Words similar to dpssm

Example sentences for: dpssm

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Fold predictions were done using the 3-D position specific score matrix (3DPSSM) [ 43 ] and the Hybrid fold method [ 44 ] . Phylogenetic analysis was carried out using the neighbor-joining algorithm, with subsequent local rearrangements using the maximum likelihood algorithm [ 45 ] . The robustness of tree topology was assessed with 10000 Resampling of Estimated Log Likelihoods (RELL) bootstrap replicates.
Both 3DPSSM and PSIPRED gave hits (E-value approximately 0.05 for 3DPSSM and probability of matching approximately 0.8 for PSIPRED) that implied a 90% certainty of the KilA-N domain adopting the same fold as the APSES domain (PDB 1bm8/1bm1).
Previously known, conserved domains were identified using PSI-BLAST derived profiles for them, with the RPS-BLAST program [ 45 ] . Sequence-structure threading was performed using the 3DPSSM server http://www.sbg.bio.ic.ac.uk/~3dpssm/.
This difference may also explain the failure of sequence-structure threading algorithms, such as the combined fold prediction and 3DPSSM [ 39], to recover any significant hits to the papain-like proteases.
Additionally, fold predictions using 3DPSSM (E-value=.