The HADDOCK2. 4 web server for integrative modeling of biomolecular complexes

RV Honorato, ME Trellet, B Jiménez-García… - Nature protocols, 2024 - nature.com
Interactions between macromolecules, such as proteins and nucleic acids, are essential for
cellular functions. Experimental methods can fail to provide all the information required to …

Protein structural bioinformatics: An overview

V de Almeida Paiva, I de Souza Gomes… - Computers in Biology …, 2022 - Elsevier
Proteins play a crucial role in organisms in nature. They are able to perform structural,
catalytic, transport and defense functions in cells, among others. We understand that a …

[HTML][HTML] ATG9A and ATG2A form a heteromeric complex essential for autophagosome formation

AR van Vliet, GN Chiduza, SL Maslen, VE Pye, D Joshi… - Molecular cell, 2022 - cell.com
Summary ATG9A and ATG2A are essential core members of the autophagy machinery.
ATG9A is a lipid scramblase that allows equilibration of lipids across a membrane bilayer …

Targeting the postsynaptic scaffolding protein PSD-95 enhances BDNF signaling to mitigate depression-like behaviors in mice

X Shi, X Zhou, G Chen, W Luo, C Zhou, T He… - Science …, 2024 - science.org
Signaling mediated by brain-derived neurotrophic factor (BDNF), which is supported by the
postsynaptic scaffolding protein PSD-95, has antidepressant effects. Conversely, clinical …

LAG3 ectodomain structure reveals functional interfaces for ligand and antibody recognition

Q Ming, DP Celias, C Wu, AR Cole, S Singh… - Nature …, 2022 - nature.com
The immune checkpoint receptor lymphocyte activation gene 3 protein (LAG3) inhibits T cell
function upon binding to major histocompatibility complex class II (MHC class II) or …

DNA G-quadruplex recognition in vitro and in live cells by a structure-specific nanobody

S Galli, L Melidis, SM Flynn, D Varshney… - Journal of the …, 2022 - ACS Publications
G-quadruplexes (G4s) are four-stranded DNA secondary structures that occur in the human
genome and play key roles in transcription, replication, and genome stability. G4-specific …

Immunoinformatics design of a structural proteins driven multi-epitope candidate vaccine against different SARS-CoV-2 variants based on fynomer

J Sarvmeili, B Baghban Kohnehrouz, A Gholizadeh… - Scientific Reports, 2024 - nature.com
The ideal vaccines for combating diseases that may emerge in the future require more than
simply inactivating a few pathogenic strains. This study aims to provide a peptide-based …

Phosphoantigen sensing combines TCR-dependent recognition of the BTN3A IgV domain and germline interaction with BTN2A1

CR Willcox, M Salim, CR Begley, MM Karunakaran… - Cell reports, 2023 - cell.com
Summary Vγ9Vδ2 T cells play critical roles in microbial immunity by detecting target cells
exposed to pathogen-derived phosphoantigens (P-Ags). Target cell expression of BTN3A1 …

Structural predictions of protein–DNA binding: MELD-DNA

R Esmaeeli, A Bauzá, A Perez - Nucleic Acids Research, 2023 - academic.oup.com
Structural, regulatory and enzymatic proteins interact with DNA to maintain a healthy and
functional genome. Yet, our structural understanding of how proteins interact with DNA is …

[HTML][HTML] Regulation of STING activity in DNA sensing by ISG15 modification

C Lin, EO Kuffour, NV Fuchs, CGW Gertzen, J Kaiser… - Cell Reports, 2023 - cell.com
Sensing of human immunodeficiency virus type 1 (HIV-1) DNA is mediated by the cyclic
GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) signaling axis. Signal …