protein structure

A static web database proposes 55 305 construct suggestions for 5328 human secreted and cell-surface proteins, using AlphaFold pLDDT and PAE, with ortholog, paralog and BLAST cross-reactivity context.

A length- and mutation-load-corrected homoplasy screen of 1,813 MDR-TB genomes flags idsA2; its loss raises pretomanid MIC fourfold, delamanid and ethambutol twofold, via isoprenoid flux redirection.

Designed protein binders to conserved MYC regions reach low-nanomolar affinity, reduce MYC-MAX proximity in cells, and are depleted from MYC-dependent cancer cells in culture and mouse pancreatic tumors.

Chaperone, a DataFrame-based framework and agent harness for protein design tools, cut tokens 86% and GPU-hours 64% while raising pass rate from 6% to 12%.

CaGE alternates guided structure prediction with sequence redesign, fading guidance each cycle, so sequences recover complex catalytic sites unaided; designed nonheme-iron and PLP-dependent enzymes were active.

Adding Boltz2 distogram edges and features to protein and RNA graph networks beats MD-correlation graphs on binding tasks and improves stability, interaction and RNA predictions without simulation.

On 489 evaluable new Mac1 complexes, AlphaFold3, Chai-1 and Boltz-2 placed over half of ligands within 2 Å, but on docking hit-lists AF3 and Boltz-2 added little over docking.

AlphaFold3 pLDDT matches AlphaFold2 at calling disordered residues (Matthews correlation 0.693 vs 0.701); on disorder-containing complexes mean DockQ is similar, but interface features explain less variance (42% vs 58%).

Brig3, a DNA glycosylase from a soil metagenome, excises 5-hydroxymethylcytosine from T-even phage DNA; the glucose hydrolase BapA extends defense to glucosylated genomes such as wild-type T4.

Cryo-EM shows human Ndc80 and Ska complexes bound to adjacent microtubule protofilaments, linked by a SKA3 tether that passes Ska's preference for GTP-like lattice and tip tracking to Ndc80.

Q208A mutations in up to four subunits of the ClpX central coupler barely slow unfolded-substrate translocation but raise ATP spent per step, weaken force generation and can abolish GFP unfolding.

A structure-conditioned nucleotide-level Potts model designs protein and coding sequences jointly, enabling tRNA adaptation and RNA motif embedding beyond synonymous codons with designability comparable to Caliby.

Cortical organoids from healthy human iPSCs, seeded with Alzheimer brain tau, form three-repeat tau filaments that cryo-EM shows are identical to Alzheimer paired helical filaments and need endogenous tau.

One Drosophila Ref(2)P polypeptide takes different structures in midgut and muscle, driving autophagy or mitochondria-associated degradation; deleting disordered region IDR2 switches muscle Ref(2)P to midgut state.

Cache sensor domains of DUF3365/Tll0287 family bind covalent c-type heme through a CXXCH insertion; a signaling member behaves like an NO sensor, a stand-alone one like a redox protein.

N-terminal positions whose residue 2 permits methionine aminopeptidase cleavage are less often buried at human assembly interfaces (37.5% vs 47.5%), yet 175 such proteins stay engaged after boundary filtering.

STED imaging quantifies luminal versus abluminal localization of blood-brain barrier proteins in vivo; tyrosine motifs drive abluminal sorting of OAT3 and MHC I, and CD31 shifts day to night.

GO enrichment of proteome-scale docking profiles shrinks the candidate target list: a held-out GO gate kept 11.32% of known targets in 1.26% of candidates; additive reranking was mixed.

A 21-case nightclub-linked meningococcal outbreak variant differed from its closest relatives by horizontal gene transfer from carriage-associated Neisseria, affecting iron acquisition and type IV pili genes.

Reward-guided inference-time search over the Proteína-Complexa sequence-structure codesign model yields validated binders across 127 targets, kinases and a free carbohydrate, with codesigned sequences outperforming ProteinMPNN redesign.

5,776,417 ColabFold-AlphaFold2 structures cover 98.9% of viral UniProt 2025_03 sequences, 16.4-fold more than earlier versions, with 75.3% high-confidence and 72.6% of viral reference proteomes fully covered.

The P450 ApyO crosslinks a 10-residue C-terminal peptide, and substitutions in the YLY motif switch the linkage among C−C, N−C and C−O bonds.

Inferring tested-but-undetected pairs from prey lists of 5,530 published interaction screens yields 97 million tested human protein pairs and 18,982,508 non-interactions (≥3 tests) for calibrating screens and predictors.

CTCF dimerization on stacked nucleosomes is resolved by cryo-EM through a ZnF6-7-8 interface. Disrupting it in mouse stem cells weakens CTCF-cohesin loops more than insulation and impairs germline differentiation.

TIGRFinder annotated 6,685 TIGR arrays; cryo-EM structures show inactive RuvC domains, and E. coli reporter assays show CsTasR and MbTasA repress transcription in a guide-dependent manner.

A web database and REST API of 124,687 AlphaFold 3 structures for human splice isoforms, annotated against canonical proteins for domains, decay, modifications, neoantigens and drug pockets.

40S subunit binding to a previously unrecognised RRM in LARP1 activates its TOP-binding HEAT repeats, licensing repression of ribosomal protein mRNA translation in human cells.

A feedforward network predicts 10,549-bit ensemble pharmacophore fingerprints from SMILES without conformers: 0.584 ms versus 5.71 s per pair comparison, with median MCC 0.860 to 0.914.

An automated pipeline turns the PDB into 178,263 repaired, protonated, restraint-minimized protein-ligand complexes; scoring functions trained on them beat HiQBind-trained ones on CASF-2016 ranking and docking power.

A public crystallographic structure and affinity dataset for enteroviral 2A protease (925 binding events, 699 compounds), with docking, cofolding and screening baselines. Fragment fine-tuning of OpenFold3-p2 improves follow-on predictions.