Equation 8 · Part 9 · Structure from Sequence: What Protein Folding Prediction Did and Did Not Settle

Symbol e_ij

P(a_1,\ldots,a_L) = \frac{1}{Z}\exp\!\left[\sum_{i} h_i(a_i) + \sum_{i<j} e_{ij}(a_i,a_j)\right],

e_{ij}

What this part means

$e_i$ j is one of the signed contributions combined to compute the quantity on the left.

Its job in the formula

$e_i$ j is one of the signed contributions combined to compute the quantity on the left.

Full expressionSymbol e_ijArticle meaning

The passage around this formula

…smallest number of direct couplings. In the maximum-entropy formulation used in this literature, the probability of a full sequence takes a Potts form, $P(a_1,\ldots,a_L) = \frac{1}{Z}\exp\!\left[\sum_{i} h_i(a_i) + \sum_{i<j} e_{ij}(a_i,a_j)\right]$ . with single-site fields $h_i$ and pair couplings $e_{ij}$ fitted so that the model reproduces the single-column and pairwise frequencies of the alignment. Marks and colleagues reported that the strength of the inferred couplings is a strong predictor of residue proximity in the folded structure, and that the top-scoring couplings are accurate and…

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