ArticleBio-protocol2021
Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom.
Article in Bio-protocol, 2021. 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.
- Collective interactions along recombinase-bound D-loops could speed repair of double-strand breaks by destabilizing flanking homoduplex tails.Nucleic acids research · 2026Article
- Plasticity and Co-Factor-Dependent Structural Changes in the RecA Nucleoprotein Filament Studied by Small-Angle X-Ray Scattering (SAXS) Measurements and Molecular Modeling.Molecules (Basel, Switzerland) · 2025Article
- Modeling the Homologous Recombination Process: Methods, Successes and Challenges.International journal of molecular sciences · 2023Review
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Protein filaments are dynamic entities that respond to external stimuli by slightly or substantially modifying the internal binding geometries between successive protomers. This results in overall changes in the filament architecture, which are difficult to model due to the helical character of the system. Here, we describe how distortions in RecA nucleofilaments and their consequences on the filament-DNA and bound DNA-DNA interactions at different stages of the homologous recombination process can be modeled using the PTools/Heligeom software and subsequent molecular dynamics simulation with NAMD. Modeling methods dealing with helical macromolecular objects typically rely on symmetric assemblies and take advantage of known symmetry descriptors. Other methods dealing with single objects, such as MMTK or VMD, do not integrate the specificities of regular assemblies. By basing the model building on binding geometries at the protomer-protomer level, PTools/Heligeom frees the building process from
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