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

  title={NAFlex: a web server for the study of nucleic acid flexibility},
  author={Adam Hospital and Ignacio Faustino and Rosana Collepardo-Guevara and Carlos Gonz{\'a}lez and Josep Llu{\'i}s Gelp{\'i} and Modesto Orozco},
  journal={Nucleic Acids Research},
  pages={W47 - W55}
We present NAFlex, a new web tool to study the flexibility of nucleic acids, either isolated or bound to other molecules. The server allows the user to incorporate structures from protein data banks, completing gaps and removing structural inconsistencies. It is also possible to define canonical (average or sequence-adapted) nucleic acid structures using a variety of predefined internal libraries, as well to create specific nucleic acid conformations from the sequence. The server offers a… 

Figures from this paper

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data
The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata, and includes backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses.
The static and dynamic structural heterogeneities of B-DNA: extending Calladine–Dickerson rules
The analysis of the simulations, which contain instances of all tetranucleotide sequences, allow us to extend Calladine–Dickerson rules used for decades to interpret the average geometry of DNA, leading to a set of rules with quantitative predictive power that encompass nonlocal sequence-dependence and anharmonic fluctuations.
cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA
The cgDNA package can serve as a highly efficient tool for studying structural variations in B-form DNA over a wide range of sequences and is in reasonable agreement with the available experimental data.
cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA
cgDNAweb, which provides browser-based interactive visualization of the sequence-dependent ground states of double-stranded DNA molecules, as predicted by the underlying cgDNA coarse-grain rigid-base model of fragments with arbitrary sequence, is presented.
The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA.
This work explains the sequence-dependent BII propensity observed in RpY steps at the tetranucleotide level with the help of a previously undetected C-H···O contact between atoms belonging to adjacent bases.
How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition.
How accurate are accurate force-fields for B-DNA?
It is found that while not all theoretical simulations are equally reliable, those obtained using last generation of AMBER force-fields show predictive power in the multi-microsecond timescale and can be safely used to reproduce global structure of DNA duplexes and fine sequence-dependent details.
A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level
A new coarse grained method for the simulation of duplex DNA using a generalized multi-harmonic model that can represent any multi-normal distribution of helical parameters, thus avoiding caveats of current mesoscopic models for DNA simulation and representing a breakthrough in the field.
The structural impact of DNA mismatches
The structure and dynamics of all the transversion and transition mismatches in three different DNA environments have been characterized by molecular dynamics simulations and NMR spectroscopy. We


Chapter 1:Modelling Nucleic Acid Structure and Flexibility: From Atomic to Mesoscopic Scale
This chapter surveys some of the recent developments in coarse-grained modelling of nucleic acids and finds that the rigid base model is consistent with a local interaction pattern, while interactions in the rigid basepair model are visibly non-local, in agreement with earlier findings.
3DNALandscapes: a database for exploring the conformational features of DNA
3DNALandscapes, located at:, is a new database for exploring the conformational features of DNA, and in contrast to most structural databases, enables searches of conformational information across multiple structures.
Conformational analysis of nucleic acids revisited: Curves+
Curves+ is described, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic Acid structures, including those with up to four strands and with either canonical or modified bases and backbones, and which provides a full analysis of groove widths and depths.
FlexServ: an integrated tool for the analysis of protein flexibility
SUMMARY FlexServ is a web-based tool for the analysis of protein flexibility. The server incorporates powerful protocols for the coarse-grained determination of protein dynamics using different
Exploring polymorphisms in B-DNA helical conformations
An in-depth statistical analysis of a very large set of MD trajectories and also of experimental structures leads to very solid evidence of bimodality, and ways to improve mesoscopic models to account for this deviation from the elastic regime are suggested.
Simulating DNA at low resolution.
  • W. Olson
  • Biology
    Current opinion in structural biology
  • 1996
Towards a molecular dynamics consensus view of B-DNA flexibility
We present a systematic study of B-DNA flexibility in aqueous solution using long-scale molecular dynamics simulations with the two more recent versions of nucleic acids force fields (CHARMM27 and
The relative flexibility of B-DNA and A-RNA duplexes: database analysis.
An extensive analysis of structural databases is carried out to investigate the relative flexibility of B-DNA and A-RNA duplexes in crystal form, showing that DNA is generally more flexible, but for some distortions A- RNA is easier to deform.
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes.
A complete set of sequence-dependent empirical energy functions suitable for describing such behavior is extracted from the fluctuations and correlations of structural parameters in DNA-protein crystal complexes, providing useful stereochemical measures of the local base step movements operative in sequence-specific recognition and protein-induced deformations.