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115 results
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Point-based probabilistic surfaces to show surface uncertainty.
Grigoryan G, Rheingans P. Grigoryan G, et al. IEEE Trans Vis Comput Graph. 2004 Sep-Oct;10(5):564-73. doi: 10.1109/TVCG.2004.30. IEEE Trans Vis Comput Graph. 2004. PMID: 15794138
Ultra-fast evaluation of protein energies directly from sequence.
Grigoryan G, Zhou F, Lustig SR, Ceder G, Morgan D, Keating AE. Grigoryan G, et al. PLoS Comput Biol. 2006 Jun 16;2(6):e63. doi: 10.1371/journal.pcbi.0020063. Epub 2006 Jun 16. PLoS Comput Biol. 2006. PMID: 16789811 Free PMC article.
Computing van der Waals energies in the context of the rotamer approximation.
Grigoryan G, Ochoa A, Keating AE. Grigoryan G, et al. Proteins. 2007 Sep 1;68(4):863-78. doi: 10.1002/prot.21470. Proteins. 2007. PMID: 17554777
Coarse-graining protein energetics in sequence variables.
Zhou F, Grigoryan G, Lustig SR, Keating AE, Ceder G, Morgan D. Zhou F, et al. Among authors: grigoryan g. Phys Rev Lett. 2005 Sep 30;95(14):148103. doi: 10.1103/PhysRevLett.95.148103. Epub 2005 Sep 29. Phys Rev Lett. 2005. PMID: 16241695
The CE coarse grains over nonsequence degrees of freedom (e.g., side-chain conformations) and thereby simplifies the problem of designing proteins, or predicting the compatibility of a sequence with a given structure, by many orders of magnitude. ...
The CE coarse grains over nonsequence degrees of freedom (e.g., side-chain conformations) and thereby simplifies the problem of desig …
Cluster expansion models for flexible-backbone protein energetics.
Apgar JR, Hahn S, Grigoryan G, Keating AE. Apgar JR, et al. Among authors: grigoryan g. J Comput Chem. 2009 Nov 30;30(15):2402-13. doi: 10.1002/jcc.21249. J Comput Chem. 2009. PMID: 19360809
Structure-based prediction of bZIP partnering specificity.
Grigoryan G, Keating AE. Grigoryan G, et al. J Mol Biol. 2006 Feb 3;355(5):1125-42. doi: 10.1016/j.jmb.2005.11.036. Epub 2005 Dec 1. J Mol Biol. 2006. PMID: 16359704
Design of protein-interaction specificity gives selective bZIP-binding peptides.
Grigoryan G, Reinke AW, Keating AE. Grigoryan G, et al. Nature. 2009 Apr 16;458(7240):859-64. doi: 10.1038/nature07885. Nature. 2009. PMID: 19370028 Free PMC article.
Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL).
Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G, Senes A. Kulp DW, et al. Among authors: grigoryan g. J Comput Chem. 2012 Jul 30;33(20):1645-61. doi: 10.1002/jcc.22968. Epub 2012 May 8. J Comput Chem. 2012. PMID: 22565567 Free PMC article.
Absolute free energies of biomolecules from unperturbed ensembles.
Grigoryan G. Grigoryan G. J Comput Chem. 2013 Dec 5;34(31):2726-41. doi: 10.1002/jcc.23448. Epub 2013 Oct 16. J Comput Chem. 2013. PMID: 24132787
Identifying and reducing error in cluster-expansion approximations of protein energies.
Hahn S, Ashenberg O, Grigoryan G, Keating AE. Hahn S, et al. Among authors: grigoryan g. J Comput Chem. 2010 Dec;31(16):2900-14. doi: 10.1002/jcc.21585. J Comput Chem. 2010. PMID: 20602445
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