Motion planning algorithms for molecular simulations: a survey

DOI10.1016/J.COSREV.2012.07.002MaRDI QIDQ465699zbMATH OpenOpenAlexFDO

Authors Ibrahim Al-Bluwi, Thierry Siméon, Juan Cortés

Publication date 24 October 2014

Published in Computer Science Review (Search for Journal in Brave)

Full work available at URL https://hal.laas.fr/hal-01982596/file/12CSR_AlBluwi.pdf

zbMATH Keywords

motion planningmolecular simulationsprotein foldingprotein flexibilityprotein-ligand interactionssampling-based algorithms

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Systems biology, networks (92C42) Research exposition (monographs, survey articles) pertaining to biology (92-02) Computational methods for problems pertaining to biology (92-08)

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Cites work

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• Equation of state calculations by fast computing machines
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• Optimization by simulated annealing
• Planning Algorithms
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• Preprocessing chains for fast dihedral rotations is hard or even impossible.
• Principal component analysis.
• Rapidly-exploring random trees: Progress and prospects
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• The Art of Molecular Dynamics Simulation

Cited in

(4)

• Identification of probabilistic approaches and map-based navigation in motion planning for mobile robots
• A motion planning approach to studying molecular motions
• A survey of algorithms for transforming molecular dynamics data into metadata for \textit{in situ} analytics based on machine learning methods
• Efficient maintenance and self-collision testing for kinematic chains

Describes a project that uses

Uses Software

• OBBTree
• AutoDock

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