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Molecular docking is a simulation technique that aims to predict the binding pose between a ligand and a receptor. The resulting multidimensional continuous optimization problem is practically unsolvable in an exact way. One possible approach is the combination of an optimization algorithm and an objective function that describes the interaction. The(More)
The prediction of possible binding geometries as well as ranking of putative protein-ligand complexes according their binding affinities is the intention of so called molecular docking approaches. To evaluate complexes against each other, scoring functions are required. In recent years knowledge-based scoring functions have been evolved. They exploit the(More)
BACKGROUND Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases (kb). RESULTS During genome sequencing projects(More)
Accurate scoring of protein-ligand interactions in molecular docking and virtual screening is still challenging. Despite great efforts, the performance of existing scoring functions strongly depends on the target structure under investigation. Recent developments in the direction of target class specific scoring methods and machine-learning-based(More)
Accurate scoring of protein-ligand interactions for docking , binding-affinity prediction and virtual screening campaigns is still challenging. Despite great efforts, the performance of existing scoring functions strongly depends on the target structure under investigation. Recent developments in the direction of target-class-specific scoring methods and(More)
The generation and evaluation of molecular complexes in order to predict binding modes of protein ligand complexes, is still a challenging task. Many different algorithms and approaches try to solve the molecular docking problem. Within this work we introduce the open source docking platform ParaDockS (Parallel Docking Suite) [1], that allows the convenient(More)
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