Sali, A. & Blundell, T. L. Compartive protein modelling by satisfaction of spatial restraints.
Sali, A. & Blundell, T. L. Comparative protein modeling by satisfaction of spatial restraints.
Sali, A. & Blundell, T.L. Comparative protein modelling by satisfaction of spatial restraints.
Sali, A. & Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints.
We review recent methodological developments in integrative structural modeling by satisfying spatial restraints on networks of FRET pairs (hybrid-FRET).
Discrete sampling schemes represent an attractive alternative for generating ensembles of conformers consistent with spatial restraints derived from empirical data.
We validated our models by confirming two sets of model-generated predictions that were independent from the spatial restraints used in model-building.
Here we review a new family of computational approaches that aim at using 3C-based data to obtain spatial restraints for modeling genomes and genomic domains.
Initially generated, homology models of the target protein are refined iteratively by including information about bioactive ligands as spatial restraints and optimising the mutual interactions between the ligands and the binding-sites.
These results provide spatial restraints for protein:DNA interactions, which enable construction of a three-dimensional pseudo-atomic model for a DNA-packaging initiation complex assembled from the terminase small subunit and the packaging region on viral DNA.
Xlink Analyzer enables automatic visualization of cross-links, identifies cross-links violating spatial restraints, calculates violation statistics, maps chemically modified surfaces, and allows interactive manipulations that facilitate analysis of XL-MS data and aid designing new experiments.
