Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] aetx_v1_0.tar.gz(122769 Kbytes)|
|Manuscript Title: SLDMOL: A tool for the structural characterization of thermally disordered membrane proteins.|
|Authors: Joseph E. Curtis, Hailiang Zhang, Hirsh Nanda|
|Program title: SLDMOL|
|Catalogue identifier: AETX_v1_0|
Distribution format: tar.gz
|Journal reference: Comput. Phys. Commun. 185(2014)3010|
|Programming language: Python.|
|Operating system: 32- and 64-bit Linux (Ubuntu 10.04, Centos 5.6) and Mac OS X (10.7 - 10.9).|
|RAM: 1 GB|
|Keywords: Neutron reflectivity, X-ray reflectivity, Membrane proteins, Disordered proteins, Computer modeling.|
External routines: Python 2.6.5, numpy 1.4.0, scipy 0.8.0, Tcl 8.5, Tk 8.5, Mac installation requires Xcode 3 development tools.
Nature of problem:
Reflectivity is a powerful technique to study the conformation of biological molecules at surface and interfaces. Open source software that facilitates computational modeling and interpretation of experimental results in terms of detailed molecular structure is currently lacking.
SLDMOL takes one or an ensemble of atomistic configurations of proteins and compares them to 1-D scattering length density (SLD) profiles determined from reflectivity experiments. Protein structures can be generated independently (e.g. molecular dynamics simulations) or through the SASSIE software package. SLDMOL performs an optimization to determine which structure best fits the SLD profile. Structures can also be averaged either directly or through a Monte-Carlo weighting algorithm. Finally SLDMOL allows the modeling of reflectivity experiments through the in-silico selective deuteration of amino acids and the calculation of SLD profiles in a number of different aqueous solvent contrasts.
Varies depending on application. Typically 10 minutes to 24 hours depending on the number of structures to be evaluated.
|Disclaimer | ScienceDirect | CPC Journal | CPC | QUB|