We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shif...

The accuracy of model selection from decoy ensembles of protein loop conformations was explored by comparing the performance of the Samudrala-Moult all-atom statistical potential (RAPDF) and the AMBER molecular mechanics force field, including the Generalized Born/surface area solvation model. Large ensembles of consistent loop conformations, represented at atomic detail with idealized geometry...

This study addresses the relation between structural and functional similarity in proteins. We introduce a novel method named tree based on root mean square deviation (T-RMSD), which uses distance RMSD (dRMSD) variations to build fine-grained structure-based classifications of proteins. The main improvement of the T-RMSD over similar methods, such as Dali, is its capacity to produce the equival...

The protein structure prediction algorithm TOUCHSTONEX that uses sparse distance restraints derived from NMR nuclear Overhauser enhancement (NOE) data to predict protein structures at low-to-medium resolution was evaluated as follows: First, a representative benchmark set of the Protein Data Bank library consisting of 1365 proteins up to 200 residues was employed. Using N/8 simulated long-range...

The electromechanical (EM) impedance technique using piezoelectric lead zirconate titanate (PZT) transducers for structural health monitoring (SHM) has attracted considerable attention in various engineering fields. In the conventional EM impedance technique, the EM admittance of a PZT transducer is used as a damage indicator. Statistical analysis methods such as root mean square deviation (RMS...

A widely used way to compare the structures of biomolecules or solid bodies is to translate and rotate one structure with respect to the other to minimize the root-mean-square deviation (RMSD). We present a simple derivation, based on quaternions, for the optimal solid body transformation (rotation-translation) that minimizes the RMSD between two sets of vectors. We prove that the quaternion me...

To improve the accuracy of TASSER models especially in the limit where threading provided template alignments are of poor quality, we have developed the TASSER algorithm which uses the templates and contact restraints from TASSER generated models for iterative structure refinement. We apply TASSER to a large benchmark set of 2,773 nonhomologous single domain proteins that are 200 in length and ...

We present the Generalized Root Mean Square Deviation (G-RMSD) method. G-RMSD is an optimization method to calculate minimal RMSD value of two atomic structures by optimal superimposition. not restricted systems with equal number atoms compare or a unique atom mapping between molecules. The can handle any type chemical structure, including transition states and which cannot be explained only va...

Tertiary structure prediction is important for understanding structure-function relationships for RNAs whose structures are unknown and for characterizing RNA states recalcitrant to direct analysis. However, it is unknown what root-mean-square deviation (RMSD) corresponds to a statistically significant RNA tertiary structure prediction. We use discrete molecular dynamics to generate RNA-like fo...