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2015 2
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Weighted ensemble: Recent mathematical developments.
Aristoff D, Copperman J, Simpson G, Webber RJ, Zuckerman DM. Aristoff D, et al. J Chem Phys. 2023 Jan 7;158(1):014108. doi: 10.1063/5.0110873. J Chem Phys. 2023. PMID: 36610976 Free PMC article.
Automated visualization of rule-based models.
Sekar JAP, Tapia JJ, Faeder JR. Sekar JAP, et al. PLoS Comput Biol. 2017 Nov 13;13(11):e1005857. doi: 10.1371/journal.pcbi.1005857. eCollection 2017 Nov. PLoS Comput Biol. 2017. PMID: 29131816 Free PMC article.
A glycan gate controls opening of the SARS-CoV-2 spike protein.
Sztain T, Ahn SH, Bogetti AT, Casalino L, Goldsmith JA, Seitz E, McCool RS, Kearns FL, Acosta-Reyes F, Maji S, Mashayekhi G, McCammon JA, Ourmazd A, Frank J, McLellan JS, Chong LT, Amaro RE. Sztain T, et al. bioRxiv [Preprint]. 2021 May 17:2021.02.15.431212. doi: 10.1101/2021.02.15.431212. bioRxiv. 2021. PMID: 33619492 Free PMC article. Updated. Preprint.
OPTIMIZING WEIGHTED ENSEMBLE SAMPLING OF STEADY STATES.
Aristoff D, Zuckerman DM. Aristoff D, et al. Multiscale Model Simul. 2020;18(2):646-673. doi: 10.1137/18m1212100. Epub 2020 May 6. Multiscale Model Simul. 2020. PMID: 34421402 Free PMC article.
BioNetGen 2.2: advances in rule-based modeling.
Harris LA, Hogg JS, Tapia JJ, Sekar JA, Gupta S, Korsunsky I, Arora A, Barua D, Sheehan RP, Faeder JR. Harris LA, et al. Bioinformatics. 2016 Nov 1;32(21):3366-3368. doi: 10.1093/bioinformatics/btw469. Epub 2016 Jul 8. Bioinformatics. 2016. PMID: 27402907 Free PMC article.
49 results