HomPRIP, RNABindRPlus, and SVMOpt Performance by Zone on RB28.

<p>HomPRIP, RNABindRPlus, and SVMOpt Performance by Zone on RB28.</p

RNABindRPlus flowchart.

<p>Flowchart showing the different components of RNABindRPlus.</p

Structure-based Methods for Predicting RNA-binding sites in Proteins.

<p>Structure-based Methods for Predicting RNA-binding sites in Proteins.</p

Evaluation of Methods on the RB111 dataset.

<p>The first 6 methods are sequence-based methods. The last 2 methods (indicated by **) are structure-based methods. Methods in each category are sorted in descending order of MCC. The highest value in each column is shown in bold font.</p

Sequence-based Methods for Predicting RNA-binding sites in Proteins.

<p>Sequence-based Methods for Predicting RNA-binding sites in Proteins.</p

Principal Components Analysis (PCA) of interface conservation scores and sequence alignment statistics.

<p>Data points in the plot correspond to the projection of a 6-dimensional vector representing the pairwise alignment of a query and homolog sequence onto a 2-dimensional space defined by the first and second principal components. Blue lines with red circles at their tips represent the axes of the original 6-dimensional space for the 6 variables used in PCA analysis: -log(E) (where is the -value), Identity Score (), Positive Score (), log(L) (where is local alignment length), alignment length fractions ( and , where and are the lengths of the query and homolog proteins, respectively). Each data point is colored according to its computed score, with higher score (red/orange) indicating higher interface conservation and lower scores (blue/green) indicating lower interface conservation. The large gray arrow indicates the direction of increasing degree of interface conservation, from Dark to Twilight to Safe Zone.</p

Evaluation of Methods on 28 proteins from the RB44 dataset.

<p>The first 11 methods are sequence-based methods. The last 3 methods are structure-based methods (indicated by **). Methods in each category are sorted in descending order of MCC. The highest value in each column is shown in bold font.</p

PDB ID: 3NCU, Chain A: RIG-I.

<p>(A) Actual interface residues, (B) Predictions made by HomPRIP, (C) Predictions made by SVMOpt, and (D) Predictions made by RNABindRPlus.</p

Evaluation of Methods on 49 proteins from the RB111 dataset.

<p>The first 7 methods are sequence-based methods. The last 2 methods are structure-based methods (indicated by **). Methods in each category are sorted in descending order of MCC. The highest value in each column is shown in bold font.</p

Comparison of SVMOpt, RNABindRPlus, and the Metapredictor

<p>on the RB44 dataset using (A) ROC curves and (B) PR curves with a 5 Å distance cut-off for interface residues.</p