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Taking all possible secondary structures of the thermodynamic equilibrium into account, McCaskill's algorithm [ 34] computes the most probable structure and calculates the probability that each site is paired.
This software compares alignments of the sample protein to other proteins with known structural information to determine a probable structure using statistics.
Using a co-ordinated approach of different structural prediction algorithms, we were able to ascertain with confidence the probable structure of the newly identified staphylococcal enzyme (FUGUE z-score 43.6, where ≥6 represents 99% confidence [ 37]).
NMR spectrum prediction is then used to select the most probable structure and compare it with other structures ranked in decreasing order of probability.
Today on Science Online, researchers describe a probable structure for one of the virus's key proteins.
The most probable structure 1 coincides with the structure determined in the publication [42].
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Gasteiger-Huckel charge was used to determine the 3-D structures of the ligands: tricetin, selgin, and tricin, which were subjected to EM by the conjugate gradient algorithm using the Tripos Force Field; these are the most probable structures in solution but are probably distorted in the actual protein.
The key to sparsifying PARSE, is to optimize only over a subset of solutions, namely probable structures and alignments defined applying fixed probability thresholds θ1, θ2 and θ3 to the above probabilities.
From the equation we can see that the lower the free energy of a structure the higher its probability, thus, the predictions within 5% from the MFE also represent the most probable structures for a given sequence, with the MFE prediction being the one with the highest probability.
Their probable structures are shown in Fig. 3a.
Possible reaction mechanisms as well as probable structures for oligomeric products are proposed.
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