An Efficient ABC_DE_Based Hybrid Algorithm for Protein–Ligand Docking
Abstract
:1. Introduction
2. Results
2.1. Data Preparation and Parameter Setting
2.2. Comparison of Energy and Root-Mean-Square Deviation (RMSD)
2.3. Convergence Analysis
2.4. Data Distribution Analysis
2.5. Hypothesis Test
3. Discussion
4. Materials and Methods
4.1. Framework of ADHDOCK
4.2. ABC Module
4.3. DE Module
4.4. APP Module
4.5. Hybrid Search of ADHDOCK
5. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
Abbreviations
ADHDOCK | an efficient ABC_DE_based hybrid algorithm for protein–ligand docking |
ABC | artificial bee colony |
DE | differential evolution |
HIGA | running history information guided genetic algorithm |
PSO | particle swarm optimization |
SODOCK | swarm optimization for highly flexible protein–ligand docking |
APP | adaptive population partition |
CADD | computer aided drug design |
SA | simulated annealing |
GA | genetic algorithm |
LGA | Lamarckian genetic algorithm |
RMSD | Root-mean-square deviation |
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ADHDOCK | |
Number of food sources | 50 |
Number of limitation | 100 |
Crossover rate | 0.80 |
Scalar number | 0.90 |
Initial partition rate | 0.50 |
ABC | |
Number of food sources | 50 |
Number of limitation | 100 |
DE | |
Crossover rate | 0.80 |
Scalar number | 0.90 |
LGA | |
Mutation rate | 0.02 |
Crossover rate | 0.80 |
Maximal iterations of local search | 300 |
HIGA | |
Mutation rate | 0.02 |
Crossover rate | 0.80 |
Maximal iterations of local search | 300 |
Number of elitists | 5 |
equilibrium factor | 0.60 |
SODOCK | |
Number of immediate neighbors | 4 |
Cognitive weight | 2.00 |
Social weight | 2.00 |
Maximal iterations of local search | 300 |
Algorithm | Success Case | Average RMSD (All Cases) | Average RMSD (RMSD < 2.0 Å) |
---|---|---|---|
ABC | 32 | 3.28 ± 1.32 | 1.84 ± 0.42 |
DE | 35 | 3.21 ± 1.37 | 1.82 ± 0.42 |
LGA | 34 | 2.55 ± 1.28 | 1.68 ± 0.40 |
HIGA | 42 | 1.87 ± 0.99 | 1.36 ± 0.51 |
SODOCK | 37 | 2.92 ± 1.08 | 1.77 ± 0.39 |
ADHDOCK | 46 | 1.68 ± 0.89 | 1.19 ± 0.33 |
PDB | Tor | ADHDOCK | ABC | DE | LGA | HIGA | SODOCK | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Energy | RMSD | Energy | RMSD | Energy | RMSD | Energy | RMSD | Energy | RMSD | Energy | RMSD | ||
3ptb | 0 | −13.25 | 1.65 | −10.95 | 1.97 | −11.23 | 1.80 | −11.53 | 1.92 | −12.22 | 1.95 | −11.57 | 2.00 |
1hdy | 0 | −10.40 | 0.80 | −8.80 | 1.47 | −8.24 | 1.05 | −8.70 | 1.78 | −9.17 | 0.98 | −9.22 | 1.49 |
1aha | 1 | −18.20 | 0.82 | −13.95 | 1.85 | −15.24 | 1.22 | −16.10 | 0.45 | −16.15 | 0.90 | −14.95 | 1.44 |
1dbb | 1 | −12.38 | 0.35 | −11.88 | 0.88 | −11.29 | 0.55 | −11.00 | 0.72 | −11.17 | 0.80 | −11.76 | 0.88 |
1mrg | 1 | −8.55 | 0.30 | −7.85 | 0.85 | −7.48 | 1.25 | −6.16 | 0.40 | −7.52 | 0.33 | −8.14 | 1.20 |
1ulb | 1 | −7.50 | 0.72 | −5.36 | 0.80 | −5.20 | 0.40 | −6.28 | 0.74 | −7.07 | 0.35 | −6.75 | 0.50 |
1tnl | 2 | −9.49 | 0.36 | −5.80 | 0.68 | −6.28 | 0.52 | −6.83 | 0.73 | −8.08 | 0.62 | −6.78 | 0.88 |
2phh | 2 | −9.21 | 0.54 | −6.98 | 1.30 | −6.95 | 1.15 | −7.54 | 0.55 | −8.20 | 0.65 | −8.16 | 0.34 |
3hvt | 2 | −17.59 | 0.55 | −15.95 | 0.68 | −15.29 | 0.47 | −17.22 | 0.33 | −18.19 | 0.45 | −16.78 | 0.58 |
1phg | 3 | −10.28 | 0.38 | −7.95 | 1.67 | −7.90 | 1.33 | −8.56 | 0.80 | −9.58 | 0.60 | −9.15 | 1.34 |
2cht | 3 | −10.37 | 1.55 | −7.87 | 1.24 | −8.16 | 1.16 | −8.89 | 0.95 | −9.10 | 1.34 | −8.77 | 1.33 |
2ctc | 3 | −9.25 | 0.78 | −6.40 | 1.66 | −6.70 | 1.67 | −7.70 | 0.89 | −8.90 | 0.80 | −8.52 | 1.21 |
4cts | 3 | −9.98 | 0.55 | −6.94 | 0.95 | −6.79 | 0.68 | −7.61 | 0.75 | −8.64 | 0.48 | −9.10 | 1.20 |
1abe | 4 | −10.10 | 0.39 | −7.99 | 0.95 | −8.15 | 1.03 | −8.75 | 0.60 | −9.44 | 0.75 | −8.73 | 0.80 |
1hsl | 4 | −15.15 | 0.56 | −11.25 | 1.36 | −11.97 | 1.60 | −12.10 | 0.56 | −13.17 | 0.66 | −12.90 | 1.23 |
2mcp | 4 | −10.35 | 1.05 | −7.85 | 1.64 | −8.10 | 1.10 | −8.22 | 1.33 | −9.35 | 1.15 | −7.72 | 1.42 |
1stp | 5 | −16.10 | 0.35 | −13.20 | 1.58 | −13.13 | 0.92 | −13.37 | 1.65 | −13.90 | 0.85 | −13.52 | 1.00 |
1tni | 5 | −9.12 | 0.74 | −6.82 | 1.25 | −6.79 | 0.67 | −8.02 | 1.65 | −8.61 | 0.90 | −7.56 | 1.34 |
2lgs | 5 | −9.23 | 0.71 | −7.25 | 1.10 | −7.11 | 0.76 | −7.30 | 0.77 | −7.83 | 1.22 | −7.18 | 1.50 |
1acm | 6 | −11.61 | 0.30 | −9.95 | 0.33 | −9.28 | 0.40 | −10.10 | 0.37 | −10.87 | 0.33 | −10.11 | 0.45 |
2cgr | 6 | −18.80 | 0.70 | −14.25 | 0.97 | −14.14 | 0.80 | −16.00 | 0.76 | −17.80 | 0.75 | −15.74 | 0.77 |
6rnt | 6 | −9.32 | 0.55 | −8.95 | 1.45 | −8.90 | 1.65 | −9.13 | 0.70 | −9.62 | 0.50 | −9.12 | 1.95 |
1lst | 7 | −16.13 | 0.36 | −12.22 | 0.96 | −12.43 | 0.95 | −13.75 | 0.55 | −15.22 | 0.46 | −14.72 | 0.66 |
2cmd | 7 | −15.14 | 0.42 | −12.70 | 0.65 | −12.42 | 0.62 | −12.26 | 0.78 | −14.05 | 0.82 | −13.28 | 0.80 |
4dfr | 7 | −13.12 | 1.04 | −10.21 | 1.97 | −10.15 | 1.20 | −11.44 | 1.23 | −12.82 | 1.56 | −11.74 | 1.67 |
1ett | 8 | −14.90 | 1.20 | −12.75 | 1.65 | −12.40 | 1.70 | −13.89 | 1.38 | −13.94 | 1.40 | −12.08 | 1.54 |
1tka | 8 | −14.02 | 0.88 | −10.33 | 1.17 | −9.89 | 1.20 | −10.23 | 0.98 | −11.60 | 1.02 | −10.25 | 1.15 |
8gch | 8 | −14.55 | 0.70 | −10.85 | 0.82 | −11.30 | 1.15 | −11.88 | 1.72 | −12.55 | 1.66 | −11.29 | 0.98 |
1hri | 9 | −12.03 | 1.13 | −10.13 | 1.67 | −9.98 | 1.56 | −10.21 | 1.87 | −11.02 | 1.18 | −10.31 | 1.68 |
1trk | 9 | −14.50 | 0.80 | −11.25 | 0.65 | −11.35 | 0.62 | −11.44 | 0.65 | −13.05 | 0.50 | −11.49 | 0.60 |
2sim | 9 | −18.25 | 0.90 | −15.93 | 1.10 | −15.50 | 1.06 | −15.61 | 0.95 | −16.24 | 1.08 | −15.05 | 1.06 |
1eap | 10 | −14.05 | 1.25 | −12.85 | 1.21 | −12.18 | 1.30 | −13.08 | 1.27 | −14.55 | 0.98 | −13.77 | 1.10 |
1fkg | 10 | −17.51 | 1.13 | −15.15 | 1.20 | −15.36 | 1.22 | −15.47 | 1.36 | −16.26 | 1.35 | −15.08 | 1.38 |
1hvr | 10 | −33.40 | 0.55 | −28.65 | 0.85 | −29.38 | 0.78 | −30.85 | 0.62 | −31.50 | 0.80 | −29.29 | 0.68 |
1lna | 10 | −15.62 | 1.10 | −13.85 | 1.82 | −13.28 | 1.67 | −13.50 | 1.75 | −15.19 | 1.29 | −13.82 | 1.22 |
1nco | 11 | −21.70 | 0.93 | −20.54 | 0.77 | −20.85 | 0.82 | −21.20 | 0.65 | −22.75 | 0.55 | −20.60 | 0.92 |
4hmg | 11 | −10.51 | 1.13 | −9.95 | 1.60 | −10.00 | 1.28 | −10.09 | 1.70 | −10.21 | 1.65 | −10.08 | 1.36 |
1bbp | 12 | −26.90 | 0.45 | −24.48 | 0.65 | −23.38 | 0.78 | −23.56 | 0.52 | −25.10 | 0.67 | −24.15 | 0.72 |
1cdg | 12 | −8.95 | 1.05 | −7.13 | 1.12 | −7.72 | 1.17 | −8.22 | 1.94 | −8.90 | 1.65 | −8.45 | 1.80 |
1rds | 12 | −18.11 | 0.75 | −16.34 | 0.92 | −15.93 | 0.86 | −16.24 | 0.80 | −17.95 | 0.77 | −16.03 | 0.67 |
1htf | 13 | −22.77 | 1.02 | −19.80 | 1.80 | −20.12 | 1.48 | −20.69 | 1.33 | −21.17 | 1.20 | −21.79 | 1.42 |
1glq | 14 | −9.83 | 1.15 | −9.23 | 1.58 | −8.53 | 1.29 | −9.27 | 1.87 | −9.65 | 1.25 | −8.83 | 1.90 |
1hpv | 14 | −16.72 | 1.96 | −15.67 | 1.91 | −15.11 | 1.92 | −15.48 | 1.88 | −17.29 | 1.60 | −15.68 | 1.75 |
1qbt | 14 | −26.75 | 0.80 | −22.69 | 1.29 | −22.93 | 1.27 | −24.20 | 1.09 | −25.20 | 0.88 | −24.63 | 1.04 |
1lic | 15 | −12.77 | 0.85 | −10.01 | 1.36 | −9.80 | 1.54 | −12.17 | 1.80 | −13.03 | 0.96 | −12.55 | 1.08 |
1tmn | 15 | −11.13 | 0.90 | −9.58 | 0.65 | −9.97 | 1.18 | −10.11 | 1.20 | −10.71 | 0.95 | −10.62 | 1.95 |
4phv | 15 | −22.44 | 1.38 | −15.62 | 1.44 | −16.08 | 1.53 | −19.18 | 1.26 | −19.89 | 0.45 | −21.78 | 0.90 |
1epo | 17 | −20.33 | 0.80 | −16.07 | 1.77 | −17.18 | 1.62 | −16.80 | 1.67 | −19.13 | 1.23 | −17.65 | 0.93 |
