Unraveling the effect of defects, domain size, and chemical doping on photophysics and charge transport in covalent organic frameworks.

Understanding the underlying physical mechanisms that govern charge transport in two-dimensional (2D) covalent organic frameworks (COFs) will facilitate the development of novel COF-based devices for optoelectronic and thermoelectric applications. In this context, the low-energy mid-infrared absorption contains valuable information about the structure-property relationships and the extent of intra- and inter-framework "hole" polaron delocalization in doped and undoped polymeric materials. In this study, we provide a quantitative characterization of the intricate interplay between electronic defects, domain sizes, pore volumes, chemical dopants, and three dimensional anisotropic charge migration in 2D COFs.

Social network analysis and whole-genome sequencing to evaluate disease transmission in a large, dynamic population: A study of avian mycobacteriosis in zoo birds.

This study combined a social network analysis and whole-genome sequencing (WGS) to test for general patterns of contagious spread of a mycobacterial infection for which pathways of disease acquisition are not well understood. Our population included 275 cases diagnosed with avian mycobacteriosis that were nested in a source population of 16,430 birds at San Diego Zoo Wildlife Alliance facilities from 1992 through mid-2014. Mycobacteria species were determined using conventional methods and whole genome sequencing (WGS).

Targeting a cell surface vitamin D receptor on tumor-associated macrophages in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is an aggressive tumor with limited treatment options and poor prognosis. We applied the in vivo phage display technology to isolate peptides homing to the immunosuppressive cellular microenvironment of TNBC as a strategy for non-malignant target discovery. We identified a cyclic peptide (CSSTRESAC) that specifically binds to a vitamin D receptor, protein disulfide-isomerase A3 (PDIA3) expressed on the cell surface of tumor-associated macrophages (TAM), and targets breast cancer in syngeneic TNBC, non-TNBC xenograft, and transgenic mouse models.

Assessing the Accuracy of the SCAN Functional for Water through a Many-Body Analysis of the Adiabatic Connection Formula.

We present a systematic analysis of the accuracy of a series of SCANα functionals for water, with varying fractions (α) of exact exchange, which are constructed through the adiabatic connection formula. Our results indicate that all SCANα functionals exhibit substantial errors in the representation of the water 2-body energies. Importantly, the inclusion of exact exchange is found to have opposite effects on the ability of the SCANα functionals to describe the interaction energies of water clusters with 2-dimensional and 3-dimensional hydrogen-bonding arrangements.

Highly Accurate Many-Body Potentials for Simulations of NO in Water: Benchmarks, Development, and Validation.

Dinitrogen pentoxide (NO) is an important intermediate in the atmospheric chemistry of nitrogen oxides. Although there has been much research, the processes that govern the physical interactions between NO and water are still not fully understood at a molecular level. Gaining a quantitative insight from computer simulations requires going beyond the accuracy of classical force fields while accessing length scales and time scales that are out of reach for high-level quantum-chemical approaches.

3DBionotes COVID-19 edition.

Summary: The web platform 3DBionotes-WS integrates multiple web services and an interactive web viewer to provide a unified environment in which biological annotations can be analyzed in their structural context. Since the COVID-19 outbreak, new structural data from many viral proteins have been provided at a very fast pace. This effort includes many cryogenic electron microscopy (cryo-EM) studies, together with more traditional ones (X-rays, NMR), using several modeling approaches and complemented with structural predictions.

Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction.

The Protein Data Bank (PDB) was established in 1971 to archive three-dimensional (3D) structures of biological macromolecules as a public good. Fifty years later, the PDB is providing millions of data consumers around the world with open access to more than 175,000 experimentally determined structures of proteins and nucleic acids (DNA, RNA) and their complexes with one another and small-molecule ligands. PDB data users are working, teaching, and learning in fundamental biology, biomedicine, bioengineering, biotechnology, and energy sciences.

Modernized uniform representation of carbohydrate molecules in the Protein Data Bank.

Since 1971, the Protein Data Bank (PDB) has served as the single global archive for experimentally determined 3D structures of biological macromolecules made freely available to the global community according to the FAIR principles of Findability-Accessibility-Interoperability-Reusability. During the first 50 years of continuous PDB operations, standards for data representation have evolved to better represent rich and complex biological phenomena. Carbohydrate molecules present in more than 14,000 PDB structures have recently been reviewed and remediated to conform to a new standardized format.

From structure to the dynamic regulation of a molecular switch: A journey over 3 decades.

It is difficult to imagine where the signaling community would be today without the Protein Data Bank. This visionary resource, established in the 1970s, has been an essential partner for sharing information between academics and industry for over 3 decades. We describe here the history of our journey with the protein kinases using cAMP-dependent protein kinase as a prototype.

The Protein Data Bank Archive.

Protein Data Bank is the single worldwide archive of experimentally determined macromolecular structure data. Established in 1971 as the first open access data resource in biology, the PDB archive is managed by the worldwide Protein Data Bank (wwPDB) consortium which has four partners-the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.

Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK.

The quantum mechanics/molecular mechanics (QM/MM) approach is an essential and well-established tool in computational chemistry that has been widely applied in a myriad of biomolecular problems in the literature. In this publication, we report the integration of the QUantum Interaction Computational Kernel (QUICK) program as an engine to perform electronic structure calculations in QM/MM simulations with AMBER. This integration is available through either a file-based interface (FBI) or an application programming interface (API).

Magnetic resonance elastography biomarkers for detection of histologic alterations in nonalcoholic fatty liver disease in the absence of fibrosis.

