Publication
Protein design and folding: Template trapping of self-assembled helical bundles
Related publications (82)
A generic framework for hierarchical de novo protein design
Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Jaume Bonet Martinez, Fabian Sesterhenn, Stéphane Rosset, Che Yang
De novo protein design enables the exploration of novel sequences and structures absent from the natural protein universe. De novo design also stands as a stringent test for our understanding of the underlying physical principles of protein folding and may ...
NATL ACAD SCIENCES2022On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction
Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. We present RADI/raDIMod, a variation of the original DCA algorithm that grou ...
OXFORD UNIV PRESS2021SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions
BackgroundStatistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein-protein interaction (PPI) structures. In previous works we deco ...
BMC2021On the exploration of novel methodological approaches for immunogen design: case studies in influenza and hepatitis C
Proteins are fundamental components in biological systems and crucial for a variety of biological functions. Over the last decades, significant progress in structural biology has facilitated the study of proteins and their interactions with molecular partn ...
EPFL2021Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization
Matteo Dal Peraro, Luciano Andres Abriata
Continuous assessment of transferable forcefields for molecular simulations is essential to identify their weaknesses and direct improvement efforts. The latest efforts focused on better describing disordered proteins while retaining proper description of ...
2021Bottom-up de novo design of functional proteins with complex structural features
Luciano Andres Abriata, Bruno Emanuel Ferreira De Sousa Correia, Sandrine Madeleine Suzanne Georgeon, Leo Scheller, Jaume Bonet Martinez, Fabian Sesterhenn, Stéphane Rosset, Che Yang, Eva Anna van Aalen
De novo protein design has enabled the creation of new protein structures. However, the design of functional proteins has proved challenging, in part due to the difficulty of transplanting structurally complex functional sites to available protein structur ...
NATURE RESEARCH2021Overexpression of transcription factor Foxa1 and target genes remediate therapeutic protein production bottlenecks in Chinese hamster ovary cells
Nicolas Mermod, Iris Bodenmann
Despite extensive research conducted to increase protein production from Chinese hamster ovary (CHO) cells, cellular bottlenecks often remain, hindering high yields. In this study, a transcriptomic analysis led to the identification of 32 genes that are co ...
WILEY2020rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics
Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Andreas Scheck, Jaume Bonet Martinez, Fabian Sesterhenn
BackgroundLarge-scale datasets of protein structures and sequences are becoming ubiquitous in many domains of biological research. Experimental approaches and computational modelling methods are generating biological data at an unprecedented rate. The deta ...
2019Allosteric Protein Switches based on Antibody Mimetics
Helen Rebecca Ostlund Farrants
Synthetic protein switches are proteins that can be controlled by an external input, and are useful tools to probe protein function. Antibody fragments and antibody mimetics can be selected to bind, activate, or inhibit several diverse protein targets. Nev ...
EPFL2019Rosetta FunFolDes - A general framework for the computational design of functional proteins
Bruno Emanuel Ferreira De Sousa Correia, Andreas Scheck, Jaume Bonet Martinez, Fabian Sesterhenn, Stéphane Rosset, Che Yang, Sarah Wehrle, Freyr Sverrisson, Sabrina Susan Vollers, Mélanie Evelyne Villard, Anne Marie-Thérèse Suzanne Billet, Roxanne Marine Lourman, Karen Schriever
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 and stability. The low success rates of computational design protocols an ...
2018