Federica Battistini

Molecular Modeling and Bioinformatics, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain. 

federica.battistini@irbbarcelona.org

BioExcel’s webinar series continues with another webinar focused on entry level users. In this case, Federica Battistini is going to talk about nucleic acid flexibility and how it could be extracted and visualized using NAFlex web server. This is also the first BioExcel – Multiscale Complex Genomics joint webinar.

Nucleic acid polymers are highly flexible entities, undergoing many conformational alterations and their structural polymorphic nature depends on the sequence and on external environmental conditions or the presence of ligands.

Experimental studies and data available in the Protein Data Bank (PDB) provide conformational information and illustrate the variety of the possible structures, but they are limited in providing information regarding flexibility. In order to explore the sequence-dependent flexibility of DNA and the effect of external factors, atomistic molecular dynamics (MD) simulations are widely used1. As computer power increases and the reliability of force fields improve, more reliable information is derived from atomistic MD simulations. Such simulations have revealed the extent, and the complexity, of DNA movements and their tight coupling to the nature and dynamics of the environment. 

Here we present NAFlex2, a web tool designed to facilitate the use of nucleic acid simulation tools for newcomers to the field. The server allows the user to study the flexibility of nucleic acids, either isolated or bound to other molecules. The server offers a variety of methods to explore nucleic acid flexibility, a base-pair resolution mesoscopic model and atomistic molecular dynamics simulations with a wide variety of protocols and force fields3,4. The trajectories can be obtained by simulations, or imported externally5. In the latter case, NAFlex is directly connected with the MDWeb technology6. MDWeb allows the user to set up their own MD simulation, helps the user during all the setup and equilibration steps, providing all the input files required to launch the simulations. Finally, the trajectory obtained (and uploaded) can be visualized and analyzed directly in NAFlex server, using a large number of tools, including standard Cartesian analysis, essential dynamics, helical analysis, local and global stiffness, energy decomposition, principal components and in silico NMR spectra. The server is accessible free of charge from the mmb.irbbarcelona.org/NAFlex webpage, and is integrated in the Multiscale Complex Genomics Virtual Research Environment (MuG-VRE).

References:

  1. Dans P.D., et al. Multiscale simulation of DNA, Current Opinion in Structural Biology. 2016; 37, 29-45.
  2. Hospital A., et al. NAFlex: a web server for the study of nucleic acid flexibility. Nucleic Acids Research. 2013, 41.
  3. Dans P.D., et al. Long-timescale dynamics of the Drew–Dickerson dodecamer. Nucleic Acids Research. 2016;44(9),4052-4066.
  4. Ivani I., et al. Parmbsc1: a refined force field for DNA simulations. Nature Meth. 2016; 13, 55-58.
  5. Hospital A., et al, BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data . Nucleic Acids Res. 2016; 44 (D1): D272-D278.
  6. Hospital A., et al. MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics. 2012; 28(9),1278–1279.

Register for webinar

Title: NAFlex, a web server for the study of nucleic acid flexibility
Date: 20th July, 2017
Time: 13:00 UTC / 14:00 BST / 15:00 CEST

Please register at: https://attendee.gotowebinar.com/register/5357843579947824899
You will then receive an email with details of how you can connect to the webinar.

Discuss this webinar View slides on SlideShare Join Interest Group