AIMC Topic: Protein Conformation
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Relationship between immunogenicity and protein structure at amino acid substitution sites of blood group antigens.
Blood
Jul 24, 2025
Polypeptide blood group antigens, many of which are created by single exofacial amino acid substitutions, have varying immunogenicities. Why some amino acid substitutions are more immunogenic than others is little understood. Using AlphaFold2, an art...
HDXRank: A Deep Learning Framework for Ranking Protein Complex Predictions with Hydrogen-Deuterium Exchange Data.
Journal of chemical theory and computation
Jul 22, 2025
Accurate modeling of protein-protein complex structures is essential for understanding biological mechanisms. Hydrogen-deuterium exchange (HDX) experiments provide valuable insights into binding interfaces. Incorporating HDX data into protein complex...
Artificial Intelligence Captures Pseudo-Intelligence Evolved in the Chemical Architecture of the Multifaceted Signal Transducer, TAK1.
Journal of chemical information and modeling
Jul 14, 2025
TAK1, a multifunctional kinase, possesses intramolecular interactions that are capacitated to recognize and process diverse forms of chemical and mechanical forces, which ultimately translate into a convergent catalytic function. By elucidating a dua...
PrankWeb 4: a modular web server for protein-ligand binding site prediction and downstream analysis.
Nucleic acids research
Jul 7, 2025
Knowledge of protein-ligand binding sites (LBSs) is crucial for advancing our understanding of biology and developing practical applications in fields such as medicine or biotechnology. PrankWeb is a web server that allows users to predict LBSs from ...
DEMO-EMol: modeling protein-nucleic acid complex structures from cryo-EM maps by coupling chain assembly with map segmentation.
Nucleic acids research
Jul 7, 2025
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...
InDeepNet: a web platform for predicting functional binding sites in proteins using InDeep.
Nucleic acids research
Jul 7, 2025
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...
HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes.
Nucleic acids research
Jul 7, 2025
Protein-protein interactions (PPIs) are fundamental to cellular functions, yet predicting and analyzing their 3D structures remains a critical and computationally demanding challenge. To address this, the HawkDock web server was developed as an integ...
StructMAn 2.0 Web: a web server for structural annotation of protein sequences and mutations.
Nucleic acids research
Jul 7, 2025
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 ...
TmDet 4.0: determining membrane orientation of transmembrane proteins from 3D structure.
Nucleic acids research
Jul 7, 2025
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 ...
FoldScript: a web server for the efficient analysis of AI-generated 3D protein models.
Nucleic acids research
Jul 7, 2025
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...
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