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Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies

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PdII2L4-type coordination cages up to three nanometers in size

Rosario Scopelliti, Kay Severin, Suzanne Maria Jansze, Matthew David Wise

The utilization of large ligands in coordination-based self-assembly represents an attractive strategy for the construction of supramolecular assemblies more than two nanometers in size. However, the implementation of this strategy is hampered by the fact ...

2017

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses

Bruno Emanuel Ferreira De Sousa Correia, Stefano Zamuner

The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based ...

Wiley-Blackwell2016

AFM-Based Single Molecule Techniques: Unraveling the Amyloid Pathogenic Species

Giovanni Dietler, Francesco Simone Ruggeri, Andrea Cerreta

Background: A wide class of human diseases and neurodegenerative disorders, such as Alzheimer's disease, is due to the failure of a specific peptide or protein to keep its native functional conformational state and to undergo a conformational change into a ...

Bentham Science Publishers2016

Viability evolutionary algorithms and applications to neuroscience and biology

Andrea Maesani

Evolutionary algorithms are heuristic methods that operate on a population of individuals, which represent candidate solutions to optimization problems. Individuals with better quality, or fitness, are reproduced at a higher rate than less fit individuals ...

EPFL2015

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Revealing the atomistic architecture of supramolecular complexes is a fundamental step toward a deeper understanding of cellular functioning. To date, this formidable task is facilitated by an emerging array of integrative modeling approaches that combine ...

Current Biology Ltd2015

Hierarchically Structured Microfibers of ‘Single Stack’ Perylene Bisimide and Quaterthiophene Nanowires

Holger Frauenrath, Roman Niklaus Marty, Ruth Szilluweit, Raffaele Mezzenga

Organic nanowires and microfibers are excellent model systems for charge transport in organic semiconductors under nanoscopic confinement and may be relevant for future nanoelectronic devices. For this purpose, however, the preparation of well-ordered orga ...

Amer Chemical Soc2013

Macromolecular Symmetric Assembly Prediction Using Swarm Intelligence Dynamic Modeling

Matteo Dal Peraro, Matteo Thomas Degiacomi

Proteins often assemble in multimeric complexes to perform a specific biologic function. However, trapping these high-order conformations is difficult experimentally. Therefore, predicting how proteins assemble using in silico techniques can be of great he ...

Cell Press2013

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In order to produce materials with tailored structures and functions via supramolecular self-assembly of molecular precursors in a predictable fashion, it is necessary to develop 'supramolecular methods' based on structurally simple 'supramolecular synthon ...

2012

Proteins have the ability to assemble in multimeric states to perform their specific biological function. Unfortunately, characterizing experimentally these structures at atomistic resolution is usually difficult. For this reason, in silico methodologies a ...

EPFL2012

We report on p- and n-type organic self-assembled monolayer held effect transistors. On the base of quaterthiophene and fullerene units, multifunctional molecules were synthesized, which have the ability to self-assemble and provide multifunctional monolay ...

2011