Aug 2026· Journal of Open Source Software· Vol 11, pp. 9938· 0 citations· 20 references
TL;DR
DynDom1D_Python, an open-source Python implementation based on the original DynDom Fortran program for the analysis of domain movements in proteins, improves on the original standalone version in a number of ways.
Abstract
Here we introduce DynDom1D_Python, an open-source Python implementation based on the original DynDom Fortran program for the analysis of domain movements in proteins. DynDom works on a single protein chain and can be used when two structures of the same protein are available representing a conformational change. If appropriate, it describes the conformational change in terms of the relative rotation of quasi-rigid regions called “dynamic domains” by way of hinge axes (more precisely, interdomain screw axes) and hinge-bending residues (more precisely, interdomain bending residues). This new implementation improves on the original standalone version in a number of ways.
This method enables rapid and accurate identification of structural repeats by calculating the distance between Cα atoms in the peptide backbone by calculating the distance between Cα atoms in the peptide backbone.
Gurleen Kaur, Madhumathi Sanjeevi, Srimaha Gandhi et al.· Journal of Applied Crystallo...· 0 citations
Ruler is a local, browser-based tool that uses inter- residue distance measurements to quickly quantify atomic displacements and map changes in internal geometry across ensembles of related protein structures, enabling rapid identification of regions undergoing coordinated motion, local rearrangement, or large-scale co...
Timothy H. Baker, M. Ohi, W. Salmen· bioRxiv· 1 citation
RPDynaFlow is presented, a flow-matching model to generate conformation ensembles of RNA–protein complexes, trained on 600 ns trajectories of molecular dynamics simulation, which could be treated as a rapid and efficient complement to MD trajectories for studying RNA–protein interactions.
An improved force field is developed, derived from its parent, Amber ff24EXP-GA, and its evaluation against Amber ff14SB and other contemporary force fields, such as CHARMM36m, in capturing the empirically determined conformational properties of unfolded systems: short peptides that serve as model systems for IDPs, and...
This work proposes BackFlip-2: a fast SE(3)-equivariant graph neural network trained to directly predict dynamical descriptors, such as directional backbone flexibility and pairwise dynamic correlations, from an equilibrium structure, and shows that the proposed equivariant architecture is especially well-suited for ca...
Vsevolod Viliuga, Leif Seute, Matteo Tadiello et al.· 1 citation
NMR structural and dynamical characterization of a two-step walk through peptide sequence space is presented; from the (cid:2) N peptide sequence, which functions to activate transcription antitermination, to a peptide sequence that inhibits antitermination.
†. RyanJ.Austin, ‡. KarinA.Crowhurst, ‡. ScottA.Ross et al.· 0 citations
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