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Fast procedure for reconstruction of full‐atom protein models from reduced representations
Author(s) -
Rotkiewicz Piotr,
Skolnick Jeffrey
Publication year - 2008
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20906
Subject(s) - computer science , representation (politics) , algorithm , atom (system on chip) , protein structure prediction , protein structure , set (abstract data type) , docking (animal) , structural bioinformatics , biological system , chemistry , biology , medicine , biochemistry , programming language , nursing , politics , political science , law , embedded system
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.