.png){kind=icon}
.png){kind=icon}
Return
iMODS: internal coordinates normal mode analysis server
.png){kind=icon}
OA
AI
DOI：10.1093/nar/gku339.png)
.png){kind=icon}
.png){kind=icon}
Share.png){kind=icon}
Save
Abstract
En 中文
Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends its applicability while implicitly maintaining stereochemistry. Vibrational analysis, motion animations and morphing trajectories can be easily carried out at different resolution scales almost interactively. The server is versatile; non-specialists can rapidly characterize potential conformational changes, whereas advanced users can customize the model resolution with multiple coarse-grained atomic representations and elastic network potentials. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. The generated all-heavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies.
Keywords:
ELASTIC NETWORK MODELS
CONFORMATIONAL TRANSITIONS
ALLOSTERIC MECHANISM
PROTEIN FLEXIBILITY
MOLECULAR-DYNAMICS
CHAPERONIN GROEL
CALCIUM-PUMP
MOTIONS
SIMULATIONS
COMPLEXES
AI Summary
Key information extracted from the uploaded paper, including a brief overview, abstract, background, key highlights, visual analysis, and future outlook.
Journal
IF:
13.1
Papers:
3.6W
Citations:
29.0W