Fast procedure for reconstruction of full-atom protein models from reduced representations.
We introduce PULCHRA, a fast and robust method for the reconstruction of full-atom protein models starting from a reduced protein representation. The algorithm is particularly suitable as an intermediate step between coarse-grained model-based structure prediction and applications requiring an all-atom structure, such as molecular dynamics, protein-ligand docking, structure-based function prediction, or assessment of quality of the predicted structure. The accuracy of the method was tested on a set of high-resolution crystallographic structures as well as on a set of low-resolution protein decoys generated by a protein structure prediction algorithm TASSER. The method is implemented as a standalone program that is available for download from http://cssb.biology.gatech.edu/skolnick/files/PULCHRA.
Rotkiewicz
Piotr
P
Burnham Institute for Medical Research, 10901 N. Torrey Pines Road, La Jolla, California 92037, USA.
Skolnick
Jeffrey
J
D000465:Algorithms; D003198:Computer Simulation; D003461:Crystallography; D008954:Models, Biological; D011237:Predictive Value of Tests; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins