Dataset statistics

The datasets used to train the binding affinity prediction models in RSAPred server are curated from the R-SIM database. A total of 2,501 RNA-small molecule pairs with experimentally measured binding affinity values were collected, consisting of 461 unique RNA targets and 1,288 unique small molecules. Among them, a subset of 1,480 datapoints with binding affinity values measured in terms of dissociation constant (Kd) were selected for model development, involving 341 unique RNA targets and 815 unique small molecules.

 

DATA DISTRIBUTIONS





Feature calculations

The features or descriptors to train the multivariate linear regression models were computed using RNA target sequence and small molecule 3D structure. The features which are part of the repRNA server and Mordred package were used to compute RNA-specific and small molecule-specific features, respectively. The list of all features computed for the RNA and small molecule are provided below. For more details on feature pruning and the feature selection procedure, please refer our associated publication. For a detailed description of each small molecule feature, please visit the Mordred documentation page.

 

Nucleotide composition-based features (Mono, Di, Tri, Tetra), Pseudo structure status composition, Pseudo dinucleotide composition, Triplet feature based on predicted secondary structure

ABC, ABCGG, nAcid, nBase, SpAbs_A, SpMax_A, SpDiam_A, SpAD_A, SpMAD_A, LogEE_A, VE1_A, VE2_A, VE3_A, VR1_A, VR2_A, VR3_A, nAromAtom, nAromBond, nAtom, nHeavyAtom, nSpiro, nBridgehead, nHetero, nH, nB, nC, nN, nO, nS, nP, nF, nCl, nBr, nI, nX, ATS0dv, ATS1dv, ATS2dv, ATS3dv, ATS4dv, ATS5dv, ATS6dv, ATS7dv, ATS8dv, ATS0d, ATS1d, ATS2d, ATS3d, ATS4d, ATS5d, ATS6d, ATS7d, ATS8d, ATS0s, ATS1s, ATS2s, ATS3s, ATS4s, ATS5s, ATS6s, ATS7s, ATS8s, ATS0Z, ATS1Z, ATS2Z, ATS3Z, ATS4Z, ATS5Z, ATS6Z, ATS7Z, ATS8Z, ATS0m, ATS1m, ATS2m, ATS3m, ATS4m, ATS5m, ATS6m, ATS7m, ATS8m, ATS0v, ATS1v, ATS2v, ATS3v, ATS4v, ATS5v, ATS6v, ATS7v, ATS8v, ATS0se, ATS1se, ATS2se, ATS3se, ATS4se, ATS5se, ATS6se, ATS7se, ATS8se, ATS0pe, ATS1pe, ATS2pe, ATS3pe, ATS4pe, ATS5pe, ATS6pe, ATS7pe, ATS8pe, ATS0are, ATS1are, ATS2are, ATS3are, ATS4are, ATS5are, ATS6are, ATS7are, ATS8are