AlphaFold predictions of fold-switched conformations are driven by structure memorization
Recent work suggests that AlphaFold (AF)–a deep learning-based model that can
accurately infer protein structure from sequence–may discern important features of folded …
accurately infer protein structure from sequence–may discern important features of folded …
New prediction categories in CASP15
Prediction categories in the Critical Assessment of Structure Prediction (CASP) experiments
change with the need to address specific problems in structure modeling. In CASP15, four …
change with the need to address specific problems in structure modeling. In CASP15, four …
Statistical Thermodynamics of the Protein Ensemble: Mediating Function and Evolution
VJ Hilser, JO Wrabl, CEF Millard… - Annual Review of …, 2025 - annualreviews.org
The growing appreciation of native state conformational fluctuations mediating protein
function calls for critical reevaluation of protein evolution and adaptation. If proteins are …
function calls for critical reevaluation of protein evolution and adaptation. If proteins are …
Structural Models of Human Norepinephrine Transporter Ensemble Reveal the Allosteric Sites and Ligand-Binding Mechanism
The norepinephrine transporter (NET) plays a pivotal role in recycling norepinephrine (NE)
from the synaptic cleft. However, the structures referring to the conformational heterogeneity …
from the synaptic cleft. However, the structures referring to the conformational heterogeneity …
AlphaFold2 has more to learn about protein energy landscapes
Recent work suggests that AlphaFold2 (AF2)–a deep learning-based model that can
accurately infer protein structure from sequence–may discern important features of folded …
accurately infer protein structure from sequence–may discern important features of folded …
Critical assessment of methods of protein structure prediction (CASP)—Round XV
Computing protein structure from amino acid sequence information has been a long‐
standing grand challenge. Critical assessment of structure prediction (CASP) conducts …
standing grand challenge. Critical assessment of structure prediction (CASP) conducts …
[HTML][HTML] Predicting Mutation-Induced Allosteric Changes in Structures and Conformational Ensembles of the ABL Kinase Using AlphaFold2 Adaptations with Alanine …
N Raisinghani, M Alshahrani, G Gupta… - International Journal of …, 2024 - mdpi.com
Despite the success of AlphaFold2 approaches in predicting single protein structures, these
methods showed intrinsic limitations in predicting multiple functional conformations of …
methods showed intrinsic limitations in predicting multiple functional conformations of …
Explaining conformational diversity in protein families through molecular motions
Proteins play a central role in biological processes, and understanding their conformational
variability is crucial for unraveling their functional mechanisms. Recent advancements in …
variability is crucial for unraveling their functional mechanisms. Recent advancements in …
A Review of RNA Structure Prediction: Exploring the Potential of Computational Approaches
RNA plays a crucial role in regulating gene expression, thereby ensuring the maintenance
of genetic integrity. RNA can fold into various structures based on alternative intra-molecular …
of genetic integrity. RNA can fold into various structures based on alternative intra-molecular …
[HTML][HTML] Integrative Modeling of Protein-Polypeptide Complexes by Bayesian Model Selection using AlphaFold and NMR Chemical Shift Perturbation Data
TL Benavides, GT Montelione - bioRxiv, 2024 - pmc.ncbi.nlm.nih.gov
Protein-polypeptide interactions, including those involving intrinsically-disordered peptides
and intrinsically-disordered regions of protein binding partners, are crucial for many …
and intrinsically-disordered regions of protein binding partners, are crucial for many …