Abstract
Loop regions in protein structures often have crucial roles, and they are much more variable in sequence and structure than other regions. In homology modeling, this leads to larger deviations from the homologous templates, and loop modeling of homology models remains an open problem. To address this issue, we have previously developed the DaReUS-Loop protocol, leading to significant improvement over existing methods. Here, a DaReUS-Loop web server is presented, providing an automated platform for modeling or remodeling loops in the context of homology models. This is the first web server accepting a protein with up to 20 loop regions, and modeling them all in parallel. It also provides a prediction confidence level that corresponds to the expected accuracy of the loops. DaReUS-Loop facilitates the analysis of the results through its interactive graphical interface and is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/DaReUS-Loop/.
Highlights
The original DaReUS-Loop protocol is based on modeling a single loop at a time: it requires an initial model and a single loop region, which is re-modeled
As shown in the flowchart, it is still based on considering a single loop region at a time, but it runs in parallel, predicting one loop while keeping the other loops constant
Results are reported on the common high confidence sub-set of loops that could be predicted by all the methods of the same class
Summary
Final energy minimisation were conducted using Gromacs 2018 [1], the CHARMM36m force field [2] and the steepest descent algorithm for 1000 steps. All bonds were constrained using the LINCS algorithm. The particle mesh Ewald algorithm was used to handle electrostatics with a 10 ̊A cutoff for the short-range part and a grid spacing of 1.2 ̊A for the long-range contribution in reciprocal space. The Verlet buffer scheme was used for non-bonded interactions, the neighbor list was updated every 20 steps
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