Irum Abbasi, I'll answer this question metaphorically

AutoDock Vina is a reliable sedan—gets you where you need to go efficiently.

RosettaDock is an all-terrain vehicle—handles rough and complex terrains but uses more fuel.

Glide and GOLD are like sports cars—high performance but come with higher costs including computational resources.

Web based such as SwissDock and GalaxyDock provide consistent results with small protein-ligand complexes

Thank you Hemant Goyal

Irum Abbasi !!

I am sharing this link (https://biochemia.uwm.edu.pl/en/docking-2/) as it may be helpful. You can also test a single ligand with a protein across multiple platforms and compare their results. This comparison might provide insights into which platform offers higher accuracy or precision.

There are numerous web servers available for molecular docking, along with various computer software tools, some of which are open-access and others that are paid. Free software options include AutoDock and PyRx, while paid software includes MVD, Schrodinger, MolSoft, and Biovia (Discovery Studio), among others. Although paid software is generally assumed to provide more accurate results, the outcomes may still vary when comparing two different paid software programs. This variation is primarily due to differences in their built-in algorithms and scripting methodologies.

Each tool or server provides accurate results based on its underlying algorithm and scripting. However, to ensure reliability, you can cross-check your results using multiple tools for validation.

Irum Abbasi

PyRx is a free molecular docking software that provides a user-friendly GUI for docking studies using AutoDock and AutoDock Vina. It allows easy ligand preparation, batch docking, and visualization through Open Babel. PyRx is widely used for small molecule docking but has limitations in handling large protein-ligand complexes and flexible docking. It lacks advanced post-docking analysis tools, requiring external software like PyMOL or Discovery Studio. Despite these limitations, it remains a popular choice for researchers due to its simplicity and efficiency. Alternatives include Glide, SwissDock, and HADDOCK, depending on the complexity of the study.