Primary Citation PubMed: 16004868
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SAMPLEX: automatic mapping of perturbed and unperturbed regions of proteins and complexes.
(2010) BMC Bioinformatics 11
PubMed: 20102599 | PubMedCentral: PMC2823710 | DOI: 10.1186/1471-2105-11-51
Since the structure of the partially unfolded state of Δ25-PYP has been solved by NMR, we investigated the dependence of the predictions on the structure used: when running SAMPLEX from the un... olded structure (PDB code 1XFQ ) [ 27 ] residues 28-29, 43-58, 63-65, 67-68, 70-74, 77-78, 97-102 are predicted as perturbed and residues 42, 66, 69, 76, 79, 103 as ambiguous.
Publication Year: 2010
Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble.
(2014) PLoS Comput Biol 10
PubMed: 25356903 | PubMedCentral: PMC4214557 | DOI: 10.1371/journal.pcbi.1003797
g003 Figure 3 Configuration from a) pG state (PDB ID: 3PHY), b) experimental signaling state of WT-PYP (PDB ID: 2XK6), c) experimental signaling state of Δ25 (PDB ID: 1XFQ), d) representative ... onfiguration from our pB ensemble.
For this mutant solution-phase NMR structural measurements have been performed and added to the PDB, PDB ID: 1XFQ  .
g004 Figure 4 Comparison of the C α deviations from the pG configuration for the experimental Δ25 configurations (PDB ID 1XFQ) in black, experimental WT-PYP pB configurations (PDB ID: 2KX6) in green, and our pB ensemble in blue.
For reference, the coordinates for the experimental Δ25 (PDB ID 1XFQ) structures are shown as dark blue *, and the experimental WT-PYP (PDB ID: 2KX6) structures as red *.
Publication Year: 2014
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