Principles for integrative structural biology studies

MP Rout, A Sali - Cell, 2019 - cell.com
Integrative structure determination is a powerful approach to modeling the structures of
biological systems based on data produced by multiple experimental and theoretical …

Leveraging crosslinking mass spectrometry in structural and cell biology

A Graziadei, J Rappsilber - Structure, 2022 - cell.com
Crosslinking mass spectrometry (crosslinking-MS) is a versatile tool providing structural
insights into protein conformation and protein-protein interactions. Its medium-resolution …

Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement

F DiMaio, Y Song, X Li, MJ Brunner, C Xu… - Nature …, 2015 - nature.com
We describe a general approach for refining protein structure models on the basis of cryo-
electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo …

[BOOK][B] Introduction to proteins: structure, function, and motion

A Kessel, N Ben-Tal - 2018 - taylorfrancis.com
Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the
structure, function, and motion of proteins for students, faculty, and researchers at all levels …

[HTML][HTML] Hybrid methods for combined experimental and computational determination of protein structure

JT Seffernick, S Lindert - The Journal of chemical physics, 2020 - pubs.aip.org
Knowledge of protein structure is paramount to the understanding of biological function,
develo** new therapeutics, and making detailed mechanistic hypotheses. Therefore …

Accurate global and local 3D alignment of cryo-EM density maps using local spatial structural features

B He, F Zhang, C Feng, J Yang, X Gao… - Nature Communications, 2024 - nature.com
Advances in cryo-electron microscopy (cryo-EM) imaging technologies have led to a rapidly
increasing number of cryo-EM density maps. Alignment and comparison of density maps …

Development of a prototype system for archiving integrative/hybrid structure models of biological macromolecules

B Vallat, B Webb, JD Westbrook, A Sali, HM Berman - Structure, 2018 - cell.com
Essential processes in biology are carried out by large macromolecular assemblies, whose
structures are often difficult to determine by traditional methods. Increasingly, researchers …

EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps

S Lindert, N Alexander, N Wötzel, M Karakaş… - Structure, 2012 - cell.com
Electron density maps of membrane proteins or large macromolecular complexes are
frequently only determined at medium resolution between 4 Å and 10 Å, either by cryo …

[HTML][HTML] Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy

AP Joseph, I Lagerstedt, A Patwardhan, M Topf… - Journal of structural …, 2017 - Elsevier
Recent developments in 3-dimensional electron microcopy (3D-EM) techniques and a
concomitant drive to look at complex molecular structures, have led to a rapid increase in the …

Advances in structure modeling methods for cryo-electron microscopy maps

E Alnabati, D Kihara - Molecules, 2019 - mdpi.com
Cryo-electron microscopy (cryo-EM) has now become a widely used technique for structure
determination of macromolecular complexes. For modeling molecular structures from …