Extensive Reliability Evaluation of Docking-Based Target-Fishing Strategies
Abstract
:1. Introduction
2. Results and Discussion
3. Materials and Methods
3.1. Database Generation
3.2. Protein Structure Alignment
3.3. Docking Procedures
3.4. Docking Score Evaluation
3.5. Consensus Docking Analysis
3.6. Evaluation of True Positive Rate and False Discovery Rate
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Type | PDB Code | Source |
---|---|---|
Acetylcholinesterase (ACHE) | 1EVE | DUD |
Aldose Reductase (ALR2) | 1AH3 | |
AmpC beta-lactamase (AmpC) | 1XGJ | |
Androgen Receptor (AR) | 1XQ2 | |
Cyclic dependent Kinase 2 (CDK2) | 1CKP | |
Cyclooxigenase 1 (COX1) | 1P4G | |
Cyclooxigenase 2 (COX2) | 1CX2 | |
Dihidrofolate Reductase (DHFR) | 2DFR | |
Epidermal Growth Factor Receptor (EGFr) | 1M17 | |
Estrogen Receptor Alpha (ERagonist) | 1L2I | |
Estrogen Receptor Alpha (ERantagonist) | 3ERT | |
Fibroblast Growth Factor Receptor 1 (FGFr1) | 1AGW | |
Coagulation Factor XA (FXa) | 1F0R | |
GAR Transformylase (GART) | 1C2T | |
Glycogen Phosphorylase (GPB) | 1AI8 | |
Glucocorticoid Receptor (GR) | 1M2Z | |
HIV-1 protease (HIVPR) | 1HPX | |
HIV-1 reverse transcriptase (HIVRT) | 1RT1 | |
HMG-CoA reductase (HMGR) | 1HW8 | |
Heat shock protein 90 (HSP90) | 1UY6 | |
Enoyl reductase (InhA) | 1P44 | |
Mineralocorticoid Receptor (MR) | 2AA2 | |
Neuraminidase (NA) | 1A4G | |
p38 MAP Kinase (P38 MAP) | 1KV2 | |
poly(ADP-ribose) Polymerase (PARP) | 1EFY | |
Purine Nucleoside Phosphorylase (PNP) | 1B8O | |
Peroxisome proliferator-activated receptor gamma (PPARg) | 1FM9 | |
Progesterone receptor (PR) | 1SR7 | |
Retinoic acid receptor RXR-alpha (RXRa) | 1MVC | |
S-adenosylhomocysteine Hydrolase (SAHH) | 1A7A | |
Tyrosine-protein kinase Src (SRC) | 2SRC | |
Thrombin | 1BA8 | |
Thymidine Kinase (TK) | 1KIM | |
Beta-Trypsin | 1BJU | |
Vascular Endothelial Growth Factor Receptor 2 (VEGFr2) | 1VR2 | |
Cathepsin G | 1KYN | MUV |
Coagulation Factor XI (FXI) | 4D76 | |
Focal Adhesion Kinase (FAK) | 4Q9S | |
Muscarinic Acetylcholine Receptor M1 | 5CXV | |
cAMP-dependent Protein Kinase (PRKACA) | 5BX6 | |
Sphingosine 1-Phosphate Receptor 1 (S1PR1) | 3V2W | |
Aurora kinase A | 4ZS0 | ChEMBL |
Beta-2 Adrenergic Receptor | 3P0G | |
Beta-secretase 1 | 4RCD | |
Cathepsin B | 3AI8 | |
Cathepsin L | 5F02 | |
Cathepsin S | 4PE6 | |
Dopamine Receptor D3 | 3PBL | |
Glycogen Phosphorylase | 3DD1 | |
Insulin-like Growth Factor 1 Receptor (IGF1R) | 5HZN | |
Leukotriene A-4 Hydrolase | 5BPP | |
Macrophage Colony-Stimulating Factor 1 Receptor | 4RTH | |
Muscarinic Acetylcholine Receptor M3 | 4DAJ | |
OX2 orexin receptor | 4S0V | |
Receptor-type tyrosine-protein kinase FLT3 | 4RT7 | |
Renin | 4RYC | |
Serine/threonine-protein kinase B-Raf | 5JRQ | |
Thymidylate synthase | 5IOQ | |
Tyrosine-protein Kinase ABL1 | 4ZOG | |
Vasopressin Receptor V1R | 1YTV |
Docking Procedures | TPR (%) | FDR (%) |
---|---|---|
Autodock | 27% | 76% |
Fred | 36% | 69% |
Dock6 | 25% | 79% |
Glamdock | 31% | 73% |
GlideSP | 36% | 67% |
GlideXP | 30% | 73% |
GoldASP | 28% | 73% |
GoldCSCORE | 29% | 74% |
GoldGSCORE | 25% | 77% |
GoldPLP | 31% | 72% |
Plants | 33% | 70% |
rDock | 28% | 76% |
Vina | 22% | 81% |
Consensus Docking | 36% | 67% |
Target | Consensus Level | Target | Consensus Level |
---|---|---|---|
ACHE | 2 | SRC | 2 |
ALR2 | 1.5 | THROMBIN | 6 |
AMPC | 2 | TK | 11 |
AR | 12 | TRYPSIN | 10 |
CDK2 | 2 | VEGFR2 | 1.5 |
COX1 | 9 | ABL1 | 2.5 |
COX2 | 6 | B-Raf | 4.5 |
DHFR | 4 | Cathepsin B | 1 |
EGFR | 1.5 | Cathepsin L | 2 |
ER_ago | 12 | Renin | 6.5 |
ER_ant | 10.5 | Glycogen Phosphorylase | 2 |
FGFR1 | 1 | Cathepsin S | 1 |
FXA | 7.5 | Beta-secretase 1 | 3 |
GART | 11.5 | FLT3 | 5 |
GPB | 4 | McsFR-1 | 1.5 |
GR | 11 | OX2 | 4 |
HIVPR | 7 | D3 | 1 |
HIVRT | 9 | V1R | 1.5 |
HMGA | 5 | Cathepsin G | 1.5 |
HSP90 | 2.5 | Aurora kinase A | 2 |
INHA | 0 | M3 | 1.5 |
MR | 12 | IGF1R | 2 |
NA | 11.5 | Leukotriene A-4 Hydrolase | 5.5 |
P38 MAP | 2.5 | Thymidylate synthase | 6.5 |
PARP | 3 | S1PR1 | 3 |
PNP | 3 | β2 Receptor | 1.5 |
PPARG | 6 | FXI | 0 |
PR | 11 | FAK | 1 |
RXR | 12 | PRKACA | 2.5 |
SAHH | 10 | M1 | 1.5 |
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Lapillo, M.; Tuccinardi, T.; Martinelli, A.; Macchia, M.; Giordano, A.; Poli, G. Extensive Reliability Evaluation of Docking-Based Target-Fishing Strategies. Int. J. Mol. Sci. 2019, 20, 1023. https://doi.org/10.3390/ijms20051023
Lapillo M, Tuccinardi T, Martinelli A, Macchia M, Giordano A, Poli G. Extensive Reliability Evaluation of Docking-Based Target-Fishing Strategies. International Journal of Molecular Sciences. 2019; 20(5):1023. https://doi.org/10.3390/ijms20051023
Chicago/Turabian StyleLapillo, Margherita, Tiziano Tuccinardi, Adriano Martinelli, Marco Macchia, Antonio Giordano, and Giulio Poli. 2019. "Extensive Reliability Evaluation of Docking-Based Target-Fishing Strategies" International Journal of Molecular Sciences 20, no. 5: 1023. https://doi.org/10.3390/ijms20051023