Related papers: Protein-protein modelling using cryo-EM restraints
Protein structure determination has long been one of the primary challenges of structural biology, to which deep machine learning (ML)-based approaches have increasingly been applied. However, these ML models generally do not incorporate…
In this paper we study the formal algebraic structure underlying the intrinsic classification algorithm, recently introduced by Hadani, Shkolnisky, Singer and Zhao, for classifying noisy projection images of similar viewing directions in…
Cryo-electron microscopy (cryo-EM) studies using single particle reconstruction are extensively used to reveal structural information on macromolecular complexes. Aiming at the highest achievable resolution, state of the art electron…
In simulations of metallic interfaces, a critical aspect of metallic behavior is missing from the some of the most widely used classical molecular dynamics force fields. We present a modification of the embedded atom method (EAM) which…
Over the past decade, cryogenic electron microscopy (cryo-EM) has emerged as a primary method for determining near-native, near-atomic resolution 3D structures of biological macromolecules. In order to meet increasing demand for cryo-EM,…
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…
The embedded atom method (EAM) potentials are probably the most widely used interatomic potentials for metals and alloys. However, the EAM potentials impose three constraints on elastic constants that are inconsistent with experiments. At a…
Protein language models have demonstrated significant potential in the field of protein engineering. However, current protein language models primarily operate at the residue scale, which limits their ability to provide information at the…
Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
Imaging single proteins has been a long-standing ambition for advancing various fields in natural science, as for instance structural biology, biophysics and molecular nanotechnology. In particular, revealing the distinct conformations of…
The choice of structural resolution is a fundamental aspect of protein modelling, determining the balance between descriptive power and interpretability. Although atomistic simulations provide maximal detail, much of this information is…
Proteins are dynamic, adopting ensembles of conformations. The nature of this conformational heterogenity is imprinted in the raw electron density measurements obtained from X-ray crystallography experiments. Fitting an ensemble of protein…
Spectroscopic mapping by scanning transmission electron microscopy coupled with electron energy loss spectroscopy (STEM-EELS) is a powerful technique for determining the structure and chemistry of a wide range of materials and interfaces.…
Effective representations of protein sequences are widely recognized as a cornerstone of machine learning-based protein design. Yet, protein bioengineering poses unique challenges for sequence representation, as experimental datasets…
Cryo-electron microscopy (cryo-EM) has become a tool of fundamental importance in structural biology, helping us understand the basic building blocks of life. The algorithmic challenge of cryo-EM is to jointly estimate the unknown 3D poses…
Scanning transmission electron microscopy (STEM) has advanced rapidly in the last decade thanks to the ability to correct the major aberrations of the probe forming lens. Now atomic-sized beams are routine, even at accelerating voltages as…
A common task in cryo-electron microscopy (cryo-EM) data processing is to compare three-dimensional density maps of macromolecules. In this paper, we propose an algorithm for aligning three-dimensional density maps that exploits common…
This comprehensive review discusses the development of scanning electron microscopy and the application of this technology in different fields such as biology, nanobiotechnology and biomedical science. Besides being a tool for high…
One of the challenges of the proteomic analysis by 2D-gel is to visualize the low abundance proteins, particularly those localized in organelles. An additional problem with nuclear proteins lies in their strong interaction with nuclear…