A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

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Excitons play an essential role in the optical response of two-dimensional materials. These are bound states showing up in the band gaps of many-body systems and are conceived as quasiparticles formed by an electron and a hole. By performing real-time simu ...

The local physical properties - such as shape and flexibility - of the DNA double-helix is today widely believed to be influenced by nucleic acid sequence in a non-trivial way. Furthermore, there is strong evidence that these properties play a role in many ...

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

The present invention relates to a computer-implemented method for engineering the interaction between a protein and a cognate peptide that are capable of forming a molecular complex, wherein the method comprises (a) preparing in silico a library of test p ...

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the su ...

DNA-binding proteins physically interact with the DNA and directly affect genomic functions. The eukaryotic genome is compacted into chromatin, limiting the DNA access to nuclear factors. In this Ph.D. thesis, I explored the dynamic mechanisms, that allow ...

The rapid progress in the field of deep learning has had a significant impact on protein design. Deep learning methods have recently produced a breakthrough in protein structure prediction, leading to the availability of high-quality models for millions of ...

The present application relates to a computer-implemented systems and methods for protein interaction design using surface fingerprints. The method comprises predicting at least one target interface site with high binding propensity, wherein, optionally, t ...

BackgroundAging in postmitotic tissues is associated with clonal expansion of somatic mitochondrial deletions, the origin of which is not well understood. Such deletions are often flanked by direct nucleotide repeats, but this alone does not fully explain ...

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

Chattez avec Graph Search

Exciton migration in two-dimensional materials

Landscapes of DNA Mechanics and Genomes

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Impact of phylogeny on structural contact inference from protein sequence data

Computer-implemented design of peptide:receptor signaling complexes for enhanced chemotaxis

De novo designed proteins: a study in engineering novel folds and functions

Generative power of a protein language model trained on multiple sequence alignments

Protein target highlights in CASP15: Analysis of models by structure providers

Development of multiplexed single-molecule imaging techniques to study chromatin invasion dynamics of chromatin effector proteins

A new age in protein design empowered by deep learning

Systems and methods for de novo design of protein interactions with learned surface fingerprints

Secondary structure of the human mitochondrial genome affects formation of deletions