Slice'N'Dice: maximizing the value of predicted models for structural biologists.

With the advent of next-generation modelling methods, such as AlphaFold2, structural biologists are increasingly using predicted structures to obtain structure solutions via molecular replacement (MR) or model fitting in single-particle cryogenic sample electron microscopy (cryoEM). Differences between the domain-domain orientations represented in a predicted model and a crystal structure are often a key limitation when using predicted models. Slice'N'Dice is a software package designed to address this issue by first slicing models into distinct structural units and then automatically placing the slices using either Phaser, MOLREP or PowerFit.

Online carbohydrate 3D structure validation with the Privateer web app.

Owing to the difficulties associated with working with carbohydrates, validating glycan 3D structures prior to deposition into the Protein Data Bank has become a staple of the structure-solution pipeline. The Privateer software provides integrative methods for the validation, analysis, refinement and graphical representation of 3D atomic structures of glycans, both as ligands and as protein modifiers. While Privateer is free software, it requires users to install any of the structural biology software suites that support it or to build it from source code.

Tertiary structure assessment at CASP15.

The results of tertiary structure assessment at CASP15 are reported. For the first time, recognizing the outstanding performance of AlphaFold 2 (AF2) at CASP14, all single-chain predictions were assessed together, irrespective of whether a template was available. At CASP15, there was no single stand-out group, with most of the best-scoring groups-led by PEZYFoldings, UM-TBM, and Yang Server-employing AF2 in one way or another.

Predicted models and CCP4.

In late 2020, the results of CASP14, the 14th event in a series of competitions to assess the latest developments in computational protein structure-prediction methodology, revealed the giant leap forward that had been made by Google's Deepmind in tackling the prediction problem. The level of accuracy in their predictions was the first instance of a competitor achieving a global distance test score of better than 90 across all categories of difficulty. This achievement represents both a challenge and an opportunity for the field of experimental structural biology.

Analytical Modeling and Optimization of CuZnSn(S,Se) Solar Cells with the Use of Quantum Wells under the Radiative Limit.

In this work, we present a theoretical study on the use of CuZnSn(S,Se) quantum wells in CuZnSnS solar cells to enhance device efficiency. The role of different well thickness, number, and S/(S + Se) composition values is evaluated. The physical mechanisms governing the optoelectronic parameters are analyzed.

The CCP4 suite: integrative software for macromolecular crystallography.

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces.

Using deep-learning predictions of inter-residue distances for model validation.

Determination of protein structures typically entails building a model that satisfies the collected experimental observations and its deposition in the Protein Data Bank. Experimental limitations can lead to unavoidable uncertainties during the process of model building, which result in the introduction of errors into the deposited model. Many metrics are available for model validation, but most are limited to consideration of the physico-chemical aspects of the model or its match to the experimental data.

Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions.

β-Galactosidases catalyse the hydrolysis of lactose into galactose and glucose; as an alternative reaction, some β-galactosidases also catalyse the formation of galactooligosaccharides by transglycosylation. Both reactions have industrial importance: lactose hydrolysis is used to produce lactose-free milk, while galactooligosaccharides have been shown to act as prebiotics. For some multi-domain β-galactosidases, the hydrolysis/transglycosylation ratio can be modified by the truncation of carbohydrate-binding modules.

ConPlot: web-based application for the visualization of protein contact maps integrated with other data.

Summary: Covariance-based predictions of residue contacts and inter-residue distances are an increasingly popular data type in protein bioinformatics. Here we present ConPlot, a web-based application for convenient display and analysis of contact maps and distograms. Integration of predicted contact data with other predictions is often required to facilitate inference of structural features.

Evaluation of model refinement in CASP14.

We report here an assessment of the model refinement category of the 14th round of Critical Assessment of Structure Prediction (CASP14). As before, predictors submitted up to five ranked refinements, along with associated residue-level error estimates, for targets that had a wide range of starting quality. The ability of groups to accurately rank their submissions and to predict coordinate error varied widely.

Helical ensembles outperform ideal helices in molecular replacement.

The conventional approach in molecular replacement is the use of a related structure as a search model. However, this is not always possible as the availability of such structures can be scarce for poorly characterized families of proteins. In these cases, alternative approaches can be explored, such as the use of small ideal fragments that share high, albeit local, structural similarity with the unknown protein.

Analysis of the information in mandatory reporting in victims of gender violence.

The healthcare professional plays a key role in the detection and subsequent channeling of a situation of violence to a judicial level for appropriate investigation. The mandatory reporting of gender violence has become a controversial issue among health care practitioners and victims. The objective of this study was to analyze the quality of the way in which injury reports on victims of gender violence is completed, through an analysis of the information they include, the readability and the degree to which the document can be understood.

