Integrating machine learning and multiscale modeling—perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences

M Alber, A Buganza Tepole, WR Cannon, S De… - NPJ digital …, 2019 - nature.com
Fueled by breakthrough technology developments, the biological, biomedical, and
behavioral sciences are now collecting more data than ever before. There is a critical need …

Biophysical experiments and biomolecular simulations: A perfect match?

S Bottaro, K Lindorff-Larsen - Science, 2018 - science.org
A fundamental challenge in biological research is achieving an atomic-level description and
mechanistic understanding of the function of biomolecules. Techniques for biomolecular …

The role of protein loops and linkers in conformational dynamics and allostery

E Papaleo, G Saladino, M Lambrughi… - Chemical …, 2016 - ACS Publications
Proteins are dynamic entities that undergo a plethora of conformational changes that may
take place on a wide range of time scales. These changes can be as small as the rotation of …

Principles of protein structural ensemble determination

M Bonomi, GT Heller, C Camilloni… - Current opinion in …, 2017 - Elsevier
Highlights•The principles of protein structural ensemble determination are described.•The
use of experimental data averaged over multiple states is analysed.•Approaches for …

Ultracompact 3D microfluidics for time-resolved structural biology

J Knoška, L Adriano, S Awel, KR Beyerlein… - Nature …, 2020 - nature.com
To advance microfluidic integration, we present the use of two-photon additive
manufacturing to fold 2D channel layouts into compact free-form 3D fluidic circuits with …

Insights from molecular dynamics simulations for computational protein design

MC Childers, V Daggett - Molecular systems design & engineering, 2017 - pubs.rsc.org
A grand challenge in the field of structural biology is to design and engineer proteins that
exhibit targeted functions. Although much success on this front has been achieved, design …

Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology

CA Brosey, JA Tainer - Current opinion in structural biology, 2019 - Elsevier
Highlights•SAXS captures architecture and dynamics to elucidate molecular
ensembles.•SAXS advances now probe key thermodynamic and kinetic properties of …

Ligand binding remodels protein side-chain conformational heterogeneity

SA Wankowicz, SH de Oliveira, DW Hogan… - Elife, 2022 - elifesciences.org
While protein conformational heterogeneity plays an important role in many aspects of
biological function, including ligand binding, its impact has been difficult to quantify …

Small, but powerful and attractive: 19F in biomolecular NMR

AM Gronenborn - Structure, 2022 - cell.com
Nuclear magnetic resonance (NMR) spectroscopy is a versatile tool for probing structure,
dynamics, folding, and interactions at atomic resolution. While naturally occurring …

An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering

DA Keedy, ZB Hill, JT Biel, E Kang, TJ Rettenmaier… - Elife, 2018 - elifesciences.org
Allostery is an inherent feature of proteins, but it remains challenging to reveal the
mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic …