2024年4月16日发(作者：)

autodock-vina对接原理

英文版

The Principles of Autodock-VINA Docking

In the field of bioinformatics and computational biology,

docking is a crucial technique that simulates the interaction

between two or more molecules, such as proteins and ligands.

Among various docking software available, Autodock-VINA

stands out as a popular choice due to its accuracy, speed, and

ease of use. Understanding the principles behind Autodock-

VINA docking is essential for researchers working in this area.

1. Overview of Autodock-VINA

Autodock-VINA (VINAstands for Very Fast Simulated

Annealing) is a docking software that predicts the preferred

binding mode of a ligand within a protein binding site. It uses a

scoring function based on the interactions between atoms of

the ligand and the protein to evaluate different conformations

of the ligand. VINA is known for its speed and accuracy, making

it a popular choice for docking studies.

2. Principles of Docking with Autodock-VINA

a. Force Field and Scoring Function

Autodock-VINA employs a force field and a scoring function

to evaluate the energetics of ligand-protein interactions. The

force field calculates the interaction energy between atoms,

considering factors like bond lengths, bond angles, and torsion

angles. The scoring function, on the other hand, assigns a

numerical value to each conformation based on its stability and

fit within the binding site.

b. Simulated Annealing

Simulated annealing is a stochastic search algorithm that

mimics the physical process of annealing in metallurgy. In the

context of docking, simulated annealing helps Autodock-VINA

explore a wide range of conformations by gradually reducing

the temperature parameter. This process allows the software to