Biology subjects

Correia, B. E.

Publications and source records attributed to Correia, B. E..

2 recordsLinked to original sources

bioRxiv2018

rstoolbox: management and analysis of computationally designed structural ensembles.

MotivationComputational protein design (CPD) calculations rely on the generation of large amounts of data on the search for the best sequences. As such, CPD workflows generally include the batch generation of designed decoys (sampling) followed by ranking and filtering stages to select those with optimal metrics (scoring). Due to these factors, the proper analysis of the decoy population is a key element for the effective selection of designs for experimental validation.\n\nResultsHere, we present a set of tools for the analysis of protein design ensembles. The tool is oriented towards protein designers with basic coding training aiming to process efficiently their decoy sets as well as for protocol developers interested in benchmarking their new approaches. Although initially devised to process Rosetta design outputs, the library is extendable to other design tools.\n\nAvailability and Implementationrstoolbox is implemented for python2.7 and 3.5+. Code is freely available at https://github.com/lpdi-epfl/rstoolbox under the MIT license. Full documentation and examples can be found at https://lpdi-epfl.github.io/rstoolbox.

bioinformatics↗

bioRxiv2018

Rosetta FunFolDes - a general framework for the computational design of functional proteins

The robust computational design of functional proteins has the potential to deeply impact translational research and broaden our understanding of the determinants of protein function, nevertheless, it remains a challenge for state-of-the-art methodologies. Here, we present a computational design approach that couples conformational folding with sequence design to embed functional motifs into heterologous proteins. We performed extensive benchmarks, where the most unexpected finding was that the design of function into proteins may not necessarily reside in the global minimum of the energetic landscape, which could have important implications in the field. We have computationally designed and experimentally characterized a distant structural template and a de novo \"functionless\" fold, two prototypical design challenges, to present important viral epitopes. Overall, we present an accessible strategy to repurpose old protein folds for new functions, which may lead to important improvements on the computational design of functional proteins.

bioinformatics↗