Motivation: The protein structure reconstruction from Nuclear Magnetic Resonance (NMR) experiments heavily relies on computational algorithms, such as matrix completion (MC). Recently, some effective low-rank matrix completion methods, like ASD and ScaledASD, have been successfully applied in image processing, which inspired us to apply them in protein structure reconstruction. Results: Here we present an efficient method for determining protein structures from experimental  NOESY distances, by combining the ASD/ ScaledASD algorithm with several afterwards procedures including chirality refinement, distance lower (upper) bound refinement and forcefield-based energy minimization (EM)  . By comparing several metrics on conformation evaluation between our results and the PDB deposits, including RMSD, TMscore, MPscore, secondary structures and Ramachandran Plot, we conclude that our method is consistent with the popular used methods. In particular, the MPscore comparison indicates that our results generally have higher validity than PDB . In the end, we compared the EM results under different forcefields, showing that our reconstructed configurations are robust to the forcefields selection. Availability and implementation: The software and its MATLAB source codes are available at URLContact: qzhaoyuping@bit.edu.cn or xubiaopeng@bit.edu.cn. Supplementary: Supplementary data are available at Bioinformatics online.
 The protein structure reconstruction from Nuclear Magnetic Resonance (NMR) experiments heavily relies on computational algorithms, such as matrix completion (MC). Recently, some effective low-rank matrix completion methods, like ASD and ScaledASD, have been successfully applied in image processing, which inspired us to apply them in protein structure reconstruction. Here we present an efficient method for determining protein structures from experimental NMR NOESY distances, by combining the ScaledASD algorithm with several afterwards procedures including chirality refinement, distance lower (upper) bound refinement , force field-based energy minimization (EM) and water refinement . By comparing several metrics on conformation evaluation between our results and the PDB deposits, we conclude that our method is consistent with the popular used methods. In particular, our results show higher validities in MPscore, Molprobity clash-score, Procheck dihedral angles G-factor than PDB models . In the end, we compared our calculation results with PDB models by checking the structural similarity to X-ray crystallographic structure for a special dataset. The software and its MATLAB source codes are available by URL
D
Motivation:
D
Results:
A
NMR
D
ASD/
R
and forcefield-based
, force field-based
A
and water refinement
D
including RMSD, TMscore, MPscore, secondary structures and Ramachandran Plot,
R
the MPscore comparison indicates that our results generally have higher validity than PDB
our results show higher validities in MPscore, Molprobity clash-score, Procheck dihedral angles G-factor than PDB models
R
the EM results under different forcefields, showing that our reconstructed configurations are robust to the forcefields selection. Availability and implementation:
our calculation results with PDB models by checking the structural similarity to X-ray crystallographic structure for a special dataset.
R
at URLContact: qzhaoyuping@bit.edu.cn or xubiaopeng@bit.edu.cn. Supplementary: Supplementary data are available at Bioinformatics online.
by URL