Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution

Bio++: efficient extensible libraries and tools for computational molecular evolution.

Efficient algorithms and programs for the analysis of the ever-growing amount of biological sequence data are strongly needed in the genomics era. The pace at which new data and methodologies are generated calls for the use of pre-existing, optimized-yet extensible-code, typically distributed as libraries or packages. This motivated the Bio++ project, aiming at developing a set of C++ libraries...

Strategies and computational tools for improving randomized protein libraries.

In the last decade, directed evolution has become a routine approach for engineering proteins with novel or altered properties. Concurrently, a trend away from purely 'blind' randomization strategies and towards more 'semi-rational' approaches has also become apparent. In this review, we discuss ways in which structural information and predictive computational tools are playing an increasingly ...

Computational Molecular Evolution

Highly extensible bio-nanocomposite fibers.

Here, we show that a poly(ethylene oxide) polymer can be physically cross-linked with silicate nanoparticles (Laponite) to yield highly extensible, bio-nanocomposite fibers that, upon pulling, stretch to extreme lengths and crystallize polymer chains. We find that both, nanometer structures and mechanical properties of the fibers respond to mechanical deformation by exhibiting strain-induced cr...

Computational and molecular tools for scalable rAAV-mediated genome editing

The rapid discovery of potential driver mutations through large-scale mutational analyses of human cancers generates a need to characterize their cellular phenotypes. Among the techniques for genome editing, recombinant adeno-associated virus (rAAV)-mediated gene targeting is suited for knock-in of single nucleotide substitutions and to a lesser degree for gene knock-outs. However, the generati...