ArticleJournal of the mechanics and physics of solids2015
Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations.
Article in Journal of the mechanics and physics of solids, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation.Journal of synchrotron radiation · 2019Article
- Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion.Journal of chemical information and modeling · 2018Article
- Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs.PLoS computational biology · 2015Article
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Authors and funding
3 authors.
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Abstract
Proteins operate and interact with partners by dynamically exchanging between functional substates of a conformational ensemble on a rugged free energy landscape. Understanding how these substates are linked by coordinated, collective motions requires exploring a high-dimensional space, which remains a tremendous challenge. While molecular dynamics simulations can provide atomically detailed insight into the dynamics, computational demands to adequately sample conformational ensembles of large biomolecules and their complexes often require tremendous resources. Kinematic models can provide high-level insights into conformational ensembles and molecular rigidity beyond the reach of molecular dynamics by reducing the dimensionality of the search space. Here, we model a protein as a kinematic linkage and present a new geometric method to characterize molecular rigidity from the constraint manifold
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