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Predicted Aligned Error information


Predicted Aligned Error
Filename extension
.json
Internet media type
application/json
Developed byDeepMind, EMBL-EBI
Type of formatBioinformatics
Websitehttps://alphafold.ebi.ac.uk/faq

The Predicted Aligned Error (PAE) is a quantitative output produced by AlphaFold, a protein structure prediction system developed by DeepMind.[1] PAE estimates the expected positional error for each residue in a predicted protein structure if it were aligned to a corresponding residue in the true protein structure. This measurement helps scientists assess the confidence in the relative positions and orientations of different parts of the predicted protein model.[2]

  1. ^ "AlphaFold Protein Structure Database". alphafold.ebi.ac.uk. 2023-06-12. Archived from the original on 2023-06-13. Retrieved 2023-06-12.
  2. ^ "AlphaFold Error Estimates". www.rbvi.ucsf.edu. Archived from the original on 2023-06-13. Retrieved 2023-06-12.

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Predicted Aligned Error

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"predicted_aligned_error": [[0, 1, 4, 7, 9, ...], ...], "max_predicted_aligned_error": 31.75 } ] In the JSON file, the field predicted_aligned_error provides...

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Mean squared error

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of observed values of the variable being predicted, with Y ^ {\displaystyle {\hat {Y}}} being the predicted values (e.g. as from a least-squares fit)...

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Mean absolute error

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make comparisons between predicted values that use different scales. The mean absolute error is a common measure of forecast error in time series analysis...

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Linear regression

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dependent variables are predicted, rather than a single scalar variable. If the explanatory variables are measured with error then errors-in-variables models...

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PAE

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Wiktionary, the free dictionary. PAE may refer to: Predicted Aligned Error, AlphaFold output file format for errors of protein structure prediction Physical Address...

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Precision and recall

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n {\displaystyle {\begin{aligned}{\text{Precision}}&={\frac {tp}{tp+fp}}\\{\text{Recall}}&={\frac {tp}{tp+fn}}\,\end{aligned}}} Recall in this context...

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Variance of the mean and predicted responses

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response (or expected response) and predicted response, also known as mean outcome (or expected outcome) and predicted outcome, are values of the dependent...

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Residual sum of squares

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(SSR) or the sum of squared estimate of errors (SSE), is the sum of the squares of residuals (deviations predicted from actual empirical values of data)...

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Kalman filter

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the predicted state from the previous estimate and similarly the function h can be used to compute the predicted measurement from the predicted state...

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Sensitivity and specificity

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is at position A (the left-hand side is predicted as negative by the model, the right-hand side is predicted as positive by the model). When the dotted...

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Logistic regression

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_{i}+\varepsilon _{1}\,\end{aligned}}} where ε 0 ∼ EV 1 ⁡ ( 0 , 1 ) ε 1 ∼ EV 1 ⁡ ( 0 , 1 ) {\displaystyle {\begin{aligned}\varepsilon _{0}&\sim \operatorname...

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AlphaFold

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Human Proteome Folding Project AlphaZero AlphaGo AlphaGeometry Predicted Aligned Error ESMFold "AlphaFold". Deepmind. Retrieved 30 November 2020. "DeepMind's...

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Ordinary least squares

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whereas the predicted response is y ^ 0 = x 0 T β ^ {\displaystyle {\hat {y}}_{0}=x_{0}^{\mathrm {T} }{\hat {\beta }}} . Clearly the predicted response is...

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Least squares

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minima in the sum of squares. Under the condition that the errors are uncorrelated with the predictor variables, LLSQ yields unbiased estimates, but even under...

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Minimum mean square error

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{\begin{aligned}C_{Y_{k}|X_{k}}&=AC_{X_{k}|Y_{1},\ldots ,Y_{k-1}}A^{T}+C_{Z}=AC_{e_{k-1}}A^{T}+C_{Z}.\end{aligned}}} . The difference between the predicted value...

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Tracking error

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'ex post' tracking error. If a model is used to predict tracking error, it is called 'ex ante' tracking error. Ex-post tracking error is more useful for...

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Extended Kalman filter

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the predicted state from the previous estimate and similarly the function h can be used to compute the predicted measurement from the predicted state...

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Euler method

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{\begin{aligned}y_{2}&=y_{1}+hf(y_{1})=2+1\cdot 2=4,\\y_{3}&=y_{2}+hf(y_{2})=4+1\cdot 4=8,\\y_{4}&=y_{3}+hf(y_{3})=8+1\cdot 8=16.\end{aligned}}} Due to...

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Weighted least squares

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i 2 {\displaystyle {\begin{aligned}S&=\sum _{i=1}^{n}W_{ii}{r_{i}}^{2},&W_{ii}&={\frac {1}{{\sigma _{i}}^{2}}}\end{aligned}}} The gradient equations for...

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Simple linear regression

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residuals (see also Errors and residuals) ε ^ i {\displaystyle {\widehat {\varepsilon }}_{i}} (differences between actual and predicted values of the dependent...

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Standard deviation

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X ) . {\displaystyle {\begin{aligned}\sigma (c)&=0\\\sigma (X+c)&=\sigma (X),\\\sigma (cX)&=|c|\sigma (X).\end{aligned}}} The standard deviation of the...

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Fraction of variance unexplained

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(dependent variable) Y which cannot be explained, i.e., which is not correctly predicted, by the explanatory variables X. Suppose we are given a regression function...

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Multinomial logistic regression

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{\begin{aligned}{\boldsymbol {\beta }}'_{k}&={\boldsymbol {\beta }}_{k}-{\boldsymbol {\beta }}_{K}\;\;\;,\;k<K\\{\boldsymbol {\beta }}'_{K}&=0\end{aligned}}}...

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Forecasting

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{\displaystyle {\begin{aligned}f_{n}(x_{t})={\dfrac {1}{(1+x_{t}^{n})}}\,,\qquad n\in {\mathbb {N} },\;x\in {\mathbb {R} }.\end{aligned}}} The short term behaviour...

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