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. 2021 Jul 28:8:721955.
doi: 10.3389/fmolb.2021.721955. eCollection 2021.

SHAPER: A Web Server for Fast and Accurate SHAPE Reactivity Prediction

Yuanzhe Zhou  1 , Jun Li  1 , Travis Hurst  1 , Shi-Jie Chen  1   2   3
Affiliations

SHAPER: A Web Server for Fast and Accurate SHAPE Reactivity Prediction

Yuanzhe Zhou et al. Front Mol Biosci. .

Abstract

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemical probing serves as a convenient and efficient experiment technique for providing information about RNA local flexibility. The local structural information contained in SHAPE reactivity data can be used as constraints in 2D/3D structure predictions. Here, we present SHAPE predictoR (SHAPER), a web server for fast and accurate SHAPE reactivity prediction. The main purpose of the SHAPER web server is to provide a portal that uses experimental SHAPE data to refine 2D/3D RNA structure selection. Input structures for the SHAPER server can be obtained through experimental or computational modeling. The SHAPER server can accept RNA structures with single or multiple conformations, and the predicted SHAPE profile and correlation with experimental SHAPE data (if provided) for each conformation can be freely downloaded through the web portal. The SHAPER web server is available at http://rna.physics.missouri.edu/shaper/.

Keywords: SHAPE reactivity prediction; coarse-grained simulation; structure analysis; structure prediction; web server.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
A schematic view of the organization and function of the SHAPER web server.
FIGURE 2
FIGURE 2
Interface of the SHAPER web server and the steps involved in submitting a job. The overview of the interface of the starting page is shown in the top left, and the area within the dashed red box is updated in each step. There are three steps: uploading and choosing parameters (Step 1), waiting the job (Step 2), and checking results of the job (Step 3).
FIGURE 3
FIGURE 3
SHAPE profiles for native (A) and selected decoy (B,D) conformations at different RMSDs. Predicted and experimental (i.e., User SHAPE) profiles are shown in red and blue curves, respectively. 2D structure in (A) corresponds to the native structure, and 2D structures shown in (B,D) were used as constraints to run the simulations. (C) The relation between PC/noise-adjusted PC (red/blue) and RMSDs relative to the native structure for 60 tested conformations (include the native structure, PDB code: 2L8H). The data point of the native conformation is shown on the top left of (C) and pointed out by an arrow.
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