Table S4. Representative data structures stored in the MongoDB analysis subsystem.
Examples correspond to NAFlex_DDD_bsc1 simulation (Drew Dickerson dodecamer). Analysis correspond to fragments labelled at position 5.
{ _id: ‘NAFlex_DDD_bsc1’, dataset: ‘ParmBSC1’, NucType: ‘DNA’, moleculeType: ‘Dna’, SubType: ‘B’, PDB: ‘1naj’, sequence: ‘CGCGAATTCGCG’, rev_sequence: ‘CGCGAATTCGCG’, Parts: ‘DNA+iones’, Chains: ‘duplex’, soluteResidues: 24, soluteAtoms: 758, soluteCharge: -22, CounterIons: ‘Na+’, IonicConcentration: ‘Electroneutrality’, totalIons: 0, totalAtoms: 758, AdditionalSolvent: ‘No’, solventResidues: 0, solventAtoms: 0, totalResidues: 24, AdditionalMolecules: ‘No’, Ligands: ‘No’, AdditionalIons: ‘No’, IonsParameters: ‘Dang’, ionsModel: ‘-’, Water: ‘TIP3P’, Author: ‘P.D.’, Temperature: 298, forceField: ‘parmbsc0’, date: ‘06/23/15’, saltConcentration: 0, totalCharge: -22, time: 10000, Format: ‘netcdf’, FrameStep: ‘20ps’, Frames: 500000, Trajectory: ‘DDD10micros_nowat.nc’, Topology: ‘DDD10micros_nowat.prmtop’, RMSd_avg: 1.734, RMSd_stdev: 0.368, Comments: , ontology: [‘101’,’202’,’301’,’401’,’502’,’703’, ’80102’,’80202’,’80301’,‘80401’, ‘80501’, ‘80601’], description: ‘DNA-B|Duplex|Naked|DDD|ParmBSC1|TIP3P|Electroneutral’ } // Analyses at base level (5-A) { _id: {frame: 0,idSim: ‘NAFlex_DDD_bsc1’,idGroup: ‘A’,nGroup: 5}, CURVES: { backbone_torsions: { BI_population: [82.26], canonical_alpha_gamma: [97.22], puckering: [4.34,6.64,88.96,0.06] } }, NMR_JC: { J1p2p-DNA: [10.011,1.764], J1p2pp-DNA: [5.213,1.430], J2p3p-DNA: [6.309,0.999], J2pp3p-DNA: [2.276,1.734], J3p4p-DNA: [1.883,1.693] }, NMR_NOE: { H1p-H2p: [3.0252,0.0806], H1p-H2pp: [2.3772,0.1157], H2p-H3p: [2.3771,0.1072], H2p-H4p: [3.7905,0.0933], H2pp-H3p: [2.7312,0.1112], H2pp-H4p: [3.9616,0.3060], H3p-H4p: [2.7804,0.1090], H1p-H4p: [3.1969,0.2762], H1p-H3p: [3.7813,0.1239], H1p-H8: [3.5212,0.6081], H2p-H8: [3.6553,0.5865], H2pp-H8: [2.4727,0.4316], H3p-H8: [4.6430,0.4418], H4p-H8: [5.7722,0.6122] } } // Analyses at base pair level (5 – AT) { _id: {frame: 0,idSim: ‘NAFlex_DDD_bsc1’,idGroup: ‘AT’,nGroup: 5}, CURVES: { axis_bp: { inclin_avg: [3.44,4.6], xdisp_avg: [-0.96,0.7], ydisp_avg: [0.14,0.5] }, helical_bp: { buckle_avg: [5.62,10.2], opening_avg: [1.87,5.4], propel_avg: [-14.99,7.7], shear_avg: [0.14,0.4], stagger_avg: [-0.01,0.4], stretch_avg: [0.03,0.1] } } } // Analyses at base-pair step level (5 – AATT) { _id: {frame: 0,’idSim: ‘NAFlex_DDD_bsc1’,idGroup: ‘AATT’,nGroup: 5}, CURVES: { grooves: { majd_avg: [5.71,1.4], majw_avg: [11.93,1.6], mind_avg: [4.95,0.7], minw_avg: [5.22,1.4] }, helical_bpstep: { rise_avg: [3.37,0.3], roll_avg: [1.21,5], shift_avg: [-0.27,0.6], slide_avg: [-0.48,0.5], tilt_avg: [-2.38,4], twist_avg: [36.35,4.6] } }, STACKING: { stW: [-7.1088648,0.982759350869257], stC: [-1.43531339999999,0.731727353308896], HB: [-11.045809,1.11398008443553] } }, STIFFNESS: { FORCE_CTES: { PROD: [0.01606], MAT: [ 2.31756, 0, 0, 0.00173, 0, 0, 0, 5.57878, 2.97746, 0, -0.01652, -0.20697, 0, 2.97747, 11.11783, 0, 0.04616, -0.16052, 0.00173, 0, 0, 0.04624, 0, 0, 0, -0.01652, 0.04616, 0, 0.03597, 0.0064, 0, -0.20696, -0.16051, 0, 0.0064, 0.06717 ], rise_avg: [11.11783], roll_avg: [0.03597], shift_avg: [2.31756], slide_avg: [5.57878], tilt_avg: [0.04624], twist_avg: [0.06717] } } }