Integrative Modeling in the Age of Machine Learning: A Summary of HADDOCK Strategies in CAPRI Rounds 47-55.

The HADDOCK team participated in CAPRI rounds 47-55 as server, manual predictor, and scorers. Throughout these CAPRI rounds, we used a plethora of computational strategies to predict the structure of protein complexes. Of the 10 targets comprising 24 interfaces, we achieved acceptable or better models for 3 targets in the human category and 1 in the server category.

ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information.

The formation of a stable complex between proteins lies at the core of a wide variety of biological processes and has been the focus of countless experiments. The huge amount of information contained in the protein structural interactome in the Protein Data Bank can now be used to characterise and classify the existing biological interfaces. We here introduce ARCTIC-3D, a fast and user-friendly data mining and clustering software to retrieve data and rationalise the interface information associated with the protein input data.

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.

We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average ~70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target.

Classification of bloodstains deposited at different times on floor tiles using hierarchical modelling and a handheld NIR spectrometer.

Bloodstains are commonly encountered at crime scenes, especially on floor tiles, and can be deposited over different periods and intervals. Therefore, it is crucial to develop techniques that can accurately identify bloodstains deposited at different times. This study builds upon a previous investigation and aims to enhance the performance of three distinct hierarchical models (HMs) designed to differentiate and identify stains of human blood (HB), animal blood (AB), and common false positives (CFPs) on nine different types of floor tiles.