Protein structure reconstruction
Protein structure reconstruction refers to constructing an atomic-resolution model of a protein structure from incomplete coarse-grained representations[1] like, for example, protein contact maps, positions of alpha carbon atoms only or backbone chain atoms only. There are many computational tools for protein structure reconstruction[1] that are usually focused on specific reconstruction tasks which include: backbone reconstruction from alpha carbons, side-chains reconstruction from backbone chain atoms, hydrogen atoms reconstruction from heavy atoms positions and recovery of protein structure from contact maps.[2]
Software[edit]
Backbone reconstruction
Side chain reconstruction
References[edit]
- ^ a b Badaczewska-Dawid, Aleksandra E.; Kolinski, Andrzej; Kmiecik, Sebastian (2020-01-01). "Computational reconstruction of atomistic protein structures from coarse-grained models". Computational and Structural Biotechnology Journal. 18: 162–176. doi:10.1016/j.csbj.2019.12.007. ISSN 2001-0370. PMC 6961067. PMID 31969975.
- ^ Vendruscolo, Michele; Kussell, Edo; Domany, Eytan (1997-10-01). "Recovery of protein structure from contact maps". Folding and Design. 2 (5): 295–306. arXiv:cond-mat/9705211. Bibcode:1997cond.mat..5211V. doi:10.1016/S1359-0278(97)00041-2. ISSN 1359-0278. PMID 9377713.
- ^ a b Rotkiewicz, Piotr; Skolnick, Jeffrey (2008). "Fast procedure for reconstruction of full-atom protein models from reduced representations". Journal of Computational Chemistry. 29 (9): 1460–1465. doi:10.1002/jcc.20906. ISSN 1096-987X. PMC 2692024. PMID 18196502.
- ^ Gront, Dominik; Kmiecik, Sebastian; Kolinski, Andrzej (2007-07-15). "Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates". Journal of Computational Chemistry. 28 (9): 1593–1597. doi:10.1002/jcc.20624. ISSN 0192-8651. PMID 17342707. S2CID 8836253.
- ^ Moore, Benjamin L.; Kelley, Lawrence A.; Barber, James; Murray, James W.; MacDonald, James T. (2013-08-15). "High-quality protein backbone reconstruction from alpha carbons using Gaussian mixture models". Journal of Computational Chemistry. 34 (22): 1881–1889. doi:10.1002/jcc.23330. PMID 23703289. S2CID 10928754.
- ^ Canutescu, Adrian A.; Shelenkov, Andrew A.; Dunbrack, Roland L. (2003). "A graph-theory algorithm for rapid protein side-chain prediction". Protein Science. 12 (9): 2001–2014. doi:10.1110/ps.03154503. ISSN 1469-896X. PMC 2323997. PMID 12930999.