, ATS0p, ATS1p, ATS2p, ATS3p, ATS4p, ATS5p, ATS6p, ATS7p, ATS8p, ATS0i, ATS1i, ATS2i, ATS3i, ATS4i, ATS5i, ATS6i, ATS7i, ATS8i, AATS0dv, AATS1dv, AATS2dv, AATS3dv, AATS4dv, AATS5dv, AATS6dv, AATS7dv, AATS8dv, AATS0d, AATS1d, AATS2d, AATS3d, AATS4d, AATS5d, AATS6d, AATS7d, AATS8d, AATS0s, AATS1s, AATS2s, AATS3s, AATS4s, AATS5s, AATS6s, AATS7s, AATS8s, AATS0Z, AATS1Z, AATS2Z, AATS3Z, AATS4Z, AATS5Z, AATS6Z, AATS7Z, AATS8Z, AATS0m, AATS1m, AATS2m, AATS3m, AATS4m, AATS5m, AATS6m, AATS7m, AATS8m, AATS0v, AATS1v, AATS2v, AATS3v, AATS4v, AATS5v, AATS6v, AATS7v, AATS8v, AATS0se, AATS1se, AATS2se, AATS3se, AATS4se, AATS5se, AATS6se, AATS7se, AATS8se, AATS0pe, AATS1pe, AATS2pe, AATS3pe, AATS4pe, AATS5pe, AATS6pe, AATS7pe, AATS8pe, AATS0are, AATS1are, AATS2are, AATS3are, AATS4are, AATS5are, AATS6are, AATS7are, AATS8are, AATS0p, AATS1p, AATS2p, AATS3p, AATS4p, AATS5p, AATS6p, AATS7p, AATS8p, AATS0i, AATS1i, AATS2i, AATS3i, AATS4i, AATS5i, AATS6i, AATS7i, AATS8i, ATSC0c, ATSC1c, ATSC2c, ATSC3c, ATSC4c, ATSC5c, ATSC6c, ATSC7c, ATSC8c, ATSC0dv, ATSC1dv, ATSC2dv, ATSC3dv, ATSC4dv, ATSC5dv, ATSC6dv, ATSC7dv, ATSC8dv, ATSC0d, ATSC1d, ATSC2d, ATSC3d, ATSC4d, ATSC5d, ATSC6d, ATSC7d, ATSC8d, ATSC0s, ATSC1s, ATSC2s, ATSC3s, ATSC4s, ATSC5s, ATSC6s, ATSC7s, ATSC8s, ATSC0Z, ATSC1Z, ATSC2Z, ATSC3Z, ATSC4Z, ATSC5Z, ATSC6Z, ATSC7Z, ATSC8Z, ATSC0m, ATSC1m, ATSC2m, ATSC3m, ATSC4m, ATSC5m, ATSC6m, ATSC7m, ATSC8m, ATSC0v, ATSC1v, ATSC2v, ATSC3v, ATSC4v, ATSC5v, ATSC6v, ATSC7v, ATSC8v, ATSC0se, ATSC1se, ATSC2se, ATSC3se, ATSC4se, ATSC5se, ATSC6se, ATSC7se, ATSC8se, ATSC0pe, ATSC1pe, ATSC2pe, ATSC3pe, ATSC4pe, ATSC5pe, ATSC6pe, ATSC7pe, ATSC8pe, ATSC0are, ATSC1are, ATSC2are, ATSC3are, ATSC4are, ATSC5are, ATSC6are, ATSC7are, ATSC8are, ATSC0p, ATSC1p, ATSC2p, ATSC3p, ATSC4p, ATSC5p, ATSC6p, ATSC7p, ATSC8p, ATSC0i, ATSC1i, ATSC2i, ATSC3i, ATSC4i, ATSC5i, ATSC6i, ATSC7i, ATSC8i, AATSC0c, AATSC1c, AATSC2c, AATSC3c, AATSC4c, AATSC5c, AATSC6c, AATSC7c, AATSC8c, AATSC0dv, AATSC1dv, AATSC2dv, AATSC3dv, AATSC4dv, AATSC5dv, AATSC6dv, AATSC7dv, AATSC8dv, AATSC0d, AATSC1d, AATSC2d, AATSC3d, AATSC4d, AATSC5d, AATSC6d, AATSC7d, AATSC8d, AATSC0s, AATSC1s, AATSC2s, AATSC3s, AATSC4s, AATSC5s, AATSC6s, AATSC7s, AATSC8s, AATSC0Z, AATSC1Z, AATSC2Z, AATSC3Z, AATSC