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AutoDock and AutoDockTools for Protein-Ligand Docking: Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1(BACE1) as a Case Study
El-Hachem N, Haibe-Kains B, Khalil A, Kobeissy FH, Nemer G.. Methods in molecular biology (Clifton, N.J.), 2017-01-01
Topic: Brain proteins, microglia and lab models
Computational docking and scoring techniques have revolutionized structural bioinformatics by providing unprecedented insights on key aspects of ligand-receptor interaction. Docking is used for optimizing known drugs and for identifying novel binders by predicting their binding mode and affinity. AutoDock and AutoDockTools are free of charge techniques that have been extensively cited in the literature as essential tools in structure-based drug design.
Key findings
- Docking is used for optimizing known drugs and for identifying novel binders by predicting their binding mode and affinity.
- AutoDock and AutoDockTools are free of charge techniques that have been extensively cited in the literature as essential tools in structure-based drug design.
- Moreover, these methods are fast enough to permit virtual screening of ligand libraries containing tens of thousands of compounds.
- However using Autodock requires some knowledge in programming which creates a limitation for biologists and makes them prone for commercial applications.
Why it matters
This paper describes computational docking tools using BACE1 as a case study for structure-based drug design. It is a methods discussion and does not report any treatment, cure, or prevention for Alzheimer's disease.
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Study details
- Evidence strengthLow
How this study scored 47/100
Published in a peer-reviewed journal. Scored zero for study design, sample size, effect reported, studied in people and randomised / blinded because the record does not state it. We have no data on journal's citation record, so that was left out: it earned 45 of the 96 points we could judge it on, which is 47 out of 100.
| Component | Points | Why |
|---|---|---|
| Journal tier | 7 / 10 | Tier 3 — peer-reviewed journal (Methods in molecular biology (Clifton, N.J.)) |
| Journal's citation record | — / 4 | No journal record from OpenAlex — left out of this score |
| Study design | 0 / 12 | No study design recorded — scores zero, not guessed (not stated in the record — scored 0) |
| Strength of evidence | 1 / 5 | Rated “low” in our summary |
| Peer-review validation | 10 / 10 | Peer-reviewed. Published as an article in a named peer-reviewed journal. |
| How recent | 2 / 5 | 2017 — within 10 year(s) of the newest study here |
| Sample size | 0 / 4 | Participant count not stated — scores zero (not stated in the record — scored 0) |
| Effect reported | 0 / 3 | No effect size reported — scores zero (not stated in the record — scored 0) |
| Studied in people | 0 / 3 | Not stated whether this was studied in people — scores zero (not stated in the record — scored 0) |
| Randomised / blinded | 0 / 2 | No randomisation or blinding stated — scores zero (not stated in the record — scored 0) |
| Times cited | 5 / 7 | Cited 231 times (OpenAlex, 2026-10-10) |
| Citations per year | 4 / 5 | 21.0 citations a year over 11 year(s) since 2017 |
| Impact for its field and year | 5 / 6 | Cited 22.7× the average for papers of its field and year (OpenAlex FWCI) |
| Cited by studies here | 0 / 6 | No other study in this library cites it |
| Still being cited | 3 / 4 | Cited 128 times in 2024–2026 (2026 still in progress; OpenAlex) |
| Senior author's track record | 2 / 4 | Last-listed author Georges M. Nemer: h-index 32 (OpenAlex, whole career) |
| Institution's track record | 2 / 3 | University of Toronto: institution h-index 1,923 (OpenAlex) |
| Multi-centre collaboration | 2 / 3 | OpenAlex lists 4 institution(s) in 3 countries |
| Indexed in PubMed | 2 / 2 | Indexed in PubMed (PMID 28508374) |
| Free to read | 0 / 2 | Behind a paywall — scores zero |
| Points | 45 / 96 | Scored on 19 of 20 parts. We have no data for the rest, so they are left out: 45 of the 96 points we could judge it on is 47 out of 100. |
| Total | 47 / 100 | — |
What each of these 20 components measures, and what this score is not →
Read the original
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Cite this study APA, Vancouver, BibTeX · download .bib or .ris
Built from the record alzhub holds for this paper, not looked up. Volume, issue and page numbers are not held in the record. Check the citation against the original before you use it.
APA 7th
El-Hachem, N., Haibe-Kains, B., Khalil, A., Kobeissy, F. H., & Nemer, G. (2017). AutoDock and AutoDockTools for Protein-Ligand Docking: Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1(BACE1) as a Case Study. Methods in molecular biology (Clifton, N.J.). https://doi.org/10.1007/978-1-4939-6952-4_20
Vancouver
El-Hachem N, Haibe-Kains B, Khalil A, Kobeissy FH, Nemer G. AutoDock and AutoDockTools for Protein-Ligand Docking: Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1(BACE1) as a Case Study. Methods in molecular biology (Clifton, N.J.). 2017. doi:10.1007/978-1-4939-6952-4_20. PMID: 28508374.
BibTeX
@article{elhachem2017-28508374,
author = {El-Hachem, N. and Haibe-Kains, B. and Khalil, A. and Kobeissy, F. H. and Nemer, G.},
title = {{AutoDock and AutoDockTools for Protein-Ligand Docking: Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1(BACE1) as a Case Study}},
journal = {Methods in molecular biology (Clifton, N.J.)},
year = {2017},
doi = {10.1007/978-1-4939-6952-4_20},
pmid = {28508374},
url = {https://doi.org/10.1007/978-1-4939-6952-4_20}
}