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
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 | ||||||