Best Molecular Modeling Software for Python
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Compare the Top Molecular Modeling Software that integrates with Python as of December 2025
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This a list of Molecular Modeling software that integrates with Python. Use the filters on the left to add additional filters for products that have integrations with Python. View the products that work with Python in the table below.
What is Molecular Modeling Software for Python?
Molecular modeling software is software used by chemists and biologists to visualize, simulate, and predict the properties of molecules. It can be used to design new drug molecules or study existing ones. The software uses computational algorithms and graphical user interfaces to depict molecular structure, as well as analyze functions such as bond lengths, angles, and energies. It can also simulate molecular dynamics processes to understand chemical reactivity on a molecular level. Compare and read user reviews of the best Molecular Modeling software for Python currently available using the table below. This list is updated regularly.
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YASARA
YASARA
YASARA is a molecular graphics, modeling, and simulation program for Windows, Linux, MacOS, and Android developed in 1993, that finally makes it really easy to answer your questions. With an intuitive user interface, photorealistic graphics, and support for affordable virtual reality headsets, shutter glasses, autostereoscopic displays, and input devices, YASARA creates a new level of interaction with the 'artificial reality', that allows you to focus on your goal and forget about the details of the program. YASARA is powered by PVL (Portable Vector Language), a new development framework that provides performance way above traditional software. PVL allows you to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard PCs, making use of GPUs if available. You can push and pull molecules around and work with dynamic models instead of static pictures.Starting Price: Free -
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Promethium
Promethium
Promethium is a GPU-powered chemistry simulation platform designed to accelerate drug and materials development by enabling faster and more accurate quantum chemistry calculations. Built from the ground up for NVIDIA datacenter GPUs like A100, it employs novel QC Ware streaming algorithms to achieve unprecedented computational speed and high throughput-to-power consumption ratios. It supports density functional theory calculations on systems with up to 2,000 atoms, allowing simulations of large molecular systems that are not feasible with legacy CPU-powered ab initio codes. For instance, a single-point calculation of a 2,056-atom protein can be completed in 14 hours on a single GPU. Promethium offers a range of capabilities, including single-point energy calculations, geometry optimization, conformer search, torsion scan, reaction path optimization, transition state optimization, interaction energy computations, and relaxed potential energy surface scans.Starting Price: $30 per hour -
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PyMOL
PyMOL
PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger. PyQt interface replaces Tcl/Tk and MacPyMOL on all platforms. Better third-party plugin and custom scripting support. A comprehensive software package for rendering and animating 3D structures. A plug-in for embedding 3D images and animations into PowerPoint presentations. PyMOL is a commercial product, but we make most of its source code freely available under a permissive license. The open-source project is maintained by Schrödinger and ultimately funded by everyone who purchases a PyMOL license. Open access incentive executables. Liberal evaluation policy. Improved fuse command (disallows hypervalent bonds, substitutes monovalent atoms instead of attaching to them) Properties inspector now supports unsetting settings with the “delete” key. Fix workspace disappearing on specific display resolutions.
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