Qian Cong

Validation and analysis of 12,000 AI-driven CAR-T designs in the Bits to Binders competition

The paper validates and analyzes 12,000 AI-designed CAR-T binders from a global competition, identifying successful designs and factors improving their performance.

AI-Based Comparison of UniProt annotations and Literature Across Human Kinases

The paper uses AI to compare biological information from UniProt records and their cited literature for human kinases, finding literature provides better coverage for certain topics.

Domain classification of archaeal proteomes reveals conserved fold repertoire

The paper classifies archaeal proteomes at the domain level, revealing that structural diversity is conserved across archaea and that unclassified proteins are due to classification limitations, not structural novelty.

Modeling the structure-conditioned sequence landscape for large-scale protein design with TriFlow

TriFlow, discrete flow-matching sequence designer with global three-track structure attention, raises in silico binder success over ProteinMPNN in RFdiffusion and BindCraft-style pipelines on 500 targets and flags functional sites.

Genomics Analysis Illuminates Morphology, Ecology, Phenology and Distribution of Two Cryptic Atrytonopsis Skippers (Hesperiidae: Hesperiinae)

The paper uses genomic analysis to distinguish two cryptic Atrytonopsis skipper species, revealing their genetic uniqueness, phylogenetic relationship, and geographic distribution.

Cataloging cysteines in ECOD domains using a protein language model

The paper develops TriCyP, a model to predict cysteine states in protein structures, achieving high accuracy and identifying new biological patterns and protein families.

ECOD: Classification of domains in AFDB Swiss-Prot structure predictions

The paper classifies over 542,000 Swiss-Prot protein structure predictions into ECOD domains, expanding domain coverage and revealing novel evolutionary groups.

NUDT5 regulates purine metabolism and thiopurine sensitivity by interacting with PPAT

This study identifies NUDT5 as a regulator of purine metabolism and thiopurine sensitivity by interacting with PPAT, independent of its known enzymatic activity.

Assessment of Protein Complex Predictions in CASP16: Are we making progress?

This paper evaluates progress in predicting protein complex structures in CASP16, finding moderate improvements but ongoing challenges in model ranking, stoichiometry prediction, and handling difficult targets.

Assessment of Nucleic Acid Structure Prediction in CASP16

Across 42 CASP16 nucleic acid targets, accuracy stayed tied to template availability; human experts (Vfold first) led servers and AlphaFold 3, though servers now improve on templates on average.

Computing the Human Interactome

The paper predicts 18,316 human protein-protein interactions with 90% precision using enhanced coevolutionary analysis and a new deep learning model.

CASP16 protein monomer structure prediction assessment

This paper assesses CASP16 monomer structure prediction, showing near-solution for single-domain folds but highlighting challenges in truncated sequences and model ranking.

Accelerating Biomolecular Modeling with AtomWorks andRF3

AtomWorks, a modular atom-level data framework, trains structure prediction and design models; the resulting RF3 improves chirality handling and performs between AF3 and Boltz.

Orthogonalized human protease control of secreted signals

This paper develops hDIRECT, a platform using human-derived proteins to control cytokine activity in cell-based therapies, demonstrating orthogonalization through protease regulation.

Genetic and microbial analysis of invasiveness for Escherichia coli strains associated with inflammatory bowel disease

This study identifies genetic factors associated with invasiveness in Escherichia coli strains from IBD patients using whole genome sequencing and a modified invasion assay.

Essential and virulence-related protein interactions of pathogens revealed through deep learning

This study uses deep learning to predict protein-protein interactions in bacterial pathogens, identifying new complexes involving essential genes and virulence factors, with half of tested predictions validated.

Structure classification of the proteins from Salmonella enterica pangenome revealed novel potential pathogenicity islands

The paper classifies proteins from Salmonella enterica pangenome, identifies potentially pathogenic proteins, and reveals their clustering in the genome.

COA8 is a COX10-binding protein involved in the early biogenesis of cytochrome c oxidase

This study identifies COA8 as a COX10-binding protein essential for COX10 stability and catalytic activity in human cytochrome c oxidase biogenesis.

ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM

The paper classifies domains in 48 proteomes from the AlphaFold Database using DPAM, finding differences in domain composition between eukaryotes and bacteria.

DPAM: A Domain Parser for AlphaFold Models

DPAM automatically parses AlphaFold models to recognize and classify protein domains, outperforming existing methods in accuracy and boundary assignment.

Computed cancer interactome explains the effects of somatic mutations in cancers

The paper uses AlphaFold to predict cancer protein-protein interactions and maps somatic mutations to these interfaces, revealing functional insights and potential drug targets.

Human mitochondrial protein complexes revealed by large-scale coevolution analysis and deep learning-based structure modeling

The paper uses deep learning to predict mitochondrial protein complexes and interactions, identifying known and novel protein pairs with structural and functional insights.

Accurate prediction of protein structures and interactions using a 3-track network

The paper introduces a 3-track network for accurate protein structure and interaction prediction, achieving performance close to DeepMind's CASP14 results and enabling rapid modeling of protein complexes from sequence data.

The meadow jumping mouse genome and transcriptome suggest mechanisms of hibernation

This study investigates the genetic basis of hibernation in the meadow jumping mouse by analyzing its genome and transcriptome, identifying key genes and pathways involved in hibernation-related processes.

Genomics of a complete butterfly continent

The paper sequences all butterfly species in North America north of Mexico to study diversification patterns and adaptation mechanisms across their evolutionary history.