OPUS-PSP

[…] he Pearson's correlation coefficients between CSF score and TM‐score in all decoy sets. The results are shown in Table . OPUS‐CSF has comparable average correlation coefficient with those of GOAP and OPUS‐PSP despite the fact that OPUS‐CSF is highly coarse‐grained and the other two are all‐atom potentials.For further analysis of the method, we use 5‐residue segment case as an example, Figure show […]

[…] C curves for the complexes using four other widely-used scoring potentials computed using the CCharPPI web server: DFIRE2 interaction energy, total FireDock energy (antibody–antigen energy function), OPUS-PSP all-atom potential, and ZRANK2 scoring function. We considered the native cognate antibody–antigen interaction pairs as the only true positives.Figure 8 In ROC curves, the area under the curv […]

[…] the CTR alone and the CTR ECD docked to the RAMP1 ECD were based on the CLR/RAMP1 ECD structure 3N7R using a Clustal Omega alignment. With Modeller v9.10, 1 000 models were generated and scored using OPUS_PSP. The best scoring model was visually inspected before minimization using the Amber99sb ILDN force-field as implemented in GROMACS. For MD simulations, the minimized protein was placed central […]

[…] , ProQ2 [], Pcons [], APOLLO [], ModelEvaluator [], ModelCheck2 – an improved version of ModelEvaluator, QApro – a weighted combination of ModelEvaluator and APOLLO, SELECTpro [], Dope [], DFIRE2 [], OPUS_PSP [], RWplus [], RF_CB_SRS_OD []). MULTICOM-CONSTRUCT used the consensus (average) ranking of the individual rankings produced by these methods to select top five models as predictions [, ]. MU […]

[…] , RWplus score (), dope score () and RF_CB_SRS_OD score (); ProQ2 (); Model check2 method produced by an improved version of ModelEvaluator (); a recalibrated SELECTpro energy (); Dope (); DFIRE2 (); OPUS_PSP (); Rwplus (); ModelEvaluator () and RF_CB_SRS_OD (). The multi-model QA methods include ModFOLDclust2 (); Pcons (); APPOLLO (); QApro—a weighted combination of ModelEvaluator and APOLLO (). […]

[…] clash, backbone clash, helix dipole, water bridge, disulfide, electrostatic kon, partial covalent bonds, Energy Ionisation, Entropy Complex . The second group of three features includes energy terms (OPUS-PSP terms 1–3) calculated in OPUS-PSP . Accessible surface area of the mutant amino acid residue is computed by NACCASS , as a descriptor to measure the changes on solvent accessibility during th […]