4Z, AATSC5Z, AATSC6Z, AATSC7Z, AATSC8Z, AATSC0m, AATSC1m, AATSC2m, AATSC3m, AATSC4m, AATSC5m, AATSC6m, AATSC7m, AATSC8m, AATSC0v, AATSC1v, AATSC2v, AATSC3v, AATSC4v, AATSC5v, AATSC6v, AATSC7v, AATSC8v, AATSC0se, AATSC1se, AATSC2se, AATSC3se, AATSC4se, AATSC5se, AATSC6se, AATSC7se, AATSC8se, AATSC0pe, AATSC1pe, AATSC2pe, AATSC3pe, AATSC4pe, AATSC5pe, AATSC6pe, AATSC7pe, AATSC8pe, AATSC0are, AATSC1are, AATSC2are, AATSC3are, AATSC4are, AATSC5are, AATSC6are, AATSC7are, AATSC8are, AATSC0p, AATSC1p, AATSC2p, AATSC3p, AATSC4p, AATSC5p, AATSC6p, AATSC7p, AATSC8p, AATSC0i, AATSC1i, AATSC2i, AATSC3i, AATSC4i, AATSC5i, AATSC6i, AATSC7i, AATSC8i, MATS1c, MATS2c, MATS3c, MATS4c, MATS5c, MATS6c, MATS7c, MATS8c, MATS1dv, MATS2dv, MATS3dv, MATS4dv, MATS5dv, MATS6dv, MATS7dv, MATS8dv, MATS1d, MATS2d, MATS3d, MATS4d, MATS5d, MATS6d, MATS7d, MATS8d, MATS1s, MATS2s, MATS3s, MATS4s, MATS5s, MATS6s, MATS7s, MATS8s, MATS1Z, MATS2Z, MATS3Z, MATS4Z, MATS5Z, MATS6Z, MATS7Z, MATS8Z, MATS1m, MATS2m, MATS3m, MATS4m, MATS5m, MATS6m, MATS7m, MATS8m, MATS1v, MATS2v, MATS3v, MATS4v, MATS5v, MATS6v, MATS7v, MATS8v, MATS1se, MATS2se, MATS3se, MATS4se, MATS5se, MATS6se, MATS7se, MATS8se, MATS1pe, MATS2pe, MATS3pe, MATS4pe, MATS5pe, MATS6pe, MATS7pe, MATS8pe, MATS1are, MATS2are, MATS3are, MATS4are, MATS5are, MATS6are, MATS7are, MATS8are, MATS1p, MATS2p, MATS3p, MATS4p, MATS5p, MATS6p, MATS7p, MATS8p, MATS1i, MATS2i, MATS3i, MATS4i, MATS5i, MATS6i, MATS7i, MATS8i, GATS1c, GATS2c, GATS3c, GATS4c, GATS5c, GATS6c, GATS7c, GATS8c, GATS1dv, GATS2dv, GATS3dv, GATS4dv, GATS5dv, GATS6dv, GATS7dv, GATS8dv, GATS1d, GATS2d, GATS3d, GATS4d, GATS5d, GATS6d, GATS7d, GATS8d, GATS1s, GATS2s, GATS3s, GATS4s, GATS5s, GATS6s, GATS7s, GATS8s, GATS1Z, GATS2Z, GATS3Z, GATS4Z, GATS5Z, GATS6Z, GATS7Z, GATS8Z, GATS1m, GATS2m, GATS3m, GATS4m, GATS5m, GATS6m, GATS7m, GATS8m, GATS1v, GATS2v, GATS3v, GATS4v, GATS5v, GATS6v, GATS7v, GATS8v, GATS1se, GATS2se, GATS3se, GATS4se, GATS5se, GATS6se, GATS7se, GATS8se, GATS1pe, GATS2pe, GATS3pe, GATS4pe, GATS5pe, GATS6pe, GATS7pe, GATS8pe, GATS1are, GATS2are, GATS3are, GATS4are, GATS5are, GATS6are, GATS7are, GATS8are, GATS1p, GATS2p, GATS3p, GATS4p, GATS5p, GATS6p, GATS7p, GATS8p, GATS1i, GATS2i, GATS3i, GATS4i, GATS5i, GATS6i, GATS7i