disordered protein
British Space Startup Launches Longevity Lab Into Orbit
The lab will beam back data to train AI models to predict how proteins behind age-related diseases like Alzheimer's and certain cancers behave. Space is becoming the next frontier in longevity research. A British startup just launched self-run chemical experiments into orbit, in the hopes zero-gravity data might shine a light on a group of disease-causing proteins too difficult to study on Earth. But first they need to check their autonomous laboratory will work in space. Mass Balance's grapefruit-sized apparatus containing chemicals, sensors and control elements to keep the chemicals functioning launched on a SpaceX transporter on Tuesday morning.
DISPROTBENCH: A Disorder-Aware, Task-Rich Benchmark for Evaluating Protein Structure Prediction in Realistic Biological Contexts
Zeng, Xinyue, Wang, Tuo, Kulkarni, Adithya, Lu, Alexander, Ni, Alexandra, Xing, Phoebe, Zhao, Junhan, Chen, Siwei, Zhou, Dawei
Recent advances in protein structure prediction have achieved near-atomic accuracy for well-folded proteins. However, current benchmarks inadequately assess model performance in biologically challenging contexts, especially those involving intrinsically disordered regions (IDRs), limiting their utility in applications such as drug discovery, disease variant interpretation, and protein interface design. We introduce DisProtBench, a comprehensive benchmark for evaluating protein structure prediction models (PSPMs) under structural disorder and complex biological conditions. DisProtBench spans three key axes: (1) Data complexity, covering disordered regions, G protein-coupled receptor (GPCR) ligand pairs, and multimeric complexes; (2) Task diversity, benchmarking twelve leading PSPMs across structure-based tasks with unified classification, regression, and interface metrics; and (3) Interpretability, via the DisProtBench Portal, which provides precomputed 3D structures and visual error analyses. Our results reveal significant variability in model robustness under disorder, with low-confidence regions linked to functional prediction failures. Notably, global accuracy metrics often fail to predict task performance in disordered settings, emphasizing the need for function-aware evaluation. DisProtBench establishes a reproducible, extensible, and biologically grounded framework for assessing next-generation PSPMs in realistic biomedical scenarios.
ProtVec: A Continuous Distributed Representation of Biological Sequences
Asgari, Ehsaneddin, Mofrad, Mohammad R. K.
We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to biological sequences in general with protein-vectors (ProtVec) for proteins (amino-acid sequences) and gene-vectors (GeneVec) for gene sequences, this representation can be widely used in applications of deep learning in proteomics and genomics. In the present paper, we focus on protein-vectors that can be utilized in a wide array of bioinformatics investigations such as family classification, protein visualization, structure prediction, disordered protein identification, and protein-protein interaction prediction. In this method, we adopt artificial neural network approaches and represent a protein sequence with a single dense n-dimensional vector. To evaluate this method, we apply it in classification of 324,018 protein sequences obtained from Swiss-Prot belonging to 7,027 protein families, where an average family classification accuracy of 93%+-0.06% is obtained, outperforming existing family classification methods. In addition, we use ProtVec representation to predict disordered proteins from structured proteins. Two databases of disordered sequences are used: the DisProt database as well as a database featuring the disordered regions of nucleoporins rich with phenylalanine-glycine repeats (FG-Nups). Using support vector machine classifiers, FG-Nup sequences are distinguished from structured protein sequences found in Protein Data Bank (PDB) with a 99.8% accuracy, and unstructured DisProt sequences are differentiated from structured DisProt sequences with 100.0% accuracy. These results indicate that by only providing sequence data for various proteins into this model, accurate information about protein structure can be determined.