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.

An antibiotic from an uncultured bacterium binds to an immutable target.

Antimicrobial resistance is a leading mortality factor worldwide. Here, we report the discovery of clovibactin, an antibiotic isolated from uncultured soil bacteria. Clovibactin efficiently kills drug-resistant Gram-positive bacterial pathogens without detectable resistance.

A new antibiotic from an uncultured bacterium binds to an immutable target.

Antimicrobial resistance is a leading mortality factor worldwide. Here we report the discovery of clovibactin, a new antibiotic, isolated from uncultured soil bacteria. Clovibactin efficiently kills drug-resistant bacterial pathogens without detectable resistance.

Polyethylene terephthalate clamps: Optimization in endodontic and restorative practices.

Background: There is a growing search for innovations in dental materials and instruments and, therefore, an increase need to optimize the instruments used in the absolute isolation. The gold standard procedure contributes significantly to the quality of restorative and endodontic procedures. Thus, the aim of the present study was to evaluate the radiopacity of polyethylene terephthalate polymer clamps and compare them to conventional metal clamps.

Regional phase angle, not whole-body, is augmented in response to pre-season in professional soccer players.

The objective of this article was to assess the effects of six-week pre-season training on whole-body and regional bioelectrical impedance analysis (BIA)-derived parameters, body composition, power, and aerobic performance in professional soccer players. Ten professional soccer athletes participated in the present study. Whole-body and regional hamstrings BIA-derived parameters [resistance, reactance, impedance, phase angle (PhA)], body composition, total body water (TBW), intracellular (ICW), and extracellular (ECW) were measured before, at mid-point, and after sixth week of the pre-season.

Hierarchical classification models and Handheld NIR spectrometer to human blood stains identification on different floor tiles.

One of the most important types of evidence in certain criminal investigations is traces of human blood. For a detailed investigation, blood samples must be identified and collected at the crime scene. The present study aimed to evaluate the potential of the identification of human blood in stains deposited on different types of floor tiles (five types of ceramics and four types of porcelain tiles) using a portable NIR instrument.

Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem.

Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three dimensional structures of biomolecules and their interactions is critical for understanding the vast majority of cellular processes, with direct applications in health and food sciences. Since 2010, the WeNMR project (www.

Information-driven modeling of biomolecular complexes.

Proteins play crucial roles in every cellular process by interacting with each other, nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental methods. In the current era of integrative modeling, it is often only by a combination of various experimental techniques and computations that three-dimensional models of those molecular machines can be obtained.

Test-retest reliability of electrical impedance myography in hamstrings of healthy young men.

Several techniques are available to assess muscle tissue status, including electrical impedance myography (EIM). Despite being used in the assessment of neuromuscular status in injury and response to exercise, reliability data for hamstrings muscles are limited. Therefore, this study aimed to determine the test-retest reliability of EIM components on hamstrings.

Differences in Handgrip Strength-Endurance and Muscle Activation Between Young Male Judo Athletes and Untrained Individuals.

The aim of this study was to compare strength-endurance handgrip performance and muscle coactivation between judo athletes and untrained young males. The sample was 38 judo athletes and 38 untrained young males, between 12 and 15 years-old. Maturational status was evaluated by age at peak height velocity.

An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45.

Our information-driven docking approach HADDOCK has demonstrated a sustained performance since the start of its participation to CAPRI. This is due, in part, to its ability to integrate data into the modeling process, and to the robustness of its scoring function. We participated in CAPRI both as server and manual predictors.

Nucleosome binding peptide presents laudable biophysical and in vivo effects.

Chromatin state is highly dependent on the nucleosome binding proteins. Herein, we used a multipronged approach employing biophysical and in vivo experiments to characterize the effects of Nucleosome Binding Peptides (NBPeps) on nucleosome and cell activity. We performed a series of structure-based calculations on the nucleosome surface interaction with GMIP1 (a novel NBPep generated in silico), and HMGN2 (nucleosome binding motif of HMGN2), which contains sites that bind DNA and the acid patch, and also LANA and H4pep (nucleosome binding motif of H4 histone tail) that only bind to the acidic patch.

MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing.

Modeling biomolecular assemblies is an important field in computational structural biology. The inherent complexity of their energy landscape and the computational cost associated with modeling large and complex assemblies are major drawbacks for integrative modeling approaches. The so-called coarse-graining approaches, which reduce the degrees of freedom of the system by grouping several atoms into larger "pseudo-atoms," have been shown to alleviate some of those limitations, facilitating the identification of the global energy minima assumed to correspond to the native state of the complex, while making the calculations more efficient.

Glutaminase Affects the Transcriptional Activity of Peroxisome Proliferator-Activated Receptor γ (PPARγ) via Direct Interaction.

Phosphate-activated glutaminases catalyze the deamidation of glutamine to glutamate and play key roles in several physiological and pathological processes. In humans, GLS encodes two multidomain splicing isoforms: KGA and GAC. In both isoforms, the canonical glutaminase domain is flanked by an N-terminal region that is folded into an EF-hand-like four-helix bundle.

The mechanism by which a distinguishing arabinofuranosidase can cope with internal di-substitutions in arabinoxylans.

Background: Arabinoxylan is an abundant polysaccharide in industrially relevant biomasses such as sugarcane, corn stover and grasses. However, the arabinofuranosyl di-substitutions that decorate the xylan backbone are recalcitrant to most known arabinofuranosidases (Abfs).

Results: In this work, we identified a novel GH51 Abf (Abf51) that forms trimers in solution and can cope efficiently with both mono- and di-substitutions at terminal or internal xylopyranosyl units of arabinoxylan.

Structural basis of exo-β-mannanase activity in the GH2 family.

The classical microbial strategy for depolymerization of β-mannan polysaccharides involves the synergistic action of at least two enzymes, endo-1,4-β-mannanases and β-mannosidases. In this work, we describe the first exo-β-mannanase from the GH2 family, isolated from pv. (XacMan2A), which can efficiently hydrolyze both manno-oligosaccharides and β-mannan into mannose.

Authenticity assessment of banknotes using portable near infrared spectrometer and chemometrics.

Spectra recorded using a portable near infrared (NIR) spectrometer, Soft Independent Modeling of Class Analogy (SIMCA) and Linear Discriminant Analysis (LDA) associated to Successive Projections Algorithm (SPA) models were applied to identify counterfeit and authentic Brazilian Real (R$20, R$50 and R$100) banknotes, enabling a simple field analysis. NIR spectra (950-1650nm) were recorded from seven different areas of the banknotes (two with fluorescent ink, one over watermark, three with intaglio printing process and one over the serial numbers with typography printing). SIMCA and SPA-LDA models were built using 1st derivative preprocessed spectral data from one of the intaglio areas.

Thioredoxin-1 Negatively Modulates ADAM17 Activity Through Direct Binding and Indirect Reductive Activity.

Aims: A disintegrin and metalloprotease 17 (ADAM17) modulates signaling events by releasing surface protein ectodomains such as TNFa and the EGFR-ligands. We have previously characterized cytoplasmic thioredoxin-1 (Trx-1) as a partner of ADAM17 cytoplasmic domain. Still, the mechanism of ADAM17 regulation by Trx-1 is unknown, and it has become of paramount importance to assess the degree of influence that Trx-1 has on metalloproteinase ADAM17.