1aaq | 20 | −23.10 | 1.10 | −15.55 | 1.20 | −16.60 | 1.75 | −17.44 | 1.70 | −20.66 | 1.05 | −19.80 | 1.34 |
1hiv | 23 | −25.60 | 0.55 | −15.45 | 1.06 | −16.20 | 0.73 | −17.95 | 1.73 | −21.25 | 1.21 | −19.74 | 1.55 |
PDB | ABC | DE | LGA | HIGA | SODOCK |
---|---|---|---|---|---|
3ptb | 4.49 × 10−8 | 3.17 × 10−4 | 2.15 × 10−3 | 7.12 × 10−3 | 3.32 × 10−4 |
1hdy | 1.18 × 10−4 | 2.39 × 10−9 | 3.04 × 10−6 | 2.50 × 10−3 | 1.02 × 10−3 |
1aha | 6.41 × 10−11 | 4.13 × 10−7 | 5.14 × 10−5 | 3.76 × 10−4 | 4.31 × 10−10 |
1dbb | 2.27 × 10−3 | 1.03 × 10−3 | 4.15 × 10−4 | 3.25 × 10−4 | 1.43 × 10−3 |
1mrg | 2.19 × 10−4 | 6.37 × 10−5 | 2.43 × 10−8 | 4.57 × 10−4 | 1.42 × 10−1 |
1ulb | 3.91 × 10−7 | 2.31 × 10−8 | 8.15 × 10−4 | 4.35 × 10−3 | 2.82 × 10−4 |
1tnl | 4.93 × 10−10 | 3.86 × 10−9 | 2.62 × 10−8 | 2.14 × 10−5 | 5.90 × 10−8 |
2phh | 1.76 × 10−5 | 2.59 × 10−5 | 3.98 × 10−4 | 1.45 × 10−3 | 2.08 × 10−3 |
3hvt | 8.99 × 10−6 | 7.34 × 10−7 | 4.12 × 10−2 | 9.98 × 10−1 | 3.06 × 10−8 |
1phg | 3.77 × 10−6 | 6.33 × 10−6 | 3.37 × 10−4 | 1.51 × 10−1 | 9.12 × 10−2 |
2cht | 1.74 × 10−8 | 2.78 × 10−7 | 4.09 × 10−5 | 2.74 × 10−4 | 6.32 × 10−5 |
2ctc | 4.86 × 10−8 | 3.96 × 10−8 | 9.25 × 10−4 | 7.46 × 10−3 | 3.74 × 10−4 |
4cts | 3.14 × 10−8 | 1.19 × 10−9 | 3.82 × 10−6 | 2.39 × 10−4 | 7.22 × 10−3 |
1abe | 3.38 × 10−12 | 4.31 × 10−10 | 2.35 × 10−6 | 3.55 × 10−3 | 2.04 × 10−6 |
1hsl | 1.19 × 10−10 | 3.08 × 10−8 | 1.05 × 10−6 | 5.32 × 10−4 | 3.91 × 10−5 |
2mcp | 4.15 × 10−9 | 9.30 × 10−6 | 3.21 × 10−6 | 2.86 × 10−4 | 8.82 × 10−9 |
1stp | 2.42 × 10−7 | 1.11 × 10−7 | 8.25 × 10−6 | 3.32 × 10−5 | 3.45 × 10−6 |
1tni | 3.14 × 10−8 | 1.43 × 10−8 | 3.71 × 10−5 | 8.46 × 10−3 | 1.58 × 10−5 |
2lgs | 2.37 × 10−5 | 1.33 × 10−9 | 2.54 × 10−8 | 4.52 × 10−5 | 2.28 × 10−4 |
1acm | 1.42 × 10−8 | 2.12 × 10−9 | 5.18 × 10−4 | 3.15 × 10−2 | 4.12 × 10−4 |
2cgr | 3.39 × 10−7 | 1.07 × 10−9 | 3.95 × 10−4 | 2.14 × 10−2 | 7.38 × 10−4 |
6rnt | 3.51 × 10−4 | 4.52 × 10−4 | 2.49 × 10−1 | 9.82 × 10−1 | 1.01 × 10−1 |
1lst | 1.78 × 10−10 | 2.91 × 10−8 | 3.53 × 10−5 | 5.54 × 10−3 | 2.32 × 10−4 |
2cmd | 4.58 × 10−7 | 9.12 × 10−7 | 2.38 × 10−8 | 1.13 × 10−3 | 3.35 × 10−5 |
4dfr | 1.26 × 10−8 | 1.09 × 10−9 | 7.74 × 10−4 | 2.52 × 10−3 | 1.34 × 10−4 |
1ett | 2.29 × 10−6 | 8.17 × 10−7 | 1.16 × 10−4 | 7.70 × 10−3 | 1.02 × 10−8 |
1tka | 4.75 × 10−8 | 3.92 × 10−10 | 2.97 × 10−7 | 3.63 × 10−5 | 2.18 × 10−7 |
8gch | 2.48 × 10−6 | 8.19 × 10−5 | 4.08 × 10−5 | 1.40 × 10−4 | 9.03 × 10−5 |
1hri | 4.12 × 10−4 | 3.88 × 10−5 | 6.11 × 10−2 | 2.54 × 10−1 | 8.42 × 10−2 |
1trk | 1.61 × 10−8 | 5.30 × 10−7 | 3.76 × 10−7 | 2.96 × 10−3 | 1.18 × 10−7 |
2sim | 3.29 × 10−5 | 3.97 × 10−5 | 1.05 × 10−6 | 4.52 × 10−2 | 7.12 × 10−6 |
1eap | 1.54 × 10−4 | 2.98 × 10−6 | 3.67 × 10−3 | 8.56 × 10−1 | 1.52 × 10−1 |
1fkg | 4.92 × 10−5 | 3.73 × 10−5 | 9.13 × 10−4 | 1.19 × 10−4 | 9.62 × 10−6 |
1hvr | 1.01 × 10−7 | 2.92 × 10−5 | 1.93 × 10−4 | 8.52 × 10−3 | 8.32 × 10−5 |
1lna | 2.29 × 10−5 | 5.37 × 10−6 | 9.10 × 10−5 | 6.13 × 10−3 | 3.40 × 10−5 |
1nco | 1.02 × 10−2 | 6.13 × 10−2 | 2.24 × 10−1 | 8.12 × 10−1 | 5.46 × 10−2 |
4hmg | 6.15 × 10−6 | 2.23 × 10−5 | 8.75 × 10−4 | 1.40 × 10−4 | 1.07 × 10−5 |
1bbp | 1.07 × 10−5 | 8.13 × 10−7 | 2.82 × 10−7 | 4.94 × 10−3 | 2.85 × 10−5 |
1cdg | 8.32 × 10−6 | 1.02 × 10−6 | 7.21 × 10−4 | 7.16 × 10−2 | 1.14 × 10−4 |
1rds | 3.91 × 10−4 | 4.27 × 10−7 | 6.15 × 10−4 | 6.26 × 10−2 | 1.08 × 10−5 |
1htf | 2.24 × 10−7 | 6.27 × 10−6 | 1.80 × 10−6 | 3.42 × 10−4 | 1.17 × 10−4 |
1glq | 7.59 × 10−5 | 8.18 × 10−8 | 2.60 × 10−5 | 1.51 × 10−4 | 3.58 × 10−7 |
1hpv | 7.12 × 10−2 | 3.92 × 10−4 | 6.15 × 10−2 | 8.15 × 10−1 | 9.33 × 10−2 |
1qbt | 8.04 × 10−9 | 2.71 × 10−9 | 1.16 × 10−6 | 2.12 × 10−4 | 5.72 × 10−4 |
1lic | 2.43 × 10−7 | 6.39 × 10−7 | 8.18 × 10−3 | 6.88 × 10−1 | 5.89 × 10−2 |
1tmn | 2.06 × 10−7 | 6.18 × 10−7 | 2.93 × 10−6 | 3.52 × 10−4 | 9.86 × 10−4 |
4phv | 1.35 × 10−11 | 5.13 × 10−9 | 4.75 × 10−6 | 6.56 × 10−6 | 1.12 × 10−4 |
1epo | 7.87 × 10−10 | 1.03 × 10−6 | 3.42 × 10−8 | 1.04 × 10−3 | 2.77 × 10−6 |
1aaq | 1.02 × 10−10 | 5.52 × 10−8 | 1.24 × 10−7 | 3.18 × 10−5 | 6.19 × 10−7 |
1hiv | 8.91 × 10−9 | 4.43 × 10−8 | 6.88 × 10−7 | 2.86 × 10−4 | 1.58 × 10−6 |
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Guan, B.; Zhang, C.; Zhao, Y. An Efficient ABC_DE_Based Hybrid Algorithm for Protein–Ligand Docking. Int. J. Mol. Sci. 2018, 19, 1181. https://doi.org/10.3390/ijms19041181
Guan B, Zhang C, Zhao Y. An Efficient ABC_DE_Based Hybrid Algorithm for Protein–Ligand Docking. International Journal of Molecular Sciences. 2018; 19(4):1181. https://doi.org/10.3390/ijms19041181
Chicago/Turabian StyleGuan, Boxin, Changsheng Zhang, and Yuhai Zhao. 2018. "An Efficient ABC_DE_Based Hybrid Algorithm for Protein–Ligand Docking" International Journal of Molecular Sciences 19, no. 4: 1181. https://doi.org/10.3390/ijms19041181