Best of Both Worlds: Uniform sampling in Cartesian and Cayley Molecular Assembly Configuration Space

Aysegul Ozkan; Meera Sitharam

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arXiv · 1409.0956

Best of Both Worlds: Uniform sampling in Cartesian and Cayley Molecular Assembly Configuration Space

Aysegul Ozkan·Meera Sitharam

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Abstract

EASAL (efficient atlasing and sampling of assembly landscapes) is a recently reported geometric method for representing, visualizing, sampling and computing integrals over the potential energy landscape tailored for small molecular assemblies. EASAL's efficiency arises from the fact that small assembly landscapes permit the use of so-called Cayley parameters (inter-atomic distances) 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, ensuring reasonable coverage of crucial but narrow regions of low effective dimension. However, this alone is inadequate for accurate computation of configurational entropy and other integrals, required for estimation of both free energy and kinetics - where it is essential to obtain uniform sampling in appropriate cartesian or moduli space parameterization. Standard adjustment of Cayley sampling via the Jacobian of the map between the two parameterizations is fraught with challenges stemming from an illconditioned Jacobian. This paper formalizes and analyzes these challenges to provide modifications to EASAL that secure the advantages of Cayley sampling while ensuring certain minimum distance and coverage relationships between sampled configurations - in Cartesian space. The modified EASAL's performance is compared with the basic EASAL and the data are presented for Human and Rat Islet Amylin Polypeptide (HiAPP, PDB-2KJ7 and RiAPP PDB-2KB8) dimerization (the two differ in only 6 out of 37 residues, but the former aggregates into fibrils, while the latter does not).

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Aysegul Ozkan, Meera Sitharam. 2014-09-03. Best of Both Worlds: Uniform sampling in Cartesian and Cayley Molecular Assembly Configuration Space. https://arxiv.org/abs/1409.0956

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