Predicting dissociation free energies of protein-DNA complexes


Sequence-specific protein–DNA interactions are crucial in processes such as DNA organization, gene regulation and DNA replication. Thor van Heesch, Peter Bolhuis and Jocelyne Vreede have developed a molecular simulation approach to quantify the sequence specificity of protein–DNA complexes, that yields results fast, and is generally applicable to any protein–DNA complex. The approach is based on molecular […]

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Structure prediction of a bacterial spore membrane protein


Dr Jocelyne Vreede of the research group Computational Chemistry at the Van ‘t Hoff Institute for Molecular Sciences (HIMS) worked together with researchers at the UvA’s Swammerdam Institute for Life Sciences (SILS) to elucidate the structure and dynamics of the spore membrane protein GerAB from the bacterium Bacillus subtilis. The study contributes to a better […]

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UvA researchers collaborate on new Handbook of Porous Materials


State-of-the-art reference work on synthesis, characterisation, and industrial application A group of authors including researchers and alumni from the Van ‘t Hoff Institute for Molecular Sciences (HIMS) have just completed a four-volume reference work covering the fundamentals and key applications of porous materials. This “Handbook of Porous Materials” will be published in November by World […]

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How does the accessibility of DNA affect the expression of genes?


Dr Jocelyne Vreede of the Computational Chemistry group at the Van ‘t Hoff Institute for Molecular Sciences has received an NWO KLEIN-2 grant for a four-year project investigating how the shape and compactness of DNA affect the expression of genes. In cooperation with Prof. Willem Kegel, professor of Self-organizing Systems at Utrecht University, experimental, theoretical […]

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