The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins

V Agarwal, AC McShan - Nature Chemical Biology, 2024 - nature.com
Artificial intelligence-driven advances in protein structure prediction in recent years have
raised the question: has the protein structure-prediction problem been solved? Here, with a …

Can AlphaFold's breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity?

B McMaster, C Thorpe, G Ogg, CM Deane, H Koohy - Nature Methods, 2024 - nature.com
T cells are essential immune cells responsible for identifying and eliminating pathogens.
Through interactions between their T-cell antigen receptors (TCRs) and antigens presented …

Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes

JM Custodio, CM Ayres, TJ Rosales… - Proceedings of the …, 2023 - National Acad Sciences
Neoepitopes arising from amino acid substitutions due to single nucleotide polymorphisms
are targets of T cell immune responses to cancer and are of significant interest in the …

Revolutionizing peptide‐based drug discovery: Advances in the post‐AlphaFold era

L Chang, A Mondal, B Singh… - Wiley …, 2024 - Wiley Online Library
Peptide‐based drugs offer high specificity, potency, and selectivity. However, their inherent
flexibility and differences in conformational preferences between their free and bound states …

EnGens: a computational framework for generation and analysis of representative protein conformational ensembles

A Conev, MM Rigo, D Devaurs… - Briefings in …, 2023 - academic.oup.com
Proteins are dynamic macromolecules that perform vital functions in cells. A protein structure
determines its function, but this structure is not static, as proteins change their conformation …

A journey to your self: The vague definition of immune self and its practical implications

B Koncz, GM Balogh… - Proceedings of the …, 2024 - National Acad Sciences
The identification of immunogenic peptides has become essential in an increasing number
of fields in immunology, ranging from tumor immunotherapy to vaccine development. The …

MHC-Fine: Fine-tuned AlphaFold for precise MHC-peptide complex prediction

E Glukhov, D Kalitin, D Stepanenko, Y Zhu, T Nguyen… - Biophysical …, 2024 - cell.com
The precise prediction of major histocompatibility complex (MHC)-peptide complex
structures is pivotal for understanding cellular immune responses and advancing vaccine …

A Computational Pipeline for Accurate Prioritization of Protein‐Protein Binding Candidates in High‐Throughput Protein Libraries

A Mondal, B Singh, RH Felkner, A De Falco… - Angewandte …, 2024 - Wiley Online Library
Identifying the interactome for a protein of interest is challenging due to the large number of
possible binders. High‐throughput experimental approaches narrow down possible binding …

RankMHC: Learning to Rank Class-I Peptide-MHC Structural Models

R Fasoulis, G Paliouras, LE Kavraki - Journal of Chemical …, 2024 - ACS Publications
The binding of peptides to class-I Major Histocompability Complex (MHC) receptors and
their subsequent recognition downstream by T-cell receptors are crucial processes for most …

[HTML][HTML] Epitope mapping via in vitro deep mutational scanning methods and its applications

MM Keen, AD Keith, EA Ortlund - Journal of Biological Chemistry, 2024 - Elsevier
Epitope mapping is a technique employed to define the region of an antigen that elicits an
immune response, providing crucial insight into the structural architecture of the antigen as …