docking experiment

USAGE SUMMARY

The phrase "docking experiment" is correct and usable in written English.
It can be used in scientific or technical contexts, particularly in fields like biology, chemistry, or computer science, where it refers to the process of studying the interaction between molecules, such as a drug and its target protein. Example: "The docking experiment revealed promising results for the new drug candidate's binding affinity to the target enzyme."

✓ Grammatically correct

Science

Human-verified examples from authoritative sources

Exact Expressions

59 human-written examples

One hundred cycles were performed per docking experiment, and for each ligand 100 independent dockings were carried out.

BioMed Research International

A possible explanation for this efficacy difference is proposed by docking experiment performed with molecular model of the receptor.

Bioorganic & Medicinal Chemistry Letters

These 284 peptides were used as the ligands for docking experiment with ACE. Figure 1 Length distribution of peptides derived from P. esculenta proteins by virtual hydrolysis.

Bioresources and Bioprocessing

For validation of docking experiment, co-crystallised inhibitor 6-methoxy-9-methyl[1,3]dioxolo[4,5-h]quinolin-8 9 h)-one was used as control molecule targeting anticancer protein aromatase (PDB: 3EQM), quinone reductase (PDB: 3G5M) (Table 7).

Chemistry Central Journal

Before docking experiment, the title compound 3 was prepared for docking by minimizing its energy at B3LYP functional and 6 311G (d,p) basis set using Gaussian 03 software.

Chemistry Central Journal

From the solvent exposed surface residues, the most notable ones (V51, L73, F75, G76, R99, P101, H102 and K103) were selected as obligatory contacts for docking experiment.

BMC Genomics

According to the CAPRI community-wide protein protein docking experiment, this type of approximation gives good results for a large fraction of complexes (Lensink and Wodak, 2013).

eLife

An in silico glycan docking experiment indicated that conserved Y468 (PglB Cj Y462) may interact with the N-acetyl group of the innermost sugar of the transferred oligosaccharide [ 11].

BMC Biotechnology

As demonstrated by the results of CAPRI (Critical Assessment of Prediction of Interactions) communitywide protein docking experiment, for such cases modern computational docking methods, including automated servers, are capable of generating docked conformations that agree well with the X-ray structure of the complex (Lensink and Wodak, 2013).

eLife

The docking parameters set to perform each docking experiment were derived from 100 different runs that were set to terminate after a maximum of 2,500,000 energy evaluations, elitism of 1, mutation rate of 0.02, cross-over rate of 0.8, and local search rate of 0.06.

BioMed Research International

Human-verified similar examples from authoritative sources

Similar Expressions

1 human-written examples

Initially, the performance of docking software was tested by re-docking experiment.

Chemistry Central Journal

Expert writing Tips

Best practice

When describing a "docking experiment", specify the software and scoring function used to ensure reproducibility and clarity in your methodology.

Common error

Avoid stating that a single successful docking result validates a hypothesis. Molecular docking requires rigorous validation, including statistical analysis and comparison with experimental data, to confirm the reliability of the findings.

Linguistic Context

The phrase "docking experiment" functions as a compound noun, typically serving as the subject or object of a sentence. As shown in Ludwig, it commonly refers to a computational method in molecular biology and drug discovery.

Expression frequency: Very common

Frequent in

Science

100%

Less common in

News & Media

0%

Formal & Business

0%

Academia

0%

Ludwig's WRAP-UP

In summary, the term "docking experiment" is a well-established phrase in scientific literature, specifically within the fields of molecular biology, chemistry, and drug discovery. According to Ludwig, the phrase is grammatically sound and very frequently used. The analysis reveals that it functions as a noun phrase, primarily used to describe a computational method for predicting molecular interactions. Given its usage in scientific contexts, the register is formal and scientific. When discussing "docking experiments", ensure you specify the software and validation methods used. Consider alternatives like "molecular docking simulation" or "in silico docking study" for greater precision. Avoid oversimplifying the validation process to maintain scientific rigor.

More alternative expressions

Phrases that express similar concepts, ordered by semantic similarity:

molecular docking simulation

Replaces "experiment" with "simulation", emphasizing the computational nature of the process. The similarity score reflects the direct relationship in meaning.

in silico docking study

Specifies that the docking is performed using computer simulations, offering more detail about the experimental method. The similarity score reflects the direct relationship in meaning.

ligand docking assay

Replaces "experiment" with "assay", a term common in biochemistry and molecular biology to describe a procedure to analyze a sample. The similarity score reflects the direct relationship in meaning.

molecular docking procedure

Uses "procedure" instead of "experiment", focusing on the standardized steps involved. The similarity score reflects the direct relationship in meaning.

virtual docking screen

Highlights the screening aspect, suggesting a process of identifying potential binding candidates, which is a common application of docking experiments. The similarity score reflects the direct relationship in meaning.

computational docking analysis

Emphasizes the analytical aspect of docking using computational methods. The similarity score reflects the direct relationship in meaning.

docking trial

Suggests a test or attempt at docking. The similarity score reflects the direct relationship in meaning.

docking investigation

Uses investigation highlighting the exploratory nature of the experiment. The similarity score reflects the direct relationship in meaning.

docking run

Focuses on a single execution of a docking simulation. The similarity score reflects the direct relationship in meaning.

docking exercise

Uses exercise suggesting a practical application of docking. The similarity score reflects the direct relationship in meaning.

FAQs

How is a "docking experiment" used in drug discovery?

A "docking experiment" is used to predict the binding affinity and orientation of small molecules to a target protein, helping researchers to identify potential drug candidates. It's a cost-effective way to screen compounds before more expensive lab experiments.

What software is commonly used for "docking experiments"?

Common software includes AutoDock Vina, Glide, and MOE. Each program uses different algorithms and scoring functions, so the choice depends on the specific research question and available resources.

How do I validate the results of a "docking experiment"?

Validation involves comparing docking scores with experimental binding affinities (e.g., IC50 or Ki values), performing mutation studies to assess the importance of key residues, and ensuring the predicted binding mode is consistent with known structural information.

What are some limitations of "docking experiments"?

Limitations include the accuracy of the force field used to calculate binding energies, the treatment of protein flexibility, and the potential for false positives. "Docking experiments" are also limited by the quality of the protein structure used.