AllosMod: Modeling of Ligand-induced Protein Dynamics and Beyond

AllosMod is a web server to set up and run simulations based on a modeled energy landscape that you create. Carefully designed energy landscapes allow efficient molecular dynamics sampling at constant temperatures, thereby providing ergodic sampling of conformational space. Use AllosMod to:

• Model energy landscapes for protein, DNA, RNA, and/or sugar with either known or modeled structures
• Sample your energy landscapes to predict often and/or rarely populated conformations
• Model energy landscapes for ligand-induced structural and/or dynamic changes, i.e. allostery
• Model energy landscapes for glycosylated proteins (For help, click here)

The AllosMod server runs in two modes: 1) single landscape and 2) batch jobs to set up many simulations at once. By creating a single landscape, the server will create input files that can be used to submit batch jobs. AllosMod will set up many short simulations for each landscape. There are two types of sampling: 1) constant temperature molecular dynamics, which will be completed overnight on a single processor on the user's computer (using MODELLER) or 2) quick, unequilibrated simulations performed on our servers within minutes to hours. Sampling is achieved efficiently by starting each simulation at different points in conformational space and by storing the energies in memory.

AllosMod has several options for conformational sampling and contains tools for simulation analysis. For more details click on the "About AllosMod" link above and read the paper listed below.

***NEW*** The AllosMod server is integrated with the FoXS server for rigid body modeling of small angle X-ray scattering profiles. Our combined server is AllosMod-FoXS.