Abstract
Model evaluation is a necessary step for better prediction and design of 3D RNA structures. For proteins, this has been widely studied and the knowledge-based statistical potential has been proved to be one of effective ways to solve this problem. Currently, a few knowledge-based statistical potentials have also been proposed to evaluate predicted models of RNA tertiary structures. The benchmark tests showed that they can identify the native structures effectively but further improvements are needed to identify near-native structures and those with non-canonical base pairs. Here, we present a novel knowledge-based potential, 3dRNAscore, which combines distance-dependent and dihedral-dependent energies. The benchmarks on different testing datasets all show that 3dRNAscore are more efficient than existing evaluation methods in recognizing native state from a pool of near-native states of RNAs as well as in ranking near-native states of RNA models.
Highlights
RNA molecules play different biological roles besides messengers between DNA and protein [1,2], e.g. regulatory functions [3]
The Ribonucleic Acids Statistical Potential (RASP) developed by Capriotti et al [17,19] and the coarse-grained and all-atom RNA KB potentials by Bernauer et al [18]
In the all-atom version of RNA KB potential, unlike RASP in which the atom types are clustered, the atom types in different nucleotides are considered to be different, so totally 85 atom types are considered rather than 23 atom types used in RASP-ALL
Summary
RNA molecules play different biological roles besides messengers between DNA and protein [1,2], e.g. regulatory functions [3]. A full atom RNA potential (FARFAR, fragment assembly of RNA with full-atom refinement) available within the ROSETTA suite was successfully used for the de novo prediction and design of noncanonical RNA 3D structures [6,11]. This full-atom potential contains weak carbon hydrogen bonding and solvation terms, as well as a complete description for potential hydrogen bonds between bases and backbone oxygen atoms
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