A. Clustering analysis for the predicted structures of the SUMO2/RBD complex using mutual Q (including inter-domain and inter-molecular residue pairs) as the structural similarity metric. B. Potential energy (blue line) and numbers of minimally frustrated contacts (red line) for the predicted SUMO2/RBD complex structures. The structure with the largest number of minimally frustrated contacts and having relatively low potential energy is selected as the representative structure (marked with a red star) and is shown in Fig 4C. C. The predicted structure of the SUMO2/RBD complex. The SUMO2 is colored in pink and the SIM in RRM1 is colored in green.</p
<p>The TRAIL-R2 structure derived from the complex with UL141 (4I9X, in cyan) is superimposed (resid...
<p>Overlap of the linker representative clusters in the binary (<b>A1 and A2</b>) and ternary (<b>B1...
<p>(A) Free energy landscape of metadynamics simulation. The brown dotted outline corresponds to the...
A. One example of the initial structure for the SUMO2/RBD complex structure prediction. The SUMO2 pr...
A. The free energy landscape for RBD plotted using Qf and PC0 as the two order parameters. Qf is the...
A. The 60 predicted structures of full length RBD that can be divided into 3 clusters using mutual Q...
A. The free energy landscape for RBD/RNA using Qf and PC0 as the two order parameters. B. The free e...
<p>The rigid body prediction before SDU2 refinement is indicated by a black circle and the SDU2 pred...
<p>(A) Structural model of the lowest scoring models from the 4 largest clusters, showing the PP2AA ...
Inaccuracies in computational molecular modeling methods are often counterweighed by brute-force gen...
<p>The red nodes represent the proteins in the true complex that are detected by the algorithm, the ...
<p>The native structure is indicated by a blue circled asterisk and the SDU2 prediction by a red squ...
<p>The clustering results are color-coded to indicate the population of the cluster in the given tim...
<p>(A) The RMSD for backbone atoms of the protein. (B) The potential energy of the system. These plo...
<p>The structures of Models 1–6 were initially generated by homology modeling, while Model 7 was gen...
<p>The TRAIL-R2 structure derived from the complex with UL141 (4I9X, in cyan) is superimposed (resid...
<p>Overlap of the linker representative clusters in the binary (<b>A1 and A2</b>) and ternary (<b>B1...
<p>(A) Free energy landscape of metadynamics simulation. The brown dotted outline corresponds to the...
A. One example of the initial structure for the SUMO2/RBD complex structure prediction. The SUMO2 pr...
A. The free energy landscape for RBD plotted using Qf and PC0 as the two order parameters. Qf is the...
A. The 60 predicted structures of full length RBD that can be divided into 3 clusters using mutual Q...
A. The free energy landscape for RBD/RNA using Qf and PC0 as the two order parameters. B. The free e...
<p>The rigid body prediction before SDU2 refinement is indicated by a black circle and the SDU2 pred...
<p>(A) Structural model of the lowest scoring models from the 4 largest clusters, showing the PP2AA ...
Inaccuracies in computational molecular modeling methods are often counterweighed by brute-force gen...
<p>The red nodes represent the proteins in the true complex that are detected by the algorithm, the ...
<p>The native structure is indicated by a blue circled asterisk and the SDU2 prediction by a red squ...
<p>The clustering results are color-coded to indicate the population of the cluster in the given tim...
<p>(A) The RMSD for backbone atoms of the protein. (B) The potential energy of the system. These plo...
<p>The structures of Models 1–6 were initially generated by homology modeling, while Model 7 was gen...
<p>The TRAIL-R2 structure derived from the complex with UL141 (4I9X, in cyan) is superimposed (resid...
<p>Overlap of the linker representative clusters in the binary (<b>A1 and A2</b>) and ternary (<b>B1...
<p>(A) Free energy landscape of metadynamics simulation. The brown dotted outline corresponds to the...