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Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies.
Alamanova D, Stegmaier P, Kel A. Alamanova D, et al. BMC Bioinformatics. 2010 May 3;11:225. doi: 10.1186/1471-2105-11-225. BMC Bioinformatics. 2010. PMID: 20438625 Free PMC article.
Dynamics of protein-protein encounter: a Langevin equation approach with reaction patches.
Schluttig J, Alamanova D, Helms V, Schwarz US. Schluttig J, et al. Among authors: alamanova d. J Chem Phys. 2008 Oct 21;129(15):155106. doi: 10.1063/1.2996082. J Chem Phys. 2008. PMID: 19045236