rsRNASP: A distance-dependent statistical potential based on residue separation for RNA 3D structure evaluation
The potentials were set to a high value of 30 kBT for atom pairs within 3 Å to exclude the structure candidates with severe steric conflicts; updated on July 23, 2024.
# Compilation
gcc rsRNASP.c -lm -o rsRNASP // scoring one conformation
or
gcc rsRNASP-batch.c -lm -o rsRNASP-batch // scoring a batch of conformations; updated on December 16, 2023 for improving the scoring efficiency
# Usage
./rsRNASP XXX.pdb energy.txt
or
./rsRNASP-batch ${path} ${N} energy_list.txt // "path" is the folder path where the batch of conformations are located, and "N" is the number of conformations to be evaluated;
// updated on December 16, 2023 for improving the scoring efficiency
Note: the subfolder "data/" and the compiled file "rsRNASP" or "rsRNASP-batch" should be in the same folder.
./rsRNASP 1a9nR.pdb energy.txt
or
N=`ls *.pdb | wc -l`
./rsRNASP-batch ./ ${N} energy_list.txt // updated on December 16, 2023 for improving the scoring efficiency
Output:
1a9nR.pdb -3055.902390 kBT
or
1h4sT.pdb -7743.385764 kBT
1a9nR.pdb -3055.902390 kBT
Please feel free to contact us if you have any question! zjtan@whu.edu.cn
Reference:
[1] Tan YL, Wang X, Shi YZ, Zhang W, & Tan ZJ. 2022. rsRNASP: A residue-separation-based statistical potential for RNA 3D structure
evaluation. Biophys J. 121(1): 142-156.