Molecular Docking Glossary
Understand the vocabulary of computational molecular docking — from binding affinity and scoring functions to virtual screening.
Run molecular docking →Molecular Docking
A computational method that predicts the preferred orientation and binding affinity of a ligand when bound to a protein target.
Read definition →Binding Affinity
The strength of interaction between a protein and ligand, typically measured as ΔG (kcal/mol) or Ki/IC50 values. More negative ΔG = stronger binding.
Read definition →RMSD
Root Mean Square Deviation — measures the average distance between atoms of superimposed structures. Used to compare docked poses against crystal structures.
Read definition →Vina (AutoDock Vina)
A widely-used open-source molecular docking program with improved scoring accuracy and speed over AutoDock4, employing a knowledge-based scoring function.
Read definition →GNINA
A deep-learning molecular docking tool that uses 3D convolutional neural networks for scoring, built on the AutoDock Vina framework.
Read definition →Virtual Screening
Computational evaluation of large compound libraries against a protein target to identify potential hits, using docking, pharmacophore, or ML-based methods.
Read definition →Protein Structure Prediction
Computational methods that predict the 3D structure of a protein from its amino acid sequence, enabling structure-based drug design.
Read definition →AlphaFold
DeepMind's AI system that predicts protein structures with near-experimental accuracy, revolutionizing structural biology and drug discovery.
Read definition →ESMFold
Meta AI's protein structure prediction model based on large language model embeddings, offering faster predictions without multiple sequence alignments.
Read definition →Protein Domain
A conserved, independently-folding region of a protein that often has a specific function, such as ligand binding or protein–protein interaction.
Read definition →Protein
A macromolecule composed of amino acid chains that performs enzymatic, structural, and regulatory functions in cells.
Read definition →Proteome
The complete set of proteins expressed by a genome, cell, tissue, or organism at a given time under specific conditions.
Read definition →IC50
The half-maximal inhibitory concentration — the concentration of a compound that inhibits a biological process by 50%, a key measure of drug potency.
Read definition →Drug Discovery
The process of identifying new therapeutic compounds through target identification, hit screening, lead optimization, and preclinical development.
Read definition →Pharmacodynamics
The study of how a drug affects the body — the relationship between drug concentration and its pharmacological effect.
Read definition →Pharmacokinetics
The study of how the body affects a drug — absorption, distribution, metabolism, and excretion (ADME) over time.
Read definition →ADME
Absorption, Distribution, Metabolism, Excretion — the four pharmacokinetic properties that determine a drug's bioavailability and dosing regimen.
Read definition →Bioavailability
The fraction of an administered drug that reaches systemic circulation, a critical parameter for oral drug formulation and dosing.
Read definition →Lead Compound
A chemical compound that shows promising biological activity and serves as the starting point for optimization into a drug candidate.
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