Objectives: To investigate associations between histology and hepatic mechanical properties measured using multiparametric magnetic resonance elastography (MRE) in adults with known or suspected nonalcoholic fatty liver disease (NAFLD) without histologic fibrosis.

Methods: This was a retrospective analysis of 88 adults who underwent 3T MR exams including hepatic MRE and MR imaging to estimate proton density fat fraction (MRI-PDFF) within 180 days of liver biopsy. Associations between MRE mechanical properties (mean shear stiffness (|G*|) by 2D and 3D MRE, and storage modulus (G'), loss modulus (G″), wave attenuation (α), and damping ratio (ζ) by 3D MRE) and histologic, demographic and anthropometric data were assessed.

Relationship between Hydrogen-Bonding Motifs and the 1b Splitting in the X-ray Emission Spectrum of Liquid Water.

The split of the 1b peak observed in the X-ray emission (XE) spectrum of liquid water has been the focus of intense research. Although several hypotheses have been proposed to explain the origin of this split, a consensus has not yet been reached. Here, we introduce a novel theoretical/computation approach which, combining path-integral molecular dynamics simulations with the MB-pol model and time-dependent density functional theory calculations, predicts the 1b splitting in liquid water and not in crystalline ice, in agreement with the experimental observations.

Design and proof-of-concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain.

Unlabelled: Development of effective vaccines against Coronavirus Disease 2019 (COVID-19) is a global imperative. Rapid immunization of the world human population against a widespread, continually evolving, and highly pathogenic virus is an unprecedented challenge, and many different vaccine approaches are being pursued to meet this task. Engineered filamentous bacteriophage (phage) have unique potential in vaccine development due to their inherent immunogenicity, genetic plasticity, stability, cost-effectiveness for large-scale production, and proven safety profile in humans.

Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development.

The Protein Data Bank (PDB) is an international core data resource central to fundamental biology, biomedicine, bioenergy, and biotechnology/bioengineering. Now celebrating its 50th anniversary, the PDB houses >175,000 experimentally determined atomic structures of proteins, nucleic acids, and their complexes with one another and small molecules and drugs. The importance of three-dimensional (3D) biostructure information for research and education obtains from the intimate link between molecular form and function evident throughout biology.

Test, Trace, and Put on the Blockchain?: A Viewpoint Evaluating the Use of Decentralized Systems for Algorithmic Contact Tracing to Combat a Global Pandemic.

The enormous pressure of the increasing case numbers experienced during the COVID-19 pandemic has given rise to a variety of novel digital systems designed to provide solutions to unprecedented challenges in public health. The field of algorithmic contact tracing, in particular, an area of research that had previously received limited attention, has moved into the spotlight as a crucial factor in containing the pandemic. The use of digital tools to enable more robust and expedited contact tracing and notification, while maintaining privacy and trust in the data generated, is viewed as key to identifying chains of transmission and close contacts, and, consequently, to enabling effective case investigations.

Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank.

The Worldwide Protein Data Bank (wwPDB) has provided validation reports based on recommendations from community Validation Task Forces for structures in the PDB since 2013. To further enhance validation of small molecules as recommended from the 2016 Ligand Validation Workshop, wwPDB, Global Phasing Ltd., and the Noguchi Institute, recently formed a public/private partnership to incorporate some of their software tools into the wwPDB validation package.

Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a human microbiome.

N-Acetylneuraminic acid is the most abundant sialic acid (SA) in humans and is expressed as the terminal sugar on intestinal mucus glycans. Several pathogenic bacteria harvest and display host SA on their own surfaces to evade Siglec-mediated host immunity. While previous studies have identified bacterial enzymes associated with SA catabolism, no reported methods permit the selective labeling, tracking, and quantitation of SA-presenting microbes within complex multi-microbial systems.

Longitudinal shear stress response in human endothelial cells to atheroprone and atheroprotective conditions.

The two main blood flow patterns, namely, pulsatile shear (PS) prevalent in straight segments of arteries and oscillatory shear (OS) observed at branch points, are associated with atheroprotective (healthy) and atheroprone (unhealthy) vascular phenotypes, respectively. The effects of blood flow-induced shear stress on endothelial cells (ECs) and vascular health have generally been studied using human umbilical vein endothelial cells (HUVECs). While there are a few studies comparing the differential roles of PS and OS across different types of ECs at a single time point, there is a paucity of studies comparing the temporal responses between different EC types.

A Practical Guide to Metabolomics Software Development.

A growing number of software tools have been developed for metabolomics data processing and analysis. Many new tools are contributed by metabolomics practitioners who have limited prior experience with software development, and the tools are subsequently implemented by users with expertise that ranges from basic point-and-click data analysis to advanced coding. This Perspective is intended to introduce metabolomics software users and developers to important considerations that determine the overall impact of a publicly available tool within the scientific community.

Interactions of large T-Antigen (LT) protein of polyomaviruses with p53 unfold their cancerogenic potential.

Polyomaviruses such as Simian Virus 40 (SV40) and John Cunningham Virus (JCV) have been extensively studied for their potential role in aiding oncogenic transformation. One of the mechanisms through which they do this is by inactivating p53, a known tumor suppressor, through one of their viral proteins, large T-antigen (LT). However, these two viruses represent only a fraction of existing polyomaviruses.

High-performance macromolecular data delivery and visualization for the web. Corrigendum.

Two citations in the article by Sehnal et al. [(2020), Acta Cryst. D76, 1167-1173] are corrected.