AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences

The AlphaFold Database Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) has significantly impacted structural biology by amassing over 214 million predicted protein structures, expanding from the initial 300k structures released in 2021. Enabled by the groundbreaking AlphaFold2 artificial intelligence (AI) system, the predictions archived in AlphaFold DB have been integrated into primary data resources such as PDB, UniProt, Ensembl, InterPro and MobiDB. Our manuscript details subsequent enhancements in data archiving, covering successive releases encompassing model organisms, global health proteomes, Swiss-Prot integration, and a host of curated protein datasets. We detail the data access mechanisms of AlphaFold DB, from direct file access via FTP to advanced queries using Google Cloud Public Datasets and the programmatic access endpoints of the database. We also discuss the improvements and services added since its initial release, including enhancements to the Predicted Aligned Error viewer, customisation options for the 3D viewer, and improvements in the search engine of AlphaFold DB.

Long-term effect of low molecular weight heparin on serum lipids in hypertriglyceridemic chronic hemodialysis patients

Although low-molecular-weight heparin (LMWH) has been reported to lower serum triglycerides and raise HDL in patients previously receiving classic heparin for hemodialysis by sparing lipoprotein lipase activation, this is not universally accepted. To evaluate this effect we studied 14 hypertriglyceridemic patients on hemodialysis for a median of 61 months (range 6-168 months); six were males and eight females, with a median age of 54 years (range 30-78). Eight patients were on bicarbonate and six on acetate HD. Eight were receiving EPO. All had been given conventional heparin, 102 +/- 5.8 IU/kg, at least for the last six months (control period) before switching to LMWH. Mean LMWH dose was 77 +/- 3.1 IU/kg. Fasting levels of total cholesterol (TC), triglycerides (TG) and HDL were measured monthly during the control period and every trimester for the next 36 months. Serum lipoproteins were measured at months 0 and 36 of the trial. TC, Lp alpha and beta showed no significant change. Serum TG and Lp pre-beta dropped significantly, to almost normal levels. EPO treatment, serum iPTH levels or dialysate buffer did not seem to influence this effect. HDL rose significantly higher in women than in men. It is concluded that LMWH substantially lowered the abnormally high serum TG and Lp pre-beta to almost normal and raised serum HDL in chronic hemodialysis patients.

AlphaFold Protein Structure Database and 3D-Beacons: New Data and Capabilities

The AlphaFold Protein Structure Database (https://alphafold.ebi.ac.uk/) has made significant strides in enhancing its utility and accessibility for the life science research community. The recent integration of AlphaMissense predictions enables access to the pathogenicity of human protein missense variants, with an innovative and interactive heatmap and 3D visualisation that display variant data at the residue level. Users can now toggle between structure model quality (pLDDT) and average pathogenicity scores, providing insights into the implications of specific residue changes. The Foldseek integration offers a rapid and accurate method for protein structure searches and comparisons. Bulk data download options further facilitate comprehensive data analysis and integration with other computational tools. The 3D-Beacons framework (https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/) has also been enhanced with detailed annotation endpoints (such as AlphaMissense data) and integrates LevyLab's dataset of homomeric AlphaFold 2 models. These advancements significantly improve the functionality and accessibility of these resources, enabling discoveries using structure data.