Coarse-grained modeling of antibodies from small-angle scattering profiles

D Corbett, M Hebditch, R Keeling, P Ke… - The Journal of …, 2017 - ACS Publications
… molecules have been interpreted using spherical models … -bead antibody model to determine
theoretical scattering profiles that … normalized profiles correspond to structure factor profiles

X-ray scattering and coarse-grained simulations for clustering and interactions of monoclonal antibodies at high concentrations

BJ Dear, JA Bollinger, A Chowdhury… - The Journal of …, 2019 - ACS Publications
… S eff (q)) with small-angle X-ray scattering (SAXS). The SAXS … on selected beads in
coarse-grained 12-bead models of the … space intensity profiles I(q) for the 12-bead model

Self-interactions of two monoclonal antibodies: small-angle X-ray scattering, light scattering, and coarse-grained modeling

S Mahapatra, M Polimeni, L Gentiluomo… - Molecular …, 2021 - ACS Publications
… accumulation on the antibody surface. By counting the average ion density in spherical
shells around the center of the simulation cell, we constructed the ion density profiles for PPI03 …

[HTML][HTML] Characterization of monoclonal antibody–protein antigen complexes using small-angle scattering and molecular modeling

MM Castellanos, JA Snyder, M Lee, S Chakravarthy… - Antibodies, 2017 - mdpi.com
… SAXS and detailed ensemble modeling is a viable method to characterize antibody–antigen …
symmetry allows a discrimination of scattering profiles for putative models. Furthermore, the …

Characterizing experimental monoclonal antibody interactions and clustering using a coarse-grained simulation library and a viscosity model

A Chowdhury, N Manohar, G Guruprasad… - The Journal of …, 2023 - ACS Publications
… from a library of coarse-grained molecular dynamics simulations. … for combining the viscosity
model and simulation library to … or structure factor from small-angle X-ray scattering. At low …

Coarse-grained antibody models for “weak” protein–protein interactions from low to high concentrations

C Calero-Rubio, A Saluja… - The Journal of Physical …, 2016 - ACS Publications
… to compute G 22 and Rayleigh scattering profiles (or osmotic compressibility) for proteins in
… other CG models and to more spatially detailed results (such as small-angle scattering) was …

Coarse-grained molecular dynamics simulations for understanding the impact of short-range anisotropic attractions on structure and viscosity of concentrated …

A Chowdhury, JA Bollinger, BJ Dear… - Molecular …, 2020 - ACS Publications
small-angle X-ray scattering experiments with those from molecular dynamics (MD) simulations.
The simulations, which utilize coarse-grained 12-bead models … (r) profiles are nearly …

Protein-protein interactions, clustering, and rheology for bovine IgG up to high concentrations characterized by small angle X-ray scattering and molecular dynamics …

A Chowdhury, G Guruprasad, AT Chen… - Journal of …, 2020 - Elsevier
… simulations of coarse-grained (CG) bead models that mimic … of antibody concentrations
modeled using a CG simulation … , 25 , 26 , 28 however, we describe the SAXS scattering profile

Electrostatically mediated protein-protein interactions for monoclonal antibodies: a combined experimental and coarse-grained molecular modeling approach

GM Ferreira, C Calero-Rubio, HA Sathish… - Journal of …, 2019 - Elsevier
… , this report employs coarse-grained (CG) molecular … these to PPI from experimental light
scattering measurements. The … (pI ∼5-6), and the profile of k D versus TIS is similar to that for …

Toward a suite of coarse-grained models for molecular simulation of monoclonal antibodies and therapeutic proteins

H Shahfar, JK Forder, CJ Roberts - The Journal of Physical …, 2021 - ACS Publications
… light scattering (SLS), dynamic light scattering, small-angle neutron scattering, X-ray scattering
The 1bC/D and DODECA models have similar profiles in Figure 6 as the models deal with …