BioPipelines: Accessible Computational Protein and Ligand Design for Chemical Biologists | Computational and Structural Biotechnology Journal

spj.science.org

De novo chemo-optogenetics through the rational design of photoresponsive molecules and selection of their artificial protein binding pairs - Nature Chemistry

Optical manipulation of proteins is central to modulating and characterizing biomolecular functions in cell biology, but tools based on natural proteins are difficult to reconfigure for desired photoc...

nature.com

UZH: PhD Position in Redox Chemical Biology

We are a dynamic, interdisciplinary, medium-size lab working at the interface of chemistry and biology. We work on the development of probes to visualize and control biological processes in living sys...

jobs.uzh.ch

A locally activatable sensor for robust quantification of organellar glutathione - Nature Chemistry

Fluorescent sensors that are responsive only in a specific subcellular location have remained elusive. Now, a chemogenetic sensing platform has been developed to sense glutathione in a user-defined or...

nature.com

BioPipelines: Accessible Computational Protein and Ligand Design for Chemical Biologists

Deep learning methods for protein structure generation, sequence design, and structure and property prediction have created unprecedented opportunities for protein engineering and drug discovery. However, using these tools often requires navigating incompatible software environments, diverse input/output formats, and high-performance computing infrastructure, any of which may hinder adoption by primarily experimental chemical biology laboratories. Here we present BioPipelines, an open-source Python framework that allows researchers to define multi-step computational design workflows in a few lines of code. Additionally, its robust yet modular architecture provides a straightforward way to expand the toolkit with different functionalities, particularly by leveraging coding agents, with little effort. The framework currently integrates over 30 tools encompassing structure generation, sequence design, structure prediction, compound screening, and analysis. The same workflow code can be prototyped interactively in a Jupyter notebook and then submitted for production-scale runs without modification. We demonstrate applications in inverse folding, gene synthesis, de novo protein design, compound library screening, iterative binding site optimization, and fusion-protein linker optimization. We hope this framework will empower researchers, allowing them to focus on the scientific question rather than computational logistics. BioPipelines is available under the MIT license at https://github.com/locbp-uzh/biopipelines. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, https://ror.org/00yjd3n13, 200021-236456

biorxiv.org

Catalytic pKa Attenuation in a Hydrolytic Metalloenzyme by Genetic Code Expansion

Hydrolytic metalloenzymes employ Lewis-acidic metal cofactors to activate water molecules, generating nucleophilic hydroxide species that facilitate catalysis. Their catalytic efficiency across a wide...

doi.org

A Ratiometric pH Sensor for Gram-Positive and Gram-Negative Bacteria

Fluctuating environments can lead to phenotypic heterogeneity within a monoclonal bacterial population, especially in response to antibiotics or the human immune system. Methods are required to analyz...

pubs.acs.org

UZH: PhD Position in Redox Chemical Biology

We are a dynamic, interdisciplinary, medium-size lab working at the interface of chemistry and biology. We work on the development of probes to visualize and control biological processes in living sys...

jobs.uzh.ch

Profiling the proteome-wide selectivity of diverse electrophiles - Nature Chemistry

Covalent inhibitors are powerful entities in drug discovery. Now the amino acid selectivity and reactivity of a diverse electrophile library have been assessed proteome-wide using an unbiased workflow...

nature.com

Two‐Color Timestamping of Gene Expression with a Chemigenetic Reporter System

A chemigenetic reporter assay is developed that enables monitoring of BiP/GRP78 expression, an important chaperone and key regulator of the unfolded protein response. The system is based on the coexp....

chemistry-europe.onlinelibrary.wiley.com

Potent Inducers of Paraptosis through Electronic Tuning of Hemicyanine Electrophiles

Paraptosis is a distinct form of programmed cell death characterized by cytoplasmic vacuolization, mitochondrial swelling, and endoplasmic reticulum (ER) dilation, offering an alternative to apoptosis...

pubs.acs.org

Fluorescence Lifetime Multiplexing with Environment‐Sensitive Chemigenetic Probes

HaloTag (HT) is a versatile self-labeling protein that has been widely adopted in fluorescence microscopy. Besides its established use as an intensity-based marker and sensor, interest in using HT fo....

chemistry-europe.onlinelibrary.wiley.com

UZH: PhD position in Chemical Biology

In the Laboratory of Chemical and Biological probes (PI: Pablo Rivera Fuentes), we do research at the interface of chemistry and biology, particularly in the fields of redox biology, development of im...

jobs.uzh.ch

Characterization of the Glutathione Redox State in the Golgi Apparatus

Redox homeostasis is crucial for cell function, and, in eukaryotic cells, studying it in a compartmentalized way is essential due to the redox variati…

sciencedirect.com

Hydrophobic tuning with non-canonical amino acids in a copper metalloenzyme

Hydrophobicity controls many aspects of protein and enzyme function. Although hydrophobic tuning can be achieved to a limited extent with canonical amino acids, the incorporation of non- canonical ami...

biorxiv.org

Characterization of the Glutathione Redox State in the Golgi Apparatus

Redox homeostasis is crucial for cell function, and, in eukaryotic cells, studying it in a compartmentalized way is essential due to the redox variations between different organelles. The redox state ...

biorxiv.org