Recent progress and development of artificial intelligence and machine learning (AI/ML) techniques have enabled addressing complex biomolecular problems. AI/ML models learn the underlying distribution of data they are trained on and when exposed to n...
Therapeutic antibodies are manufactured, stored and administered in the free state; this makes understanding the unbound form key to designing and improving development pipelines. Prediction of unbound antibodies is challenging, specifically modellin...
International journal of molecular sciences
39859213
We test here the prediction capabilities of the new generation of deep learning predictors in the more challenging situation of multistate multidomain proteins by using as a case study a coiled-coil family of Nucleotide-binding Oligomerization Domain...
Proceedings of the National Academy of Sciences of the United States of America
39951500
Understanding the dynamic evolution of protein structures is crucial for uncovering their biological functions. Yet, real-time prediction of these dynamic structures remains a significant challenge. Two-dimensional infrared (2DIR) spectroscopy is a p...
Journal of chemical information and modeling
39950947
Recent studies have reported long-range charge transport in peptide- and protein-based fibers and wires, rendering this class of materials as promising charge-conducting interfaces between biological systems and electronic devices. In the complex mol...
Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling the determination of biomolecular structures that are challenging to resolve using conventional methods. Interpreting a cryo-EM map requires accurate modeling of the...
This review highlights recent advances in AI-driven methods for generating Boltzmann-weighted structural ensembles, which are crucial for understanding biomolecular dynamics and drug discovery. With the rise of deep learning models such as AlphaFold2...
Artificial intelligence (AI) and deep learning are making groundbreaking strides in protein structure prediction. AlphaFold is remarkable in this arena for its outstanding accuracy in modelling proteins fold based solely on their amino acid sequences...
Protein-ligand structure prediction methods, aiming to predict the three-dimensional complex structure and binding energy of a compound and target protein, are essential in many structure-based drug discovery pipelines, including virtual screening an...
Protein science : a publication of the Protein Society
39865355
Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression...