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Bottom-up de novo design of functional proteins with complex structural features

Publications associées (39)

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Rationalizing the structure and structure–property relations for complex materials such as polymers or biomolecules relies heavily on the identification of local atomic motifs, e.g., hydrogen bonds and secondary structure patterns, that are seen as buildin ...

2019

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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

Unintended specificity of an engineered ligand-binding protein facilitated by unpredicted plasticity of the protein fold

Kai Johnsson, Alberto Schena

Attempts to create novel ligand-binding proteins often focus on formation of a binding pocket with shape complementarity against the desired ligand (particularly for compounds that lack distinct polar moieties). Although designed proteins often exhibit bin ...

OXFORD UNIV PRESS2018

Inferring interaction partners from protein sequences using mutual information

Anne-Florence Raphaëlle Bitbol

Functional protein-protein interactions are crucial in most cellular processes. They enable multi-protein complexes to assemble and to remain stable, and they allow signal transduction in various pathways. Functional interactions between proteins result in ...

2018

Molecular Imaging of Biopolymers Enabled by Electrospray-Ion Beam Deposition

Sabine Abb

Biomolecular functional complexes often serve as inspiration for the development of artificial molecular nanostructures. The functionality of the biomolecular structures is based on complex and adaptable binding motifs that have evolved over billions of ye ...

EPFL2017

Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics

Matteo Dal Peraro, Luciano Andres Abriata, Enrico Spiga

Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known e ...

Cell Press2016

Phage Selection of Bicyclic Peptide Ligands of the Notch1 Receptor

Freddy Radtke, Christian Heinis, Charlotte Marie Urech-Varenne

Precise regulation of the Notch signaling pathway is crucial, as increases or deficiencies in signaling are associated with diseases, including a wide range of cancers. Recent studies have demonstrated that monoclonal antibodies that bind and stabilize the ...

Wiley-Blackwell2015

Approximation Algorithms for the Interval Constrained Coloring Problem

We consider the interval constrained coloring problem, which appears in the interpretation of experimental data in biochemistry. Monitoring hydrogen-deuterium exchange rates via mass spectroscopy experiments is a method used to obtain information about pro ...

2011

Discrete breathers in protein structures

Francesco Piazza

Recently, using a numerical surface cooling approach, we have shown that highly energetic discrete breathers (DBs) can form in the stiffest parts of nonlinear network models of large protein structures. In the present study, using an analytical approach, w ...

2008

Solute energy based REMD

Molecular dynamics (MD) simulations have increasingly contributed to the understanding of biomolecular processes, allowing for predictions of thermodynamic and structural properties. Unfortunately, the holy grail of protein structure prediction was soon fo ...

EPFL2008