NAFlex: a web server for the study of nucleic acid flexibility

Area of Science:

• Structural Biology
• Computational Biology
• Biophysics

Background:

• Understanding nucleic acid flexibility is crucial for biological processes.
• Existing tools may lack comprehensive features for analyzing nucleic acid dynamics.

Purpose of the Study:

• To introduce NAFlex, a versatile web server for studying nucleic acid flexibility.
• To provide a platform for incorporating, modeling, and analyzing nucleic acid structures.

Main Methods:

• Utilizes protein data bank structures, canonical structures, and user-defined conformations.
• Employs colorless wormlike-chain, mesoscopic, and atomistic molecular dynamics simulations.
• Offers extensive analysis tools including helical analysis, principal components, and in silico NMR spectra.

Main Results:

• NAFlex enables detailed exploration of nucleic acid flexibility in various contexts.
• The server integrates structure preparation, diverse simulation methods, and advanced analysis.
• Provides visualization and analysis of simulation trajectories and imported data.

Conclusions:

• NAFlex is a valuable, free resource for researchers studying nucleic acid dynamics.
• The tool facilitates a deeper understanding of nucleic acid structure-function relationships.
• Accessible via mmb.irbbarcelona.org/NAFlex, it supports isolated and bound nucleic acid studies.