The article describes the development of Membrane Builder, an automated web-based tool for constructing realistic protein/membrane complexes for molecular dynamics (MD) simulations. Membrane Builder is part of the CHARMM-GUI website and provides a graphical user interface (GUI) to help users build complex systems involving membrane proteins. The tool automates the process of system size determination, lipid bilayer generation, pore water, bulk water, and ion generation, allowing users to create realistic membrane systems in as little as 5 minutes to 2 hours depending on the system size. The tool is designed to be user-friendly, with default values that provide reasonable starting points for both non-expert and expert users. It supports two main methods for building membrane systems: the replacement method, which involves inserting a protein into a lipid bilayer, and the insertion method, which involves creating a hole in a pre-equilibrated lipid bilayer and inserting the protein into it. The tool has been tested with 12 transmembrane and 3 interfacial membrane proteins, and the resulting systems are available on the CHARMM-GUI website. The tool also includes a pore water generation method to ensure that water molecules are properly solvated in the transmembrane region of the protein. The article highlights the advantages of using Membrane Builder, including its ease of use, automation, and the ability to generate realistic membrane systems with minimal user intervention. The tool is particularly useful for researchers who are not experienced with MD simulation software, as it provides a intuitive and efficient way to build and simulate biologically important membrane systems. The article also discusses the limitations of the two main methods used in building membrane systems, and how Membrane Builder addresses these limitations through its automated and user-friendly approach. The tool has been tested with a variety of membrane proteins, and the results show that it is effective in generating realistic membrane systems that can be used for MD simulations. The article concludes with a discussion of the future development of Membrane Builder, including the addition of more lipid types and the incorporation of new simulation methods. Overall, the article highlights the importance of automated tools in the field of MD simulations, particularly for membrane proteins, and the benefits of using such tools for researchers who may not have extensive experience with simulation software.The article describes the development of Membrane Builder, an automated web-based tool for constructing realistic protein/membrane complexes for molecular dynamics (MD) simulations. Membrane Builder is part of the CHARMM-GUI website and provides a graphical user interface (GUI) to help users build complex systems involving membrane proteins. The tool automates the process of system size determination, lipid bilayer generation, pore water, bulk water, and ion generation, allowing users to create realistic membrane systems in as little as 5 minutes to 2 hours depending on the system size. The tool is designed to be user-friendly, with default values that provide reasonable starting points for both non-expert and expert users. It supports two main methods for building membrane systems: the replacement method, which involves inserting a protein into a lipid bilayer, and the insertion method, which involves creating a hole in a pre-equilibrated lipid bilayer and inserting the protein into it. The tool has been tested with 12 transmembrane and 3 interfacial membrane proteins, and the resulting systems are available on the CHARMM-GUI website. The tool also includes a pore water generation method to ensure that water molecules are properly solvated in the transmembrane region of the protein. The article highlights the advantages of using Membrane Builder, including its ease of use, automation, and the ability to generate realistic membrane systems with minimal user intervention. The tool is particularly useful for researchers who are not experienced with MD simulation software, as it provides a intuitive and efficient way to build and simulate biologically important membrane systems. The article also discusses the limitations of the two main methods used in building membrane systems, and how Membrane Builder addresses these limitations through its automated and user-friendly approach. The tool has been tested with a variety of membrane proteins, and the results show that it is effective in generating realistic membrane systems that can be used for MD simulations. The article concludes with a discussion of the future development of Membrane Builder, including the addition of more lipid types and the incorporation of new simulation methods. Overall, the article highlights the importance of automated tools in the field of MD simulations, particularly for membrane proteins, and the benefits of using such tools for researchers who may not have extensive experience with simulation software.