molecular docking protocol

USAGE SUMMARY

The phrase "molecular docking protocol" is correct and usable in written English.
It can be used in scientific or research contexts, particularly in biochemistry or pharmacology, to refer to a method for predicting how molecules, such as drugs, interact with biological targets. Example: "The researchers followed a molecular docking protocol to evaluate the binding affinity of the new compound to the target protein."

✓ Grammatically correct

Science

Human-verified examples from authoritative sources

Exact Expressions

3 human-written examples

Twenty-two HLA-B*57 01 HLA-B*57 01inders were identified using the molecular docking protocol.

Journal of Cheminformatics

This 3D model together with the reported structure of Diva [22] were used in the molecular docking protocol, which also included information from the NMR data on the interacting surface in Diva as experimental restraints (Materials and Methods).

Plosone

In contrast, the molecular docking protocol performed poorly with enrichment factors <30% in all cases.

BioMed Research International

Human-verified similar examples from authoritative sources

Similar Expressions

57 human-written examples

Developing molecular docking protocols that effectively identify hits can be a challenging undertaking, especially when it comes to the preparation of complex proteins, such as HLA [37].

Journal of Cheminformatics

Filtered structures were then used in more sophisticated molecular docking simulations protocols (i.e., Glide/SP; Glide/XP; Glide/IFD; Glide/QPLD, and GOLD).

Journal of Molecular Graphics and Modelling

At first, the complex obtained after molecular docking using Glide XP protocol was solvated in a triclinic periodic box of TIP3 water and then neutralized with appropriate number of counter-ions.

BMC Cancer

In this paper, the binding modes of them against the wild type and mutant SMO receptors were identified to gain insights into the resistant and non-resistant factors, based on a comprehensive protocol involving molecular docking, molecular dynamic simulations, free energy calculation and decomposition.

Pharmacological Research

In this study, we sketched and validated a possible virtual screening protocol using molecular docking as the main technique.

ChemMedChem

Different binding models of the substrate enantiomers to the active site of CRL were investigated by applying a computational protocol based on molecular docking, conformational analysis, and energy minimization procedures.

Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology

The root mean square deviation (RMSD) of all atoms between these two conformations was 1.58 Å, indicating that the protocol set for molecular docking is accurate.

BioMed Research International

The root mean squared deviations (RMSD) of all atoms between these two conformations (redocked and original crystal structure from protein data bank) were found to be 1.87 Å only, suggesting that the protocol set for molecular docking is fairly efficient and faithfully reproduces the crystallographic complex with a high degree of similarity.

BioMed Research International

Expert writing Tips

Best practice

When describing a "molecular docking protocol", clearly specify the software and parameters used to ensure reproducibility.

Common error

Avoid describing the "molecular docking protocol" in overly general terms. Always provide specific details about the software, force fields, and search parameters used to ensure clarity and reproducibility.

Linguistic Context

The phrase "molecular docking protocol" functions as a noun phrase, typically serving as the subject or object of a sentence. It refers to a specific set of procedures used in computational biology to predict the binding of molecules. Ludwig AI provides examples of its use in scientific contexts.

Expression frequency: Rare

Frequent in

Science

100%

Less common in

News & Media

0%

Formal & Business

0%

Ludwig's WRAP-UP

The phrase "molecular docking protocol" is a noun phrase used in scientific contexts to describe a set of computational procedures for predicting molecular binding. Ludwig AI analysis confirms its grammatical correctness and notes its primary usage in science, particularly in cheminformatics and molecular modeling. It is most effectively used when specifying the software and parameters to ensure reproducibility. While grammatically sound, it's important to avoid overgeneralization and provide specific details when using this phrase. Related terms include "docking simulation procedure" and "computational docking method".

More alternative expressions

Phrases that express similar concepts, ordered by semantic similarity:

docking simulation procedure

Replaces "molecular" with "docking simulation" and "protocol" with "procedure", emphasizing the simulation aspect while keeping the procedural nature.

computational docking method

Uses "computational" to highlight the computational aspect of molecular docking, substituting "protocol" with "method".

in silico docking strategy

Replaces "molecular" with "in silico" to underscore the computational environment and uses "strategy" as a more general term for protocol.

molecular binding simulation workflow

Substitutes "docking" with "binding simulation" and "protocol" with "workflow", focusing on the binding aspect within a structured process.

ligand docking process

Uses "ligand docking" to specify the ligand-receptor interaction and "process" as a more general term for protocol.

molecular docking technique

Replaces "protocol" with "technique", highlighting the technical aspect of the docking process.

structure-based docking approach

Emphasizes the structure-based aspect of molecular docking, using "approach" instead of protocol to suggest a broader methodology.

virtual screening docking plan

Uses "virtual screening" to contextualize the docking within a screening process and "plan" as a simplified term for protocol.

docking experiment design

Focuses on the experimental aspect of docking, substituting "molecular" with "docking experiment" and "protocol" with "design".

simulation docking guideline

Highlights the simulation aspect and uses "guideline" to suggest a less rigid structure than protocol.

FAQs

How is a "molecular docking protocol" used in research?

A "molecular docking protocol" is used to predict the binding orientation of a ligand to a protein or other biomolecule. This helps researchers understand molecular interactions and can be used in drug discovery to identify potential drug candidates.

What are the key components of a "molecular docking protocol"?

Key components include target protein preparation, ligand preparation, defining the search space, selecting a docking algorithm, setting scoring functions, and analyzing the results. Each step requires careful consideration to ensure accurate and reliable predictions.

What is the difference between a "molecular docking method" and a "molecular docking protocol"?

While the terms are often used interchangeably, a "molecular docking method" refers to the general technique of predicting ligand-protein interactions, while a "molecular docking protocol" is a detailed, step-by-step plan for conducting a specific docking experiment. Therefore, a "molecular docking method" describes a wider area while a "molecular docking protocol" defines a specific process.

Which software is commonly used to perform a "molecular docking protocol"?

Common software includes AutoDock Vina, Glide, GOLD, and MOE. Each program has its own strengths and weaknesses, so the choice depends on the specific research question and available resources.