Macromolecular modeling and design in Rosetta: recent methods and frameworks.

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities.

Releasing a preprint is associated with more attention and citations for the peer-reviewed article.

Preprints in biology are becoming more popular, but only a small fraction of the articles published in peer-reviewed journals have previously been released as preprints. To examine whether releasing a preprint on bioRxiv was associated with the attention and citations received by the corresponding peer-reviewed article, we assembled a dataset of 74,239 articles, 5,405 of which had a preprint, published in 39 journals. Using log-linear regression and random-effects meta-analysis, we found that articles with a preprint had, on average, a 49% higher Altmetric Attention Score and 36% more citations than articles without a preprint.

Cox regression increases power to detect genotype-phenotype associations in genomic studies using the electronic health record.

Background: The growth of DNA biobanks linked to data from electronic health records (EHRs) has enabled the discovery of numerous associations between genomic variants and clinical phenotypes. Nonetheless, although clinical data are generally longitudinal, standard approaches for detecting genotype-phenotype associations in such linked data, notably logistic regression, do not naturally account for variation in the period of follow-up or the time at which an event occurs. Here we explored the advantages of quantifying associations using Cox proportional hazards regression, which can account for the age at which a patient first visited the healthcare system (left truncation) and the age at which a patient either last visited the healthcare system or acquired a particular phenotype (right censoring).

Simphony: simulating large-scale, rhythmic data.

Simulated data are invaluable for assessing a computational method's ability to distinguish signal from noise. Although many biological systems show rhythmicity, there is no general-purpose tool to simulate large-scale, rhythmic data. Here we present Simphony, an R package for simulating data from experiments in which the abundances of rhythmic and non-rhythmic features (e.

Commonly used fluoroquinolones cross-react with urine drug screens for opiates, buprenorphine, and amphetamines.

Objectives: Fluoroquinolone antibiotics are commonly used in the treatment of infections and have previously been confirmed to cross-react with previous generations of opiates immunoassays. In this work we evaluated the cross-reactivity of the three fluoroquinolones in use at our institution with a panel of 10 urine drug screens.

Design And Methods: Drug preparations of levofloxacin, ciprofloxacin, and moxifloxacin that were designed for intravenous delivery were added to drug-free urine at varying concentrations.

RosettaLigandEnsemble: A Small-Molecule Ensemble-Driven Docking Approach.

RosettaLigand is a protein-small-molecule (ligand) docking software capable of predicting binding poses and is used for virtual screening of medium-sized ligand libraries. Structurally similar small molecules are generally found to bind in the same pose to one binding pocket, despite some prominent exceptions. To make use of this information, we have developed RosettaLigandEnsemble (RLE).

Predictive Power of Different Types of Experimental Restraints in Small Molecule Docking: A Review.

Incorporating experimental restraints is a powerful method of increasing accuracy in computational protein small molecule docking simulations. Different algorithms integrate distinct forms of biochemical data during the docking and/or scoring stages. These so-called hybrid methods make use of receptor-based information such as nuclear magnetic resonance (NMR) restraints or small molecule-based information such as structure-activity relationships (SARs).