High levels of auxin signalling define the stem-cell organizer of the vascular cambium.

Wood, a type of xylem tissue, originates from cell proliferation of the vascular cambium. Xylem is produced inside, and phloem outside, of the cambium. Morphogenesis in plants is typically coordinated by organizer cells that direct the adjacent stem cells to undergo programmed cell division and differentiation.

Phosphate Starvation-Dependent Iron Mobilization Induces CLE14 Expression to Trigger Root Meristem Differentiation through CLV2/PEPR2 Signaling.

Low inorganic phosphate (Pi) availability causes terminal differentiation of the root apical meristem (RAM), a phenomenon known as root meristem exhaustion or determined growth. Here, we report that the CLE14 peptide acts as a key player in this process. Low Pi stress induces iron mobilization in the RAM through the action of LPR1/LPR2, causing expression of CLE14 in the proximal meristem region.

Production of [Formula: see text] and [Formula: see text] in proton-proton collisions at [Formula: see text] 7 TeV.

The production of the strange and double-strange baryon resonances ([Formula: see text], [Formula: see text]) has been measured at mid-rapidity ([Formula: see text][Formula: see text]) in proton-proton collisions at [Formula: see text] [Formula: see text] 7 TeV with the ALICE detector at the LHC. Transverse momentum spectra for inelastic collisions are compared to QCD-inspired models, which in general underpredict the data. A search for the [Formula: see text] pentaquark, decaying in the [Formula: see text] channel, has been carried out but no evidence is seen.

Identification of a new Alcaligenes faecalis strain MOR02 and assessment of its toxicity and pathogenicity to insects.

We report the isolation of a bacterium from Galleria mellonella larva and its identification using genome sequencing and phylogenomic analysis. This bacterium was named Alcaligenes faecalis strain MOR02. Microscopic analyses revealed that the bacteria are located in the esophagus and intestine of the nematodes Steinernema feltiae, S.

Exclusive J/ψ photoproduction off protons in ultraperipheral p-Pb collisions at √(s(NN))=5.02 TeV.

We present the first measurement at the LHC of exclusive J/ψ photoproduction off protons, in ultraperipheral proton-lead collisions at sqrt[s_{NN}]=5.02  TeV. Events are selected with a dimuon pair produced either in the rapidity interval, in the laboratory frame, 2.

Measurement of prompt D-meson production in p-Pb collisions at √(s(NN))=5.02 TeV.

The p_{T}-differential production cross sections of the prompt charmed mesons D^{0}, D^{+}, D^{*+}, and D_{s}^{+} and their charge conjugate in the rapidity interval -0.96 View Article and Find Full Text PDF

Measurement of quarkonium production at forward rapidity in [Formula: see text] collisions at [Formula: see text]TeV.

The inclusive production cross sections at forward rapidity of [Formula: see text], [Formula: see text], [Formula: see text](1S) and [Formula: see text](2S) are measured in [Formula: see text] collisions at [Formula: see text] with the ALICE detector at the LHC. The analysis is based on a data sample corresponding to an integrated luminosity of 1.35 pb[Formula: see text].

Prevention of infective endocarditis: a review of the American Heart Association guidelines.

Ever since the last American Heart Association (AHA) publication on prevention of infective endocarditis (IE) many medical societies and physicians have questioned the efficacy of prophylaxis in patients that undergo a dental, genitourinary (GU) or gastrointestinal (GI) procedures. In 1997 AHA recognize that most cases of IE were not related to invasive procedures but as a result of arbitrarily occurring bacteremia from routine daily activities as well as recognition of the possibility of IE prophylaxis failure. This assumptions as well as review of numerous published studies over the past two decades caused that AHA to revise the guidelines of 1997.

Acupuncture as a complementary therapy to the pharmacological treatment of osteoarthritis of the knee: randomised controlled trial.

Objectives: To analyse the efficacy of acupuncture as a complementary therapy to the pharmacological treatment of osteoarthritis of the knee, with respect to pain relief, reduction of stiffness, and increased physical function during treatment; modifications in the consumption of diclofenac during treatment; and changes in the patient's quality of life.

Design: Randomised, controlled, single blind trial, with blinded evaluation and statistical analysis of results.

Setting: Pain management unit in a public primary care centre in southern Spain, over a period of two years.

[Prescription of drugs in family medicine: on the trail of efficiency].

Objective: To analyse the effect of various factors on the efficiency of drug prescription by general practitioners (GPs).

Design: Descriptive, cross-sectional study.

Setting: Primary care in Murcia, Cartagena, and Lorca, in which 535 GPs work in the care of 921,281 people.