Cysteine residues play key roles in protein structure and function and can serve as targets for chemical probes and even drugs. Chemoproteomic studies have revealed that heightened cysteine reactivity toward electrophilic probes, such as iodoacetamid...
The N-heptad repeat (NHR) of the HIV-1 gp41 prehairpin intermediate (PHI) is an attractive potential vaccine target with high sequence conservation across diverse strains. However, despite the potency of NHR-targeting peptides and clinical efficacy o...
Journal of chemical information and modeling
Jul 14, 2025
Generative design of functional RNAs presents revolutionary opportunities for diverse RNA-based biotechnologies and biomedical applications. To this end, RNA inverse folding is a promising strategy for generatively designing new RNA sequences that ca...
Atomic structure modeling is a crucial step in determining the structures of protein complexes using cryo-electron microscopy (cryo-EM). This work introduces DEMO-EMol, an improved server that integrates deep learning-based map segmentation and chain...
Predicting functional binding sites in proteins is crucial for understanding protein-protein interactions (PPIs) and identifying drug targets. While various computational approaches exist, many fail to assess PPI ligandability, which often involves c...
StructMAn is a method for protein structural annotation. It describes each position of a protein sequence or specific variants in it in terms of their importance for the three-dimensional (3D) structure of the protein and its interactions with other ...
During the structural determination of transmembrane proteins, one crucial piece of information is lost: the orientation of the protein within the lipid bilayer. The TmDet algorithm was developed in the early 2000s to determine the relative position ...
Artificial intelligence (AI)-based 3D protein modelling software have revolutionized structural biology, often predicting protein structures with unprecedented confidence. However, to get the most out of AI, it is advisable to consider the informatio...
Journal of the American Society for Mass Spectrometry
Jun 4, 2025
Hydroxyl radical protein footprinting (HRPF) coupled with mass spectrometry yields information about residue solvent exposure and protein topology. However, data from these experiments are sparse and require computational interpretation to generate u...
MOTIVATION: Allostery, the process by which binding at one site perturbs a distant site, is being rendered as a key focus in the field of drug development with its substantial impact on protein function. The identification of allosteric pockets (site...
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