TL;DR
This chapter focuses on three methods developed for intermediate resolution maps, DiffModeler, DMcloud, and VESPER, presenting their usages through the web server.
Cryo-electron microscopy (cryo-EM) has become one of the most powerful techniques for macromolecular structure determination. However, accurate model building from cryo-EM maps remains challenging, particularly for nucleic acids. Here, we present EM3DFold, a unified de novo model-building framework for accurate structu...
Single-particle cryo-electron microscopy (cryo-EM) has become a widely adopted technique for biomolecular structure determination. The conventional cryo-EM computational pipeline first combines many particle images to reconstruct an electrostatic potential (ESP) map and then fits an atomic model to the recovered map. D...
The STEM framework demonstrates how information from condition-dependent experiments can be integrated to yield a coherent mechanistic picture of RNA folding by demonstrating how information from condition-dependent experiments can be integrated to yield a coherent mechanistic picture of RNA folding.
With cryogenic electron microscopy (cryo‐EM) on track to surpass X‐ray crystallography as the preferred method for determining macromolecular structures, it is important to evaluate and compare the quality of structure models obtained by these methods. This allows us to assess whether the rapidly growing numbers (quant...
Continuous protein conformations are essential for understanding fundamental biological processes and supporting drug discovery. Although cryo-EM can resolve individual states at high resolution, recovering continuous heterogeneity from 2D particle images remains challenging. High noise, motion blur, and limited struct...
Unravelling protein-folding mechanisms and kinetics is a key challenge to biochemical science. The variational approach for Markov processes (VAMP) is a powerful tool to build Markov Models that capture key kinetic and structural information despite the conformational complexity and long time scales associated with pro...
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