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4 papers
BEND: Benchmarking DNA Language Models on biologically meaningful tasks
Frederikke Isa Marin, Felix Teufel, Marc Horlacher +4
The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation o…
Improvements to the APBS biomolecular solvation software suite
Elizabeth Jurrus, Dave Engel, Keith Star +21
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact i…
In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB
Martin R. Hediger, Luca De Vico, Julie B. Rannes +4
Our previously presented method for high throughput computational screening of mutant activity (Hediger et al., arXiv:1203.2950) is benchmarked against experimentally measured amid…
A Computational Methodology to Screen Activities of Enzyme Variants
Martin R. Hediger, Luca De Vico, Allan Svendsen +2
We present a fast computational method to efficiently screen enzyme activity. In the presented method, the effect of mutations on the barrier height of an enzyme-catalysed reaction…