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PLOS statement on recent US Executive Orders

February 27, 2025

PLOS statement on recent US Executive Orders

PLOS remains committed to the principles of open science: integrity, transparency, inclusivity, and collaboration. Read more on our blog.

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08/11/2025

research article

Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics

The authors present an approach that integrates AI with cryo-EM density-guided simulations to fit ligands into experimental maps. Using three inputs: 1) a protein amino acid sequence, 2) a ligand specification, and 3) an experimental cryo-EM map, they validated the approach on a set of biomedically relevant protein-ligand complexes including kinases, GPCRs, and solute transporters.

Image credit: Haloi, Howard, Lindahl

Cryo-EM ligand building using AlphaFold3-like model and molecular dynamics

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Current Issue July 2025

08/05/2025

research article

COEXIST: Coordinated single-cell integration of serial multiplexed tissue images

The authors developed COEXIST, a computational algorithm that combines shared molecular profiles with spatial information to match cells across serial sections, enabling more complete and accurate tissue profiling. COEXIST improves MTI utility, enhances single-cell resolution, and offers opportunities for integrating MTI with spatial transcriptomics for deeper biological insight.

Image credit: Heussner et al

COEXIST: Coordinated single-cell integration of serial multiplexed tissue images

08/04/2025

research article

Mutations in tumor signaling, metastases, and synthetic lethality establish distinct patterns

The authors developed a framework to discover mutations that co-exist in different oncoproteins, and those that are excluded, likely encoding oncogene-induced senescence. First, mapping the proteins onto pathways assists combinatorial drug selections and helps to detect metastases. Second, it provides the molecular basis for synthetic lethality, to date investigated at the genome level.

Image credit: Yavuz et al

Mutations in tumor signaling, metastases, and synthetic lethality establish distinct patterns

07/18/2025

Education

Ten simple rules for navigating AI in science

It can be hard to navigate the vast body of literature surrounding AI techniques and the latest developments. As scientists using AI in diverse fields, from plant biology to neuroscience and physics, the authors have faced these and similar questions over the years. In this paper, they share some of the key aspects of their learning journeys.

Ten simple rules for navigating AI in science

Image credit: Crilly et al

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