Related papers: Determination of protein structural ensembles usin…
We present an information-theoretic approach inspired by distributional clustering to assess the structural heterogeneity of particulate systems. Our method identifies communities of particles that share a similar local structure by…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
Recent years have seen tremendous developments in the use of machine learning models to link amino acid sequence, structure and function of folded proteins. These methods are, however, rarely applicable to the wide range of proteins and…
Cryo-Electron Microscopy (cryo-EM) has become an extremely powerful method for resolving structural details of large biomolecular complexes. However, challenging problems in single-particle methods remain open because of (1) the low…
The computational pipelines of single-particle cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) include an early particle-picking stage, in which a micrograph or tomogram is scanned to extract candidate particles,…
In this perspective article, we present a multidisciplinary approach for characterizing protein structure networks. We first place our approach in its historical context and describe the manner in which it synthesizes concepts from quantum…
Proteins are sequences of amino acids that serve as the basic building blocks of living organisms. Despite rapidly growing databases documenting structural and functional information for various protein sequences, our understanding of…
Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance…
The understanding of protein structure, folding, and interaction with other proteins remains one of the grand challenges of modern biology. Tremendous progress has been made thanks to X-ray- or electron-based techniques that have provided…
Machine learning (ML) is widely used to explore crystal materials and predict their properties. However, the training is time-consuming for deep-learning models, and the regression process is a black box that is hard to interpret. Also, the…
The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the Literature, although the number of statistically significant structural studies supporting this is surprisingly low. At variance with…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
Multiple phenotypic protein expressions arising from one genome represent variations in the protein relative abundance and their stoichiometry. A lack of definite compositional parts challenges the modeling of protein megacomplexes and…
Cryo-electron tomography enables 3D visualization of cells in a near native state at molecular resolution. The produced cellular tomograms contain detailed information about all macromolecular complexes, their structures, their abundances…
Cryo-Electron Microscopy (Cryo-EM) is a Nobel prize-winning technology for determining the 3D structure of particles at near-atomic resolution. A fundamental step in the recovering of the 3D single-particle structure is to align its 2D…
We put forward the idea of establishing a novel interdisciplinary field of research at the interface between quantum mechanics and proteomics. The new field, called quantum proteomics, is defined as the large-scale study of the electronic…
Cryo-electron microscopy (cryo-EM) enables the atomic-resolution visualization of biomolecules; however, modern direct detectors generate data volumes that far exceed the available storage and transfer bandwidth, thereby constraining…
Cryo-electron microscopy (cryo-EM) has recently emerged as a powerful tool for obtaining three-dimensional (3D) structures of biological macromolecules in native states. A minimum cryo-EM image data set for deriving a meaningful…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
Many complex systems in nature and society can be described in terms of networks capturing the intricate web of connections among the units they are made of. A key question is how to interpret the global organization of such networks as the…