Martin Mann

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BACKGROUND The principles of protein folding and evolution pose problems of very high inherent complexity. Often these problems are tackled using simplified protein models, e.g. lattice proteins. The CPSP-tools package provides programs to solve exactly and completely the problems typical of studies using 3D lattice protein models. Among the tasks addressed(More)
Small RNAs (sRNAs) constitute a large and heterogeneous class of bacterial gene expression regulators. Much like eukaryotic microRNAs, these sRNAs typically target multiple mRNAs through short seed pairing, thereby acting as global posttranscriptional regulators. In some bacteria, evidence for hundreds to possibly more than 1,000 different sRNAs has been(More)
  • A Dayem Ullah, L Kapsokalivas, M Mann, K Steinhöfel
  • 2009
We propose a two-stage optimization approach for protein folding simulation in the FCC lattice, inspired from the phenomenon of hydrophobic collapse. Given a protein sequence, the first stage of the approach produces compact protein structures with the maximal number of contacts among hydrophobic monomers, using the CPSP tools for optimal structure(More)
UNLABELLED Studies on proteins are often restricted to highly simplified models to face the immense computational complexity of the associated problems. Constraint-based protein structure prediction (CPSP) tools is a package of very fast algorithms for ab initio optimal structure prediction and related problems in 3D HP-models [cubic and face centered cubic(More)
Knowledge of a protein's three-dimensional native structure is vital in determining its chemical properties and functionality. However, experimental methods to determine structure are very costly and time-consuming. Computational approaches such as folding simulations and structure prediction algorithms are quicker and cheaper but lack consistent accuracy.(More)
Lattice models are a common abstraction used in the study of protein structure, folding, and refinement. They are advantageous because the discretisation of space can make extensive protein evaluations computationally feasible. Various approaches to the protein chain lattice fitting problem have been suggested but only a single backbone-only tool is(More)
CopraRNA (Comparative prediction algorithm for small RNA targets) is the most recent asset to the Freiburg RNA Tools webserver. It incorporates and extends the functionality of the existing tool IntaRNA (Interacting RNAs) in order to predict targets, interaction domains and consequently the regulatory networks of bacterial small RNA molecules. The CopraRNA(More)
Lattice protein models, as the Hydrophobic-Polar (HP) model , are a common abstraction to enable exhaustive studies on structure, function, or evolution of proteins. A main issue is the high number of optimal structures, resulting from the hydrophobicity-based energy function applied. We introduce an equivalence relation on protein structures that(More)
Global and co-translational protein folding may both occur in vivo, and understanding the relationship between these folding mechanisms is pivotal to our understanding of protein-structure formation. Within this study, over 1.5 million hydrophobic-polar sequences were classified based on their ability to attain a unique, but not necessarily minimal energy(More)