, GATS8i, BCUTc-1h, BCUTc-1l, BCUTdv-1h, BCUTdv-1l, BCUTd-1h, BCUTd-1l, BCUTs-1h, BCUTs-1l, BCUTZ-1h, BCUTZ-1l, BCUTm-1h, BCUTm-1l, BCUTv-1h, BCUTv-1l, BCUTse-1h, BCUTse-1l, BCUTpe-1h, BCUTpe-1l, BCUTare-1h, BCUTare-1l, BCUTp-1h, BCUTp-1l, BCUTi-1h, BCUTi-1l, BalabanJ, SpAbs_DzZ, SpMax_DzZ, SpDiam_DzZ, SpAD_DzZ, SpMAD_DzZ, LogEE_DzZ, SM1_DzZ, VE1_DzZ, VE2_DzZ, VE3_DzZ, VR1_DzZ, VR2_DzZ, VR3_DzZ, SpAbs_Dzm, SpMax_Dzm, SpDiam_Dzm, SpAD_Dzm, SpMAD_Dzm, LogEE_Dzm, SM1_Dzm, VE1_Dzm, VE2_Dzm, VE3_Dzm, VR1_Dzm, VR2_Dzm, VR3_Dzm, SpAbs_Dzv, SpMax_Dzv, SpDiam_Dzv, SpAD_Dzv, SpMAD_Dzv, LogEE_Dzv, SM1_Dzv, VE1_Dzv, VE2_Dzv, VE3_Dzv, VR1_Dzv, VR2_Dzv, VR3_Dzv, SpAbs_Dzse, SpMax_Dzse, SpDiam_Dzse, SpAD_Dzse, SpMAD_Dzse, LogEE_Dzse, SM1_Dzse, VE1_Dzse, VE2_Dzse, VE3_Dzse, VR1_Dzse, VR2_Dzse, VR3_Dzse, SpAbs_Dzpe, SpMax_Dzpe, SpDiam_Dzpe, SpAD_Dzpe, SpMAD_Dzpe, LogEE_Dzpe, SM1_Dzpe, VE1_Dzpe, VE2_Dzpe, VE3_Dzpe, VR1_Dzpe, VR2_Dzpe, VR3_Dzpe, SpAbs_Dzare, SpMax_Dzare, SpDiam_Dzare, SpAD_Dzare, SpMAD_Dzare, LogEE_Dzare, SM1_Dzare, VE1_Dzare, VE2_Dzare, VE3_Dzare, VR1_Dzare, VR2_Dzare, VR3_Dzare, SpAbs_Dzp, SpMax_Dzp, SpDiam_Dzp, SpAD_Dzp, SpMAD_Dzp, LogEE_Dzp, SM1_Dzp, VE1_Dzp, VE2_Dzp, VE3_Dzp, VR1_Dzp, VR2_Dzp, VR3_Dzp, SpAbs_Dzi, SpMax_Dzi, SpDiam_Dzi, SpAD_Dzi, SpMAD_Dzi, LogEE_Dzi, SM1_Dzi, VE1_Dzi, VE2_Dzi, VE3_Dzi, VR1_Dzi, VR2_Dzi, VR3_Dzi, BertzCT, nBonds, nBondsO, nBondsS, nBondsD, nBondsT, nBondsA, nBondsM, nBondsKS, nBondsKD, PNSA1, PNSA2, PNSA3, PNSA4, PNSA5, PPSA1, PPSA2, PPSA3, PPSA4, PPSA5, DPSA1, DPSA2, DPSA3, DPSA4, DPSA5, FNSA1, FNSA2, FNSA3, FNSA4, FNSA5, FPSA1, FPSA2, FPSA3, FPSA4, FPSA5, WNSA1, WNSA2, WNSA3, WNSA4, WNSA5, WPSA1, WPSA2, WPSA3, WPSA4, WPSA5, RNCG, RPCG, RNCS, RPCS, TASA, TPSA, RASA, RPSA, C1SP1, C2SP1, C1SP2, C2SP2, C3SP2, C1SP3, C2SP3, C3SP3, C4SP3, HybRatio, FCSP3, Xch-3d, Xch-4d, Xch-5d, Xch-6d, Xch-7d, Xch-3dv, Xch-4dv, Xch-5dv, Xch-6dv, Xch-7dv, Xc-3d, Xc-4d, Xc-5d, Xc-6d, Xc-3dv, Xc-4dv, Xc-5dv, Xc-6dv, Xpc-4d, Xpc-5d, Xpc-6d, Xpc-4dv, Xpc-5dv, Xpc-6dv, Xp-0d, Xp-1d, Xp-2d, Xp-3d, Xp-4d, Xp-5d, Xp-6d, Xp-7d, AXp-0d, AXp-1d, AXp-2d, AXp-3d, AXp-4d, AXp-5d, AXp-6d, AXp-7d, Xp-0dv, Xp-1dv, Xp-2dv, Xp-3dv, Xp-4dv, Xp-5dv, Xp-6dv, Xp-7dv, AXp-0dv, AXp-1dv, AXp-2dv, AXp-3dv, AXp-4dv, AXp-5dv, AXp-6dv, AXp-7dv, SZ, Sm, Sv, Sse, Spe, Sare, Sp, Si, MZ, Mm, Mv, Mse, Mpe, Mare, Mp, Mi, SpAbs_Dt, SpMax_Dt, SpDiam_Dt, SpAD_Dt, SpMAD_Dt, LogEE_Dt, SM1_Dt, VE1_Dt, VE2_Dt, VE3_Dt, VR1_Dt, VR2_Dt, VR3_Dt, DetourIndex, SpAbs_D, SpMax_D, SpDiam_D, SpAD_D, SpMAD_D, LogEE_D, VE1_D, VE2_D, VE3_D, VR1_D, VR2_D, VR3_D, NsLi, NssBe, NssssBe, NssBH, NsssB, NssssB, NsCH3, NdCH2, NssCH2, NtCH, NdsCH, NaaCH, NsssCH, NddC, NtsC, NdssC, NaasC, NaaaC, NssssC, NsNH3, NsNH2, NssNH2, NdNH, NssNH, NaaNH, NtN, NsssNH, NdsN, NaaN, NsssN, NddsN, NaasN, NssssN, NsOH, NdO, NssO, NaaO, NsF, NsSiH3, NssSiH2, NsssSiH, NssssSi, NsPH2, NssPH, NsssP, NdsssP, NsssssP, NsSH, NdS, NssS, NaaS, NdssS, NddssS, NsCl, NsGeH3, NssGeH2, NsssGeH, NssssGe, NsAsH2, NssAsH, NsssAs, NsssdAs, NsssssAs, NsSeH, NdSe, NssSe, NaaSe, NdssSe, NddssSe, NsBr, NsSnH3, NssSnH2, NsssSnH, NssssSn, NsI, NsPbH3, NssPbH2, NsssPbH, NssssPb, SsLi, SssBe, SssssBe, SssBH, SsssB, SssssB, SsCH3, SdCH2, SssCH2, StCH, SdsCH, SaaCH, SsssCH, SddC, StsC, SdssC, SaasC, SaaaC, SssssC, SsNH3, SsNH2, SssNH2, SdNH, SssNH, SaaNH, StN, SsssNH, SdsN, SaaN, SsssN, SddsN, SaasN, SssssN, SsOH, SdO, SssO, SaaO, SsF, SsSiH3, SssSiH2, SsssSiH, SssssSi, SsPH2, SssPH, SsssP, SdsssP, SsssssP, SsSH, SdS, SssS, SaaS, SdssS, SddssS, SsCl, SsGeH3, SssGeH2, SsssGeH, SssssGe, SsAsH2, SssAsH, SsssAs, SsssdAs, SsssssAs, SsSeH, SdSe, SssSe, SaaSe, SdssSe, SddssSe, SsBr, SsSnH3, SssSnH2, SsssSnH, SssssSn, SsI, SsPbH3, SssPbH2, SsssPbH, SssssPb, MAXsLi, MAXssBe, MAXssssBe, MAXssBH, MAXsssB, MAXssssB, MAXsCH3, MAXdCH2, MAXssCH2, MAXtCH, MAXdsCH, MAXaaCH, MAXsssCH, MAXddC, MAXtsC, MAXdssC, MAXaasC, MAXaaaC, MAXssssC, MAXsNH3, MAXsNH2, MAXssNH2, MAXdNH, MAXssNH, MAXaaNH, MAXtN, MAXsssNH, MAXdsN, MAXaaN, MAXsssN, MAXddsN, MAXaasN, MAXssssN, MAXsOH, MAXdO, MAXssO, MAXaaO, MAXsF, MAXsSiH3, MAXssSiH2, MAXsssSiH, MAXssssSi, MAXsPH2, MAXssPH, MAXsssP, MAXdsssP, MAXsssssP, MAXsSH, MAXdS, MAXssS, MAXaaS, MAXdssS, MAXddssS, MAXsCl, MAXsGeH3, MAXssGeH2, MAXsssGeH, MAXssssGe, MAXsAsH2, MAXssAsH, MAXsssAs, MAXsssdAs, MAXsssssAs, MAXsSeH, MAXdSe, MAXssSe, MAXaaSe, MAXdssSe, MAXddssSe, MAXsBr, MAXsSnH3, MAXssSnH2, MAXsssSnH, MAXssssSn, MAXsI, MAXsPbH3, MAXssPbH2, MAXsssPbH, MAXssssPb, MINsLi, MINssBe, MINssssBe, MINssBH, MINsssB, MINssssB, MINsCH3, MINdCH2, MINssCH2, MINtCH, MINdsCH, MINaaCH, MINsssCH, MINddC, MINtsC, MINdssC, MINaasC, MINaaaC, MINssssC, MINsNH3, MINsNH2, MINssNH2, MINdNH, MINssNH, MINaaNH, MINtN, MINsssNH, MINdsN, MINaaN, MINsssN, MINddsN, MINaasN, MINssssN, MINsOH, MINdO, MINssO, MINaaO, MINsF, MINsSiH3, MINssSiH2, MINsssSiH, MINssssSi, MINsPH2, MINssPH, MINsssP, MINdsssP, MINsssssP, MINsSH, MINdS, MINssS, MINaaS, MINdssS, MINddssS, MINsCl, MINsGeH3, MINssGeH2, MINsssGeH, MINssssGe, MINsAsH2, MINssAsH, MINsssAs, MINsssdAs, MINsssssAs, MINsSeH, MINdSe, MINssSe, MINaaSe, MINdssSe, MINddssSe, MINsBr, MINsSnH3, MINssSnH2, MINsssSnH, MINssssSn, MINsI, MINsPbH3, MINssPbH2, MINsssPbH, MINssssPb, ECIndex, ETA_alpha, AETA_alpha, ETA_shape_p, ETA_shape_y, ETA_shape_x, ETA_beta, AETA_beta, ETA_beta_s, AETA_beta_s, ETA_beta_ns, AETA_beta_ns, ETA_beta_ns_d, AETA_beta_ns_d, ETA_eta, AETA_eta, ETA_eta_L, AETA_eta_L, ETA_eta_R, AETA_eta_R, ETA_eta_RL, AETA_eta_RL, ETA_eta_F, AETA_eta_F, ETA_eta_FL, AETA_eta_FL, ETA_eta_B, AETA_eta_B, ETA_eta_BR, AETA_eta_BR, ETA_dAlpha_A, ETA_dAlpha_B, ETA_epsilon_1, ETA_epsilon_2, ETA_epsilon_3, ETA_epsilon_4, ETA_epsilon_5, ETA_dEpsilon_A, ETA_dEpsilon_B, ETA_dEpsilon_C, ETA_dEpsilon_D, ETA_dBeta, AETA_dBeta, ETA_psi_1, ETA_dPsi_A, ETA_dPsi_B, fragCpx, fMF, GeomDiameter, GeomRadius, GeomShapeIndex, GeomPetitjeanIndex, GRAV, GRAVH, GRAVp, GRAVHp, nHBAcc, nHBDon, IC0, IC1, IC2, IC3, IC4, IC5, TIC0, TIC1, TIC2, TIC3, TIC4, TIC5, SIC0, SIC1, SIC2, SIC3, SIC4, SIC5, BIC0, BIC1, BIC2, BIC3, BIC4, BIC5, CIC0, CIC1, CIC2, CIC3, CIC4, CIC5, MIC0, MIC1, MIC2, MIC3, MIC4, MIC5, ZMIC0, ZMIC1, ZMIC2, ZMIC3, ZMIC4, ZMIC5, Kier1, Kier2, Kier3, Lipinski, GhoseFilter, FilterItLogS, VMcGowan, Mor01, Mor02, Mor03, Mor04, Mor05, Mor06, Mor07, Mor08, Mor09, Mor10, Mor11, Mor12, Mor13, Mor14, Mor15, Mor16, Mor17, Mor18, Mor19, Mor20, Mor21, Mor22, Mor23, Mor24, Mor25, Mor26, Mor27, Mor28, Mor29, Mor30, Mor31, Mor32, Mor01m, Mor02m, Mor03m, Mor04m, Mor05m, Mor06m, Mor07m, Mor08m, Mor09m, Mor10m, Mor11m, Mor12m, Mor13m, Mor14m, Mor15m, Mor16m, Mor17m, Mor18m, Mor19m, Mor20m, Mor21m, Mor22m, Mor23m, Mor24m, Mor25m, Mor26m, Mor27m, Mor28m, Mor29m, Mor30m, Mor31m, Mor32m, Mor01v, Mor02v, Mor03v, Mor04v, Mor05v, Mor06v, Mor07v, Mor08v, Mor09v, Mor10v, Mor11v, Mor12v, Mor13v, Mor14v, Mor15v, Mor16v, Mor17v, Mor18v, Mor19v, Mor20v, Mor21v, Mor22v, Mor23v, Mor24v, Mor25v, Mor26v, Mor27v, Mor28v, Mor29v, Mor30v, Mor31v, Mor32v, Mor01se, Mor02se, Mor03se, Mor04se, Mor05se, Mor06se, Mor07se, Mor08se, Mor09se, Mor10se, Mor11se, Mor12se, Mor13se, Mor14se, Mor15se, Mor16se, Mor17se, Mor18se, Mor19se, Mor20se, Mor21se, Mor22se, Mor23se, Mor24se, Mor25se, Mor26se, Mor27se, Mor28se, Mor29se, Mor30se, Mor31se, Mor32se, Mor01p, Mor02p, Mor03p, Mor04p, Mor05p, Mor06p, Mor07p, Mor08p, Mor09p, Mor10p, Mor11p, Mor12p, Mor13p, Mor14p, Mor15p, Mor16p, Mor17p, Mor18p, Mor19p, Mor20p, Mor21p, Mor22p, Mor23p, Mor24p, Mor25p, Mor26p, Mor27p, Mor28p, Mor29p, Mor30p, Mor31p, Mor32p, LabuteASA, PEOE_VSA1, PEOE_VSA2, PEOE_VSA3, PEOE_VSA4, PEOE_VSA5, PEOE_VSA6, PEOE_VSA7, PEOE_VSA8, PEOE_VSA9, PEOE_VSA10, PEOE_VSA11, PEOE_VSA12, PEOE_VSA13, SMR_VSA1, SMR_VSA2, SMR_VSA3, SMR_VSA4, SMR_VSA5, SMR_VSA6, SMR_VSA7, SMR_VSA8, SMR_VSA9, SlogP_VSA1, SlogP_VSA2, SlogP_VSA3, SlogP_VSA4, SlogP_VSA5, SlogP_VSA6, SlogP_VSA7, SlogP_VSA8, SlogP_VSA9, SlogP_VSA10, SlogP_VSA11, EState_VSA1, EState_VSA2, EState_VSA3, EState_VSA4, EState_VSA5, EState_VSA6, EState_VSA7, EState_VSA8, EState_VSA9, EState_VSA10, VSA_EState1, VSA_EState2, VSA_EState3, VSA_EState4, VSA_EState5, VSA_EState6, VSA_EState7, VSA_EState8, VSA_EState9, MDEC-11, MDEC-12, MDEC-13, MDEC-14, MDEC-22, MDEC-23, MDEC-24, MDEC-33, MDEC-34, MDEC-44, MDEO-11, MDEO-12, MDEO-22, MDEN-11, MDEN-12, MDEN-13, MDEN-22, MDEN-23, MDEN-33, MID, AMID, MID_h, AMID_h, MID_C, AMID_C, MID_N, AMID_N, MID_O, AMID_O, MID_X, AMID_X, MOMI-X, MOMI-Y, MOMI-Z, PBF, MPC2, MPC3, MPC4, MPC5, MPC6, MPC7, MPC8, MPC9, MPC10, TMPC10, piPC1, piPC2, piPC3, piPC4, piPC5, piPC6, piPC7, piPC8, piPC9, piPC10, TpiPC10, apol, bpol, nRing, n3Ring, n4Ring, n5Ring, n6Ring, n7Ring, n8Ring, n9Ring, n10Ring, n11Ring, n12Ring, nG12Ring, nHRing, n3HRing, n4HRing, n5HRing, n6HRing, n7HRing, n8HRing, n9HRing, n10HRing, n11HRing, n12HRing, nG12HRing, naRing, n3aRing, n4aRing, n5aRing, n6aRing, n7aRing, n8aRing, n9aRing, n10aRing, n11aRing, n12aRing, nG12aRing, naHRing, n3aHRing, n4aHRing, n5aHRing, n6aHRing, n7aHRing, n8aHRing, n9aHRing, n10aHRing, n11aHRing, n12aHRing, nG12aHRing, nARing, n3ARing, n4ARing, n5ARing, n6ARing, n7ARing, n8ARing, n9ARing, n10ARing, n11ARing, n12ARing, nG12ARing, nAHRing, n3AHRing, n4AHRing, n5AHRing, n6AHRing, n7AHRing, n8AHRing, n9AHRing, n10AHRing, n11AHRing, n12AHRing, nG12AHRing, nFRing, n4FRing, n5FRing, n6FRing, n7FRing, n8FRing, n9FRing, n10FRing, n11FRing, n12FRing, nG12FRing, nFHRing, n4FHRing, n5FHRing, n6FHRing, n7FHRing, n8FHRing, n9FHRing, n10FHRing, n11FHRing, n12FHRing, nG12FHRing, nFaRing, n4FaRing, n5FaRing, n6FaRing, n7FaRing, n8FaRing, n9FaRing, n10FaRing, n11FaRing, n12FaRing, nG12FaRing, nFaHRing, n4FaHRing, n5FaHRing, n6FaHRing, n7FaHRing, n8FaHRing, n9FaHRing, n10FaHRing, n11FaHRing, n12FaHRing, nG12FaHRing, nFARing, n4FARing, n5FARing, n6FARing, n7FARing, n8FARing, n9FARing, n10FARing, n11FARing, n12FARing, nG12FARing, nFAHRing, n4FAHRing, n5FAHRing, n6FAHRing, n7FAHRing, n8FAHRing, n9FAHRing, n10FAHRing, n11FAHRing, n12FAHRing, nG12FAHRing, nRot, RotRatio, SLogP, SMR, TopoPSA(NO), TopoPSA, GGI1, GGI2, GGI3, GGI4, GGI5, GGI6, GGI7, GGI8, GGI9, GGI10, JGI1, JGI2, JGI3, JGI4, JGI5, JGI6, JGI7, JGI8, JGI9, JGI10, JGT10, Diameter, Radius, TopoShapeIndex, PetitjeanIndex, Vabc, VAdjMat, MWC01, MWC02, MWC03, MWC04, MWC05, MWC06, MWC07, MWC08, MWC09, MWC10, TMWC10, SRW02, SRW03, SRW04, SRW05, SRW06, SRW07, SRW08, SRW09, SRW10, TSRW10, MW, AMW, WPath, WPol, Zagreb1, Zagreb2, mZagreb1, mZagreb2

 

Model performance

The performance of the linear regression models was quantified using the Pearson's correlation coefficient (r) and mean absolute error (MAE). The following table summarizes the training and jack-knife (JK) test metrics for all the models. For details on the performance of the models on external blind test datasets, please refer our associated publication.

 

RNA category No. of features in the final model Training r Training MAE Jack-knife r Jack-knife MAE
Aptamers 12 0.72973 0.61946 0.70277 0.63058
miRNAs 8 0.89650 0.40791 0.88178 0.43425
Repeats 13 0.92097 0.31474 0.88856 0.37246
Ribosomal RNAs 11 0.83111 0.66296 0.80973 0.69770
Riboswitches 13 0.92306 0.46634 0.89618 0.54090
Viral RNAs 8 0.79620 0.59059 0.77895 0.61609

 

Regression plots

 

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