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Protein structure reconstruction

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Reconstruction of proteins from incomplete representations
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Protein structure reconstruction refers to constructing an atomic-resolution model of a protein structure from incomplete coarse-grained representations 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 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.

Software

Backbone reconstruction

  • Pulchra
  • BBQ
  • PD2

Side chain reconstruction

  • Pulchra
  • SCWRL

References

  1. ^ 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.
  2. 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.
  3. ^ 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.
  4. 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.
  5. 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.
  6. 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.


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