Kolja Stahl

Technische Universität Berlin | TUB · Institute of Biotechnology

Iron is essential for most organisms. However, two problems are associated with the use of iron for aerobically growing organisms: (i) its accumulation leads to the formation of toxic reactive oxygen species and (ii) it is present mainly as the highly insoluble ferric iron which makes the access to iron difficult. As a consequence, a tight regulati...

Scarcity of structural and evolutionary information on protein complexes poses a challenge to deep learning-based structure modelling. We integrated experimental distance restraints obtained by crosslinking mass spectrometry (MS) into AlphaFold-Multimer, by extending AlphaLink to protein complexes. Integrating crosslinking MS data substantially imp...

While AlphaFold2 can predict accurate protein structures from the primary sequence, challenges remain for proteins that undergo conformational changes or for which few homologous sequences are known. Here we introduce AlphaLink, a modified version of the AlphaFold2 algorithm that incorporates experimental distance restraint information into its net...

Both the Chamberlin–Courant and Monroe rules are voting rules that solve the problem of fully proportional representation: given a set of candidates and a set of voters, they select committees of candidates whose members represent the voters so that the voters’ total dissatisfaction is minimized. These two rules suffer from a common disadvantage, n...

Background: Accurately predicted contacts allow to compute the 3D structure of a protein. Since the solution space of native residue-residue contact pairs is very large, it is necessary to leverage information to identify relevant regions of the solution space, i.e. correct contacts. Every additional source of information can contribute to narrowi...

Determining the structure of a protein by any method requires various contributions from experimental and computational sides. In a recent study, high-density cross-linking/mass spectrometry (HD-CLMS) data in combination with ab initio structure prediction determined the structure of human serum albumin (HSA) domains, with an RMSD to X-ray structur...

Both the Chamberlin--Courant and Monroe rules are voting rules solving the problem of so-called fully proportional representation: they select committees whose members represent the voters so that voters' satisfaction with their assigned representatives is maximized. These rules suffer from a common disadvantage, being that it is computationall...

We consider the following problem. Given a graph and a rational number \(\mu \), \(0 < \mu \le 1\), find a connected subgraph of density at least \(\mu \) with the largest number of vertices. Here, the density of an \(n\)-vertex graph with \(m\) edges is \(m/\left( {\begin{array}{c}n\\ 2\end{array}}\right) \). This problem arises in many applicatio...