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Page 1
Atlasing of Assembly Landscapes using Distance Geometry and Graph Rigidity.
J Chem Inf Model. 2020 Oct 26;60(10):4924-4957. doi: 10.1021/acs.jcim.0c00763. Epub 2020 Sep 16.
J Chem Inf Model. 2020.
PMID: 32786706
Rapid prediction of crucial hotspot interactions for icosahedral viral capsid self-assembly by energy landscape atlasing validated by mutagenesis.
Wu R, Prabhu R, Ozkan A, Sitharam M.
Wu R, et al. Among authors: sitharam m.
PLoS Comput Biol. 2020 Oct 20;16(10):e1008357. doi: 10.1371/journal.pcbi.1008357. eCollection 2020 Oct.
PLoS Comput Biol. 2020.
PMID: 33079933
Free PMC article.
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Baseline Comparisons of Complementary Sampling Methods for Assembly Driven by Short-Ranged Pair Potentials toward Fast and Flexible Hybridization.
Ozkan A, Sitharam M, Flores-Canales JC, Prabhu R, Kurnikova M.
Ozkan A, et al. Among authors: sitharam m.
J Chem Theory Comput. 2021 Mar 9;17(3):1967-1987. doi: 10.1021/acs.jctc.0c00945. Epub 2021 Feb 12.
J Chem Theory Comput. 2021.
PMID: 33576635
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Corner-Sharing Tetrahedra for Modeling Micro-structure.
Sitharam M, Youngquist J, Nolan M, Peters J.
Sitharam M, et al.
Comput Aided Des. 2019 Sep;114:164-178. doi: 10.1016/j.cad.2019.05.015. Epub 2019 May 14.
Comput Aided Des. 2019.
PMID: 33776067
Free PMC article.
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Enumeration of viral capsid assembly pathways: tree orbits under permutation group action.
Bóna M, Sitharam M, Vince A.
Bóna M, et al. Among authors: sitharam m.
Bull Math Biol. 2011 Apr;73(4):726-53. doi: 10.1007/s11538-010-9606-4. Epub 2010 Dec 21.
Bull Math Biol. 2011.
PMID: 21174231
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Modeling virus self-assembly pathways: avoiding dynamics using geometric constraint decomposition.
Sitharam M, Agbandje-McKenna M.
Sitharam M, et al.
J Comput Biol. 2006 Jul-Aug;13(6):1232-65. doi: 10.1089/cmb.2006.13.1232.
J Comput Biol. 2006.
PMID: 16901239
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