DNA & RNA Structure and Helical Parameters Analyses (NAFlex)
----Tutorial 2 -- Global analysis (XCGY)
Tutorial 3 -- Meta-trajectory (XCGY)
Tutorial 4 -- Experimental vs MD analysis
----All trajectory data submitted to BIGNASim needs to be accompanied by its metadata. It can be easily generated through the web site forms, following the standard deposition procedure. However, a more authomatic way to produce such information is also made available though the use of metadata files. They are CSV files composed by:
The list of accepted tags are the following:
datasetName | Acronim for a dataset which groups one or several trajectory files. Format: alphanumeric chain of 4>length>7 |
datasetDescription | Short title or description for the dataset |
publDateSys | Method to define the dataset publication date. Options are "release": submitted data will be made public immediately after validation, "hold": data will be on-hold until [publDate] is reached |
publDate | Date on which submitted data will be release given [publDateSys]="hold". Format: yyy/mm/dd |
pubSys | Method to define how the dataset reference publication is given. Options are "document": the dataset is referenced by uploaded files. "reference": the dataset is referenced by a public study. [pubTitle], [pubAuth], [pubJourn], [pubYear], [pubVol] and [pubDOI] require to be specified |
pubTitle | Title of the dataset reference publication. Mantadory if [pubSys]="reference" |
pubAuth | List of authors (comma separated) if the dataset reference publication. Mantadory if [pubSys]="reference" |
pubJourn | Journal where the dataset reference publication is published. Mantadory if [pubSys]="reference" |
pubYear | Year of the dataset reference publication year. Mantadory if [pubSys]="reference" |
pubVol | Volume of the Journal where the dataset reference publication is published. Mantadory if [pubSys]="reference" |
pubDOI | DOI identifier for the the dataset reference publication. Mantadory if [pubSys]="reference" |
trajFormat | Format of the trajectory file uploaded. Options are "traj_crd": AMBER CRD, "traj_dcd": CHARMM/NAMD DCD, "traj_cdf": AMBER NetCDF, "traj_gro": AMBER BINPOS, "traj_xtc": Gromacs XTC. |
topFormat | Format of the topology file uploaded. Options are "top_pdb": PDB, "top_prmtop": AMBER PRMTOP, "top_psf": NAMD PSF, "top_top": GROMACS TOPi, "top_itp": GROMACS ITP, "top_rtp": GROMACS RTP |
PDB | Protein Data Bank identifier for the reference experimental structure of the trajectory |
NDB | Nucleic Data Bank identifier for the reference experimental structure of the trajectory |
ligandNames | Comma separated list of ligands included in the trajectory |
additionalSolvent | Comma separated list of additional solvent molecules of the trajectory |
counterions | Comma separated list of counterions molecules and their concentrations |
trajLength | Total trajectory length in nanoseconds. If the trajectory is splitted into multiple files, the sum of them. |
frames | Number of frames |
frameStep | Time step taken between frames in nanoseconds |
trajTemperature | Trajectory temperature in kelvin degrees |
comments | Any comment valuable for the submission that may help to the correct classification of the data |
rmsd | all-heavy atoms mass weighted RMSD (%) |
rmsd_bp | all-heavy atoms mass weighted RMSD per base pair (%/bp) |
Rgyr | Radius of gyration (%/bp) |
lostWC | Percentage of lost Watson and Crick bonds |
lostContacts | Percentage of lost 3D contacts |
fraying | Presence of fraying. Options are "yes", "no" |
avgTwist | Global average Twist (degrees) |
avgRoll | Global average Roll (degrees) |
minorGrooveSize | Minor groove dimensions . Format: width x depth |
majorGrooveSize | Major groove dimensions . Format: width x depth |
grooveSizeMethod | Method use to compute the groove dimensions |