SAXS Data Analysis with BILBOMD

About this Application

BILBOMD allows you to determine the three-dimensional domain structure of proteins based on conformational sampling using a molecular dynamics (MD) approach. Conformational sampling is followed by structure validation using FoXS and ensemble analysis using Minimal Ensemble Search (MES).

Pelikan M, Hura GL, Hammel M. "Structure and flexibility within proteins as identified through small angle X-ray scattering." Gen Physiol Biophys. 2009 Jun;28(2):174-89link out

Instructions

Start a job by filling out this form.

First name your BILBOMD run in the title field. This will help you keep track of multiple runs. Input your PDB segments, one chain at a time. Make sure each segment is complete and is not missing any loops or tails.

The const.inp file is required. You can either upload one or use our interactive const.inp file creation tool. Hit the 'Create const.inp FIle' button and fill out the form defining which regions of your PDB chains you want to hold rigid and which regions you want to allow flexibility. Each Domain block will be held together as one rigid body which moves independently of other domains. Multiple sections within a domain will allow you to exclude flexible loops from the rigid body. As you fill out the const.inp form, a cartoon representation of your simulation will become visible.

Upload your experimental X-ray scattering profile. Define the Max q value in units of inverse Angstroms (Å -1) (This cannot be higher than the maximal q of your experimental data).

The Length of Conformational Sampling defines the number of simulated confirmations produced for each Rg step. The higher the number, the longer the run will take.

(1 = 200 conformations per Rg value)
(2 = 400 conformations per Rg value)
(3 = 600 conformations per Rg value)
(4 = 800 conformations per Rg value)

Define the range of Rg values you wish to explore in your MD simulation. If you are unsure, start with the experimental Rg in the center of your range.

Add your email to be notified when your job is complete and download your results.

If you have recently submitted multiple jobs, you can go here to check their status of all your recent jobs.