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Nucleic acid structure prediction

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Identifying the origin of local flexibility in a carbohydrate polymer

Klaus Kern, Stephan Rauschenbach, Sabine Abb

Correlating the structures and properties of a polymer to its monomer sequence is key to understanding how its higher hierarchy structures are formed and how its macroscopic material properties emerge. Carbohydrate polymers, such as cellulose and chitin, a ...

National Academy of Sciences2021

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez

Structure-based antibody and antigen design has advanced greatly in recent years, due not only to the increasing availability of experimentally determined structures but also to improved computational methods for both prediction and design. Constant improv ...

AMER CHEMICAL SOC2021

SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions

Jaume Bonet Martinez

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 ...

2021

Silk granular hydrogels self-reinforced with regenerated silk fibroin fibers

Dominique Pioletti, Pierre-Etienne Bourban, Peyman Karami, Céline Samira Wyss, Adrien Julien Demongeot

Granular hydrogels with high stability, strength, and toughness are laborious to develop. Post-curing is often employed to bind microgels chemically and enhance mechanical properties. Here a unique strategy was investigated to maintain microgels together w ...

2021

On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction

Jaume Bonet Martinez

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 PRESS2021

Structural and analytical identifications of biomolecules by cold ion spectroscopy of non-covalent complexes

Erik Saparbayev

Non-covalent interactions are ubiquitous in nature. The diversity and functionality of these interactions are employed by nature as a universal tool for building the molecular mechanism of life. Although weak, these interactions play a key role in both for ...

EPFL2021

The DEAD-box RNA helicase CshA is required for fatty acid homeostasis inStaphylococcus aureus

Bianca Marie Petrignani

Staphylococcus aureusis an opportunistic pathogen that can grow in a wide array of conditions: on abiotic surfaces, on the skin, in the nose, in planktonic or biofilm forms and can cause many type of infections. Consequently,S.aureusmust be able to adapt r ...

PUBLIC LIBRARY SCIENCE2020

A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments

Matteo Dal Peraro, Luciano Andres Abriata, Giorgio Elikem Tamo

We present our assessment of tertiary structure predictions for hard targets in Critical Assessment of Structure Prediction round 13 (CASP13). The analysis includes (a) assignment and discussion of best models through scores-aided visual inspection of mode ...

WILEY2019

Electronic Relaxation Dynamics of UV-Photoexcited 2-Aminopurine-Thymine Base Pairs in Watson-Crick and Hoogsteen Conformations

Rebecca Ann Ingle, Hugo Jean Baptiste Marroux

The fluorescent analogue 2-aminopurine (2AP) of the canonical nucleobase adenine (6-aminopurine) base-pairs with thymine (T) without disrupting the helical structure of DNA. It therefore finds frequent use in molecular biology for probing DNA and RNA struc ...

AMER CHEMICAL SOC2019

Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank

Michele Ceriotti, Piero Gasparotto, Benjamin Aaron Helfrecht, Federico Giberti

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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Electronic Relaxation Dynamics of UV-Photoexcited 2-Aminopurine-Thymine Base Pairs in Watson-Crick and Hoogsteen Conformations

Rebecca Ann Ingle, Hugo Jean Baptiste Marroux

AMER CHEMICAL SOC2019

On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction

Jaume Bonet Martinez

OXFORD UNIV PRESS2021

Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank

Michele Ceriotti, Piero Gasparotto, Benjamin Aaron Helfrecht, Federico Giberti

2019

A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments

Matteo Dal Peraro, Luciano Andres Abriata, Giorgio Elikem Tamo

WILEY2019