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Related Concept Videos

The Significance of Membrane Transport01:44

The Significance of Membrane Transport

The transport of solutes across the cell membrane is essential for metabolic processes, like maintaining cell size and volume, generating the action potential, exchanging nutrients and gases, etc. Membrane transport can be either passive or active. It can be simple diffusion, facilitated, or mediated transport aided by transport proteins such as transporters and channels.
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Primary Active Transport

In contrast to passive transport, active transport involves a substance being moved through membranes in a direction against its concentration or electrochemical gradient. There are two types of active transport: primary active transport and secondary active transport. Primary active transport utilizes chemical energy from ATP to drive protein pumps embedded in the cell membrane. With energy from ATP, the pumps transport ions against their electrochemical gradients—a direction they would not...
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Cell membranes are composed of phospholipids, proteins, and carbohydrates loosely attached to one another through chemical interactions. Molecules are generally able to move about in the plane of the membrane, giving the membrane its flexible nature called fluidity. Two other features of the membrane contribute to membrane fluidity: the chemical structure of the phospholipids and the presence of cholesterol in the membrane.Fatty acids tails of phospholipids can be either saturated or...
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A Method for Determination and Simulation of Permeability and Diffusion in a 3D Tissue Model in a Membrane Insert System for Multi-well Plates
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A curated reference database of membrane-permeability annotations for biological dyes.

Bo Wang1, Binhao Li1, Zilong Yuan1

  • 1School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.

Scientific Data
|July 10, 2026
PubMed
Summary

DyePermDB is a new database standardizing membrane permeability information for 251 biological dyes. This resource integrates chemical structures and evidence for improved dye analysis and cell permeability studies.

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Area of Science:

  • Biochemistry
  • Chemical Biology
  • Bioinformatics

Background:

  • Cellular labeling, imaging, and functional assays rely heavily on fluorescent and chromogenic dyes.
  • Existing data on dye membrane permeability is fragmented and inconsistently documented.
  • A standardized resource is needed to consolidate this critical information.

Purpose of the Study:

  • To create DyePermDB, a curated dataset of 251 biologically relevant dyes.
  • To provide standardized chemical identifiers, literature-supported membrane permeability annotations, and structural information.
  • To address the gap in consistent and accessible dye membrane permeability data.

Main Methods:

  • Developed a two-level annotation framework for intrinsic permeability status and context-dependent permeability.
  • Integrated structured annotation fields for chemical form, evidence, localization, and conditions.
  • Standardized chemical structures using an RDKit-based workflow with quality control.
  • Organized data into four linked datasets: core annotations, structure validation, supplementary data, and cross-references.

Main Results:

  • Established DyePermDB with 251 dyes, including standard identifiers and permeability annotations.
  • Implemented a detailed annotation framework capturing nuanced permeability contexts.
  • Provided standardized structures with quality metadata for cheminformatics analysis.
  • Validated the dataset's internal classification signal using FP4 fingerprint analyses.

Conclusions:

  • DyePermDB offers a reusable resource for reviewing dye annotations and assessing structure quality.
  • The database facilitates computational studies on membrane permeability.
  • Integrating traceable evidence, standardized structures, and quality control enhances data reliability and usability.