###SASSIE-web Based Framework for Atomistic Modeling to Interpret AUC & Scattering Data
#####December 8, 2015
#####La Trobe Institute of Molecular Science, Melbourne, Australia
Molecular simulation is an important technique to analyze and interpret
molecular phenomena across many disciplines. Analytical ultracentrifugation (AUC) & Small-angle scattering (SAS) utilizing either X-ray or neutron sources are valuable methods to
characterize shape, interactions, and properties of many soft-matter
systems. Modeling of AUC & SAS data is typically done using analytical
functions and/or dummy-ball (DB) models. While these methods are simple,
they have proven to be quite robust and have allowed for a tremendous
expansion of these studies to a wide variety of systems.
Atomistic modeling can be used to interpret AUC & SAS data and inherently provides structural and
physical knowledge that are unavailable using analytical or DB models. In
additional, atomistic models can allow the use of experimental and
computational constraints on the data.
The goal of this one day introductory course is to use modern
simulation methods and software tools to predict and analyze AUC & small-angle
scattering data of soft-matter systems, focussing particularly on
biological systems. Participants will be familiarized with SASSIE, a
software framework designed to facility the use of atomistic modeling to
interpret scattering data. SASSIE-web, a product of the CCP-SAS
consortium, will be the primary tool used during the course.
The course will involves the completion of "labs" by the students.
Examples will involve various protein, dna, and their complexes.
The emphasis will be on ensemble molecular
simulation, calculation of AUC & scattering profiles and comparison to
experimental data.
---
###NOTE: Files to carry out the labs are no longer available below. Please see more recent courses for updated labs and files.
---
---
####Tuesday 12/8/2015
| Time | Lead | Activity | File
| ------------- |--------|-------|------|
| 8:30 - 9:00 AM | EHB | Software Installation and SASSIE-web | [lab_0.pdf](files/lab_0.pdf)
| 9:00 - 10:30 AM | EHB | Lab I: VMD and PDB Scan | [lab_I.pdf](files/lab_I.pdf)
| 10:30 - 11:00 AM | | **Break**
| 11:00 - 1:00 PM | EHB | Lab II: SASSIE-web Quick Start | [lab_II.pdf](files/lab_II.pdf)
| 1:00 - 2:00 PM | | **Lunch** |
| 2:00 - 3:45 PM | EHB | Lab III: SASSIE-web Advanced Monte Carlo & Simulation | [lab_III.pdf](files/lab_III.pdf)
| 3:45 - 4:15 PM | | **Break**
| 4:15 - 6:00 PM | EHB | Links to US-SOMO |
---
---
###[SASSIE-web: Quick Start](sassie-web-quick-start/quick-start.html)
###[How to Use Visual Molecular Dynamics (VMD)](vmd/vmd.html)
###[Build](http://sassie-web.chem.utk.edu/docs/build/build.html)
###[PDB Scan](build/pdbscan/pdbscan.html)
---
Go to top
