Chemical Biology Gateways to Mapping Location, Association, and Pathway Responsivity

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Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

Protein–ligand interactions (PLIs) determine the efficacy and safety profiles of small molecule drugs. Existing methods rely on either structural information or resource-intensive computations to predict PLI, casting doubt on whether it is possible to perf ...

Cell-free biology is increasingly utilized for engineering biological systems, incorporating novel functionality, and circumventing many of the complications associated with cells. The central dogma describes the information flow in biology consisting of t ...

Motivation: Large-scale kinetic models are an invaluable tool to understand the dynamic and adaptive responses of biological systems. The development and application of these models have been limited by the availability of computational tools to build and ...

Protein stabilization has a crucial rule sustaining biological functionality, disease prevention, and pharmaceutical formulation stabilization, and yet its stabilization mechanism by small molecules such as amino acids is not fully understood. In this work ...

Increasing the protein production capacity of the PURE cell-free transcription-translation (TX-TL) system will be key to implementing complex synthetic biological circuits, and to establishing a fully self-regenerating system as a basis for the development ...

The beginning of the 21st century was marked by the advent of disruptive technologies, which ushered an era of groundbreaking advances in fundamental sciences, carried by the great pace at which computational capabilities spread and evolved. But the new ce ...

Posttranslational modifications (PTMs) of proteins play central roles in regulating the protein structure, interactome, and functions. A notable modification site is the aromatic side chain of Tyr, which undergoes modifications such as phosphorylation and ...

Neuroscience incorporates knowledge from a range of scales, from single molecules to brain wide neural networks. Modeling is a valuable tool in understanding processes at a single scale or the interactions between two adjacent scales and researchers use a ...

Modelling and analysis of biological systems is crucial in order to quantitatively explain and predict their behaviour. The importance of modelling in systems biology becomes even more evident when tackling complex, large systems. Approaches that rely on ...

Published by American Chemical Society.Controlling cellular shape with micropatterning extracellular matrix (ECM) proteins on hydrogels has been shown to improve the reproducibility of the cell structure, enhancing our ability to collect statistics on sing ...

Bacteria are ubiquitous single cellular organisms. Compared to eukaryotic cells, bacteria have two unique characteristics: the membrane-less nucleoid and the cell wall built of peptidoglycan (PG). In most bacteria, a single circular chromosome is compacted ...

Single-cell transcriptomics (scRNA-seq) started a technological revolution in biology by enabling through the plethora of methods to assess a molecular state of the cell on systems level without the strict necessity of the prior knowledge of the cell state ...

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

On January 22-24, 2020, scientific luminaries across the far-flung corners of chemical biology gathered in Geneva, Switzerland, to deliver their latest and greatest discoveries in the field. Generously supported by the Swiss National Science Foundation (SN ...

G-protein-coupled receptors (GPCRs) are key regulators of human physiology and are the targets of many small-molecule research compounds and therapeutic drugs. While most of these ligands bind to their target GPCR with high affinity, selectivity is often l ...

Transient associations between numerous organelles-e.g., the endoplasmic reticulum and the mitochondria-forge highly-coordinated, particular environments essential for cross-compartment information flow. Our perspective summarizes chemical-biology tools th ...

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of conserved network mot ...

A spinal cord injury (SCI) triggers a cascade of molecular and cellular responses involving inflammatory cell infiltration and cytokine release, apoptosis, demyelination, excitotoxicity, ischemia, and the formation of a fibrotic scar surrounded by an astro ...

Chemical Biology Gateways to Mapping Location, Association, and Pathway Responsivity

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Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

G–PLIP: Knowledge graph neural network for structure-free protein–ligand bioactivity prediction

Biochemistry of Aminoacyl tRNA Synthetase and tRNAs and Their Engineering for Cell-Free and Synthetic Cell Applications

Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models

Hydrophobic Interaction and its Small Molecule effect

Improved Cell-Free Transcription-Translation Reactions in Microfluidic Chemostats Augmented with Hydrogel Membranes for Continuous Small Molecule Dialysis

New and improved methods for integrated models of metabolism and gene expression

A Versatile Method for Site-Specific Chemical Installation of Aromatic Posttranslational Modification Analogs into Proteins

A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience

Modelling the Intracellular Environment under Uncertainty, from Post-translational Modification to Metabolic Networks

Cell Architecture and Dynamics of Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes (hiPSC-CMs) on Hydrogels with Spatially Patterned Laminin and N-Cadherin

Resolving bacterial cell biology: from replisome dynamics to cell wall synthesis

Developing new tools to study and program cell fate at the single-cell level

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Empowering Global Chemical Biology at the Dawn of the New Decade

Antibodies expand the scope of angiotensin receptor pharmacology

Neighborhood watch: tools for defining locale-dependent subproteomes and their contextual signaling activities

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

MPGM: Scalable and Accurate Multiple Network Alignment

Multimodal transcriptomic atlases of mouse spinal cord injury