Denitsa Alamanova

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Knowledge of transcription factor-DNA binding patterns is crucial for understanding gene transcription. Numerous DNA-binding proteins are annotated as transcription factors in the literature, however, for many of them the corresponding DNA-binding motifs remain uncharacterized. The position weight matrices (PWMs) of transcription factors from different(More)
We study the formation of protein-protein encounter complexes with a Langevin equation approach that considers direct, steric, and thermal forces. As three model systems with distinctly different properties we consider the pairs barnase:barstar, cytochrome c-cytochrome c peroxidase, and p53:MDM2. In each case, proteins are modeled either as spherical(More)
We study the structure and energetics of AuN clusters by means of parameterfree density-functional calculations (N ≤ 8), jellium calculations (N ≤ 60), embeddedatom calculations (N ≤ 150), and parameterized density-functional calculations (N ≤ 40) in combination with different methods for determining the structure of the lowest total energy. By comparing(More)
c © 2007 by John von Neumann Institute for Computing Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior(More)
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