Fast and Flexible Geometric Method For Enhancing MC Sampling of Compact   Configurations For Protein Docking Problem
  EASAL (Efficient Atlasing and Sampling of Assembly Landscapes) is a geometric method for sampling and computing integrals over the potential energy landscape of small molecular assemblies. EASAL's efficiency arises from the fact that small assembly landscapes permit the use of so-called Cayley (inter-atomic distance based) parameters for geometric representation and sampling of the assembly configuration space regions; this results in their isolation, convexification, customized sampling and systematic traversal using a comprehensive topological roadmap.   We define custom-designed measurements to investigate and compare various sampling characteristics of EASAL and the traditional Monte Carlo (MC) sampling, including (i) sampling speed, (ii) efficiency and accuracy of uniform grid coverage, (iii) accuracy of weighted coverage at covering low energy regions, (iv) ability to localize sampling to macrostates, and (v) flexibility in sampling distributions.   In particular, we compare the sampling characteristics of EASAL and MC in sampling the assembly landscape of 2 trans-membrane helices, with short-range pair-potentials. We demonstrate that EASAL provides a reasonable coverage of crucial but narrow regions of the energy landscape of low effective dimension, with much fewer samples and computational resources than MC sampling. Promising avenues for combining the complementary advantages of the two methods are discussed. 
Aysegul Ozkan, Jose C. Flores-Canales, Rahul Prabhu, Meera Sitharam,   Maria Kurnikova
physics.chem-ph physics.bio-ph