Controlled-advancement rigid-body optimization of nanosystems

Petr Popov, Sergei Grudinin, Andrii Kurdiuk, Pavel Buslaev, Stephane Redon

    Research output: Contribution to journalArticlepeer-review

    Abstract

    In this study, we propose a novel optimization algorithm, with application to the refinement of molecular complexes. Particularly, we consider optimization problem as the calculation of quasi-static trajectories of rigid bodies influenced by the inverse-inertia-weighted energy gradient and introduce the concept of advancement region that guarantees displacement of a molecule strictly within a relevant region of conformational space. The advancement region helps to avoid typical energy minimization pitfalls, thus, the algorithm is suitable to work with arbitrary energy functions and arbitrary types of molecular complexes without necessary tuning of its hyper-parameters. Our method, called controlled-advancement rigid-body optimization of nanosystems (Carbon), is particularly useful for the large-scale molecular refinement, as for example, the putative binding candidates obtained with protein–protein docking pipelines. Implementation of Carbon with user-friendly interface is available in the SAMSON platform for molecular modeling at https://www.samson-connect.net.

    Original languageEnglish
    Pages (from-to)2391-2399
    Number of pages9
    JournalJournal of Computational Chemistry
    Volume40
    Issue number27
    DOIs
    Publication statusPublished - 15 Oct 2019

    Keywords

    • energy landscape
    • molecular docking
    • rigid-body modeling
    • structural optimization

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