run of our simple local optimization algorithm. Sometimes it happens that the SA algorithm only finds a slightly worse solution compared to the maxent-stress algorithm. In this case we ignore the SA solution and only run the simple optimization algorithm.

Experiments {#sec:experiments}
===========

In this section we present a representative subset of our experiments and their results. To this end, we implemented our algorithm in C++ based on NetworKit [@staudtSM14], an open-source toolkit for graph algorithms and in particular interactive large-scale network analysis. We call our algorithm (for **M**axent-stress **O**ptimization of **Bi**omolecular models) and compare it with  [@more1997] (C/Fortran code) and  [@leung2009sdp] (compiled Matlab code), two of the very few publicly available established tools that can handle inexact inputs with intervals.

All experiments are done on a machine that has 256 GB of main memory and 2 sockets, each equipped with an 8-core Intel Xeon CPU E5-2680 clocked at 2.7 GHz (hyperthreading enabled). We compile our code with g++ version 4.8.1 and OpenMP 3.1. The MATLAB version installed on the system is MATLAB R2015a (8.5.0.197613) 64-bit.

Instances {#sub:exp-settings}
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To test the accuracy and efficiency of our approach in a real-world setting, we work on 10 proteins of different sizes 