No Single Tool Does It All.

Molecular modelling has no one-size-fits-all engine — each tool excels at something different. Plexus Labs brings the leading open-source and commercial interfaces together in one preconfigured workspace, so you can pick the right expert for every task, run multiple tools and versions side by side, and compare their results without ever leaving the platform. No installation, no dependency management, no operational overhead — just the science.

function Descriptor Interfaces gps_fixed Docking Interfaces neurology P-L Prediction Interfaces animation MD Interfaces

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Descriptor Interfaces

Generate molecular descriptors and fingerprints from structures at scale. Mix and match toolkits to capture the chemical features that matter for your models.

RDKit

Open-source cheminformatics toolkit for descriptors, fingerprints and 2D/3D handling.

PaDEL

Computes a broad set of 1D, 2D and 3D descriptors plus fingerprints.

Mordred

Fast calculator covering 1800+ two- and three-dimensional descriptors.

CDK

Chemistry Development Kit providing descriptors and structure utilities.

BlueDesc

Command-line descriptor calculator producing model-ready feature sets.

Open Babel

Chemical toolbox for format conversion and descriptor extraction.

Chemopy

Python library for computing molecular descriptors and fingerprints.

gps_fixed

Docking Interfaces

Predict binding poses and score protein-ligand interactions. Run established docking engines side by side without local setup.

DOCK

Classic molecular docking suite for pose prediction and screening.

AutoDock

Widely used engine for automated ligand-receptor docking.

rDock

Fast, configurable docking for proteins and nucleic acids.

FlexAID

Flexible docking handling side-chain and ligand flexibility.

Vg GPU

VinaGPU

GPU-accelerated AutoDock Vina for high-throughput docking.

neurology

P-L Prediction Interfaces

Deep-learning models that predict protein-ligand binding directly from structure. State-of-the-art approaches ready to run on demand.

Dd AI/ML

DiffDock

Diffusion generative model for blind protein-ligand docking.

Db AI/ML

DynamicBind

Predicts ligand-specific conformations with dynamic receptor states.

Tb AI/ML

TankBind

Trigonometry-aware model for fast binding structure prediction.

Eb AI/ML

EquiBind

Geometric deep learning for direct-shot binding pose prediction.

NP AI/ML

NeuralPLexer

Generative model predicting protein-ligand complex structures.

animation

MD Interