[PDF][PDF] Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

D Liebschner, PV Afonine, ML Baker… - … Section D: Structural …, 2019 - journals.iucr.org
Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods
to determine three-dimensional macromolecular structures, which are required to …

Self-assembly, interfacial properties, interactions with macromolecules and molecular modelling and simulation of microbial bio-based amphiphiles (biosurfactants). A …

N Baccile, C Seyrig, A Poirier, S Alonso-de Castro… - Green …, 2021 - pubs.rsc.org
Chemical surfactants are omnipresent in consumer products, but they are the subject of
environmental concerns. For this reason, the complete replacement of petrochemical …

[PDF][PDF] ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

TI Croll - Acta Crystallographica Section D: Structural Biology, 2018 - journals.iucr.org
This paper introduces ISOLDE, a new software package designed to provide an intuitive
environment for high-fidelity interactive remodelling/refinement of macromolecular models …

Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning

SR Maddhuri Venkata Subramaniya, G Terashi… - Nature …, 2019 - nature.com
Although structures determined at near-atomic resolution are now routinely reported by cryo-
electron microscopy (cryo-EM), many density maps are determined at an intermediate …

Automated cryo-EM structure refinement using correlation-driven molecular dynamics

M Igaev, C Kutzner, LV Bock, AC Vaiana, H Grubmüller - Elife, 2019 - elifesciences.org
We present a correlation-driven molecular dynamics (CDMD) method for automated
refinement of atomistic models into cryo-electron microscopy (cryo-EM) maps at resolutions …

How to learn from inconsistencies: Integrating molecular simulations with experimental data

S Orioli, AH Larsen, S Bottaro… - Progress in Molecular …, 2020 - Elsevier
Molecular simulations and biophysical experiments can be used to provide independent
and complementary insights into the molecular origin of biological processes. A particularly …

[PDF][PDF] Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM

RA Nicholls, M Tykac, O Kovalevskiy… - … Section D: Structural …, 2018 - journals.iucr.org
Recent advances in instrumentation and software have resulted in cryo-EM rapidly
becoming the method of choice for structural biologists, especially for those studying the …

Cryo-EM for small molecules discovery, design, understanding, and application

G Scapin, CS Potter, B Carragher - Cell chemical biology, 2018 - cell.com
We present a perspective of our view of the application of cryoelectron microscopy (cryo-EM)
to structure-based drug design (SBDD). We discuss the basic needs and requirements for …

Bayesian reweighting of biomolecular structural ensembles using heterogeneous cryo-EM maps with the cryoENsemble method

T Włodarski, JO Streit, A Mitropoulou, LD Cabrita… - Scientific Reports, 2024 - nature.com
Cryogenic electron microscopy (cryo-EM) has emerged as a powerful method for the
determination of structures of complex biological molecules. The accurate characterisation …

Molecular dynamics to predict cryo-EM: capturing transitions and short-lived conformational states of biomolecules

Ł Nierzwicki, G Palermo - Frontiers in molecular biosciences, 2021 - frontiersin.org
Single-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the
structural biology, providing an access to the atomic resolution structures of large …