AlphaFold, artificial intelligence (AI), and allostery

R Nussinov, M Zhang, Y Liu, H Jang - The Journal of Physical …, 2022 - ACS Publications
AlphaFold has burst into our lives. A powerful algorithm that underscores the strength of
biological sequence data and artificial intelligence (AI). AlphaFold has appended projects …

Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell

G Wei, W Xi, R Nussinov, B Ma - Chemical reviews, 2016 - ACS Publications
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

Fuzziness and frustration in the energy landscape of protein folding, function, and assembly

S Gianni, MI Freiberger, P Jemth… - Accounts of chemical …, 2021 - ACS Publications
Conspectus Are all protein interactions fully optimized? Do suboptimal interactions
compromise specificity? What is the functional impact of frustration? Why does evolution not …

Single-molecule FRET spectroscopy and the polymer physics of unfolded and intrinsically disordered proteins

B Schuler, A Soranno, H Hofmann… - Annual Review of …, 2016 - annualreviews.org
The properties of unfolded proteins have long been of interest because of their importance
to the protein folding process. Recently, the surprising prevalence of unstructured regions or …

Sulfur in dynamic covalent chemistry

AG Orrillo, RLE Furlan - Angewandte Chemie, 2022 - Wiley Online Library
Sulfur has been important in dynamic covalent chemistry (DCC) since the beginning of the
field. Mainly as part of disulfides and thioesters, dynamic sulfur‐based bonds (DSBs) have a …

Designing multi-epitope vaccine against Staphylococcus aureus by employing subtractive proteomics, reverse vaccinology and immuno-informatics approaches

MT ul Qamar, S Ahmad, I Fatima, F Ahmad… - Computers in Biology …, 2021 - Elsevier
Staphylococcus aureus is a deadly human bacterial pathogen that causes a wide variety of
clinical manifestations. Invasive S. aureus infections in hospitals and the community are one …

Predicting protein conformational motions using energetic frustration analysis and AlphaFold2

X Guan, QY Tang, W Ren, M Chen, W Wang… - Proceedings of the …, 2024 - pnas.org
Proteins perform their biological functions through motion. Although high throughput
prediction of the three-dimensional static structures of proteins has proved feasible using …

Computational and theoretical advances in studies of intrinsically disordered proteins

RB Best - Current opinion in structural biology, 2017 - Elsevier
Highlights•Improvements in all-atom simulations and implicit solvent models now allow IDP
simulations with realistic dimensions to be performed.•Native-centric coarse-grained …

Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics

RG Parra, NP Schafer, LG Radusky… - Nucleic acids …, 2016 - academic.oup.com
The protein frustratometer is an energy landscape theory-inspired algorithm that aims at
localizing and quantifying the energetic frustration present in protein molecules. Frustration …

Structural origin of slow diffusion in protein folding

HS Chung, S Piana-Agostinetti, DE Shaw, WA Eaton - Science, 2015 - science.org
Experimental, theoretical, and computational studies of small proteins suggest that
interresidue contacts not present in the folded structure play little or no role in the self …