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Table 5 Comparative analysis of predictions based on different modes of binding against experimental data. All 16 GNN DNA targets and their respective experimentally reported helices from Qiang et al. 2002 [17] are used to find the corresponding hydrogen bond energy for Approach (1) assuming modular mode of binding and the other approach assuming synergistic mode of binding (2). Evidently the energy values for Approach 2 appear more reliable than Approach 1, even though both approaches predict with reasonable efficiency

From: Exploiting the recognition code for elucidating the mechanism of zinc finger protein-DNA interactions

Experimentally reported data Approach 2 : consensus amino acid and synergistic binding mode Approach 1: consensus amino acid and modular binding mode
Target GNN triplet (5' - 3') Qiang et al. 2002 [17] Zinc Finger Protein Helix H bond energy for experimental helix - target DNA complex Helices predicted for DNA H bond energy for predicted helix - Target DNA complex H bond energy for experimental helix - target DNA complex Helices predicted for DNA H bond energy for predicted helix - Target DNA complex
F1 F2 F3 F1 F2 F3 F1 F2 F3
GAAGAAGAA QNR QNR QNR −4.05 DSGNLTT DSGNLTT DSGNLTT −8.19 −6.62 QHR RHR DDT −11.91
GATGATGAT QNR TNR TNR −3.19 HSGALTT HSGALTT HSGALTT −5.52 −9.5 QHR RSN RHQ −16.31
GAGGAGGAG RNR RNR RNR −9.27 HSGTLTN HSGTLTN HSGTLTN −14.59 −4.8 AAK NVK ADK −8.37
GACGACGAC DNR DNR DNR −8.8 RSGSLTQ RSGSLTQ RSGSLTQ −12.69 −10.99 NHR RDK TSR −19.22
GTAGTAGTA QAR QAR QAR −11.13 QSGTLTK QSGTLTK QSGTLTK −13.76 −5.09 RDA QSR HHR −8.17
GTTGTTGTT TAR TAR TAR −2.88 ASGHLTT ASGHLTT ASGHLTT −3.99 −12.52 AAR DTT RHR −20.47
GTGGTGGTG RAR RAR RAR −6.32 RSGALTQ RSGALTQ RSGALTQ −4.29 −7.98 ASR QNQ TDR −14.23
GTCGTCGTC DAR DAR DAR −7.3 HSGSLTR HSGSLTR HSGSLTR −11.97 −10.11 THV QVT DHR −16.58
GGAGGAGGA QHR QHR QHR −9.65 NSGNLTR NSGNLTR NSGNLTR −14.91 −7.95 QVR RVR QHK −13.14
GGTGGTGGT QHR THR THR −9.07 NSGVLTQ NSGVLTQ NSGVLTQ −12.05 −11.45 AST NDR TDR −20.40
GGGGGGGGG RHR RHR RHR −14.67 RSGSLTR RSGSLTR RSGSLTR −19.44 −8.6 RHE THR NHR −12.83
GGCGGCGGC DHR DHR DHR −9.77 TSGHLTQ TSGHLTQ TSGHLTQ −10.29 −7.1 RVK DTR HDR −12.48
GCAGCAGCA QSR QDR QDR −5.36 ASGTLTK ASGTLTK ASGTLTK −6.00 −7.62 RHE DHR HHR −12.71
GCTGCTGCT QDR QDR QDR −9.43 ASGALTK ASGALTK ASGALTK −12.37 −10.71 THK QSV RSR −18.53
GCGGCGGCG RDR RDR RDR −10.54 RSGNLTK RSGNLTK RSGNLTK −10.36 −10.72 QHR RDR RSQ −18.75
GCCGCCGCC ETR DDR DDR −6 NSGSLTT NSGSLTT NSGSLTT −9.72 −8.62 ATR RHR NSK −14.48