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SLDMOL: A Tool for the Structural Characterization of Thermally Disordered Membrane Proteins
Published
Author(s)
Joseph E. Curtis, Hailiang Zhang, Hirsh Nanda
Abstract
SLDMOL is a program for modeling the one-dimensional scattering length density (SLD) profile of proteins at the lipid membrane-solution interface or adsorbed to other surfaces. The program reads experimental SLD data from neutron or X-ray reflectivity measurements and compares the results to a trajectory of protein structures, finding the conformation and orientation that best fits the experimental data. SLDMOL is a freely distributed open source program written in python that can be run independently using command lines or with a GUI integrated in the larger SASSIE package. Sample environment conditions can be replicated including H2O/D2O solvent contrasts, specific amino acid deuteration and complex molecular assemblies. Ensembles of protein conformations can be generated independently (e.g. molecular dynamics simulations) or with SASSIE. For each individual structure a best-fit SLD profile is outputted along with a goodness of fit parameter, protein depth penetration and surface coverage. In addition to individual comparisons SLD profiles can be calculated over ensemble averages of protein structures. As a result SLDMOL provides a detailed molecular interpretation of reflectivity data or conversely can be used to predict experimental outcomes for different protein conformation and specific deuteration schemes prior to measurements.
Curtis, J.
, Zhang, H.
and , H.
(2014),
SLDMOL: A Tool for the Structural Characterization of Thermally Disordered Membrane Proteins, Computer Physics Communications, [online], https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=915263
(Accessed October 8, 2025)