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Lipid membrane simulation software tools

Molecular dynamics (MD) simulations have had a profound impact on studies of membrane proteins during past two decades, but the accuracy of MD simulations of membranes is limited by the quality of membrane models and the applied force fields.…
TSTMP
Dataset

TSTMP Target Selection for human TransMembrane Proteins

Helps the target selection of human transmembrane proteins for structural…

Helps the target selection of human transmembrane proteins for structural genomics projects. TSTMP was built by sorting out proteins from the human transmembrane proteome with known structure and…

CGenFF
Web
Desktop

CGenFF CHARMM General Force Field

Performs atom typing and assignment of parameters and charges by analogy in a…

Performs atom typing and assignment of parameters and charges by analogy in a fully automated fashion. The CGenFF atom typer uses a programmable decision tree. Assignment of bonded parameters is…

FATSLiM
Desktop

FATSLiM Fast Analysis Toolbox for Simulations of Lipid Membranes

Extracts physical properties from molecular dynamics (MD) simulations of…

Extracts physical properties from molecular dynamics (MD) simulations of membranes (with or without interacting proteins). As opposed to existing tools, FATSLiM relies on the calculation of normals…

TMFoldWeb
Web

TMFoldWeb

Predicts the topology of transmembrane proteins and sequence to structure…

Predicts the topology of transmembrane proteins and sequence to structure alignment. TMFoldWeb uses statistical potentials and utilizes topology filtering and a gapless threading algorithm. It ranks…

MEMBPLUGIN
Desktop

MEMBPLUGIN MEMBrane PLUGIN

A membrane analysis tool for molecular-dynamics simulations. MEMBPLUGIN is a…

A membrane analysis tool for molecular-dynamics simulations. MEMBPLUGIN is a collection of visual and command-line tools that can be run within the Visual Molecular Dynamics (VMD) environment to…

MemGen
Web

MemGen

A web app that is capable of setting up simulation systems of heterogenous…

A web app that is capable of setting up simulation systems of heterogenous lipid membranes. MemGen is not restricted to certain lipid force fields or lipid types, but instead builds membranes from…

GridMAT-MD
Desktop

GridMAT-MD Grid based Membrane Analysis Tool for use with Molecular Dynamics

Helps in the analysis of lipid bilayers from molecular dynamics simulations.…

Helps in the analysis of lipid bilayers from molecular dynamics simulations. GridMAT-MD can also account for proteins or small molecules within the headgroups of the lipids, closely approximating…

MemBuilder
Web

MemBuilder

A web app to automate and simplify the building process of heterogeneous lipid…

A web app to automate and simplify the building process of heterogeneous lipid bilayers as well as providing molecular topologies for included lipids based on both united and all-atom force fields.…

CHARMM-GUI…
Web

CHARMM-GUI Membrane Builder

Helps user to generate a series of CHARMM inputs necessary to build a…

Helps user to generate a series of CHARMM inputs necessary to build a protein/membrane complex for molecular dynamics simulations. CHARMM-GUI Membrane Builder helps a wide range of scientists who…

APL@Voro
Desktop

APL@Voro

Supports the process of analyzing membrane simulations. The values calculated…

Supports the process of analyzing membrane simulations. The values calculated on the geometric structures can be visualized in a user-friendly interactive environment and, then, plotted and exported…

Desmond
Desktop

Desmond

Provides a high-performance of molecular dynamics simulations. Desmond includes…

Provides a high-performance of molecular dynamics simulations. Desmond includes protein-ligand complexes, small molecules in mixed solvents, organic solids, and synthetic macromolecular complexes.…

Lipidbook
Dataset

Lipidbook

A public database for force-field parameters with a special emphasis on lipids,…

A public database for force-field parameters with a special emphasis on lipids, detergents and similar molecules that are of interest when simulating biological membrane systems. Lipidbook stores…

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