase compared with half of the tetramer was analyzed using the program DynDom (Hayward et al., 1997).”
Simultaneous optimization of biomolecular energy function on features from small molecules and macromolecules (2016, methodology): “Drawing off expertise from our first experiments, the target function for second run was modified: [3] Compared to the previous optimization (Eqn.”
The Buccaneer software for automated model building. 1. Tracing protein chains. (2006, methodology): “The Ramachandran data used here is from the 'Top 500' structures database of Lovell et al. (2003).”
Developments in the CCP4 molecular-graphics project. (2004, neutral): “…(cid:119)(cid:111)(cid:114)(cid:107) (cid:105)(cid:110) (cid:70)(cid:82)(cid:79)(cid:68)(cid:79) (cid:40)(cid:74)(cid:111)(cid:110)(cid:101)(cid:115)(cid:44) (cid:49)(cid:57)(cid:55)(cid:56)(cid:41) (cid:97)(cid:110)(cid:100) (cid:105)(cid:116)(cid:115)…”
An estimated 5% of new protein structures solved today represent a new Pfam family (2013, methodology): “It was used, for example, as a source of novel domain targets by the Protein Structure Initiative (PSI-2; Chandonia & Brenner, 2005; Dessailly et al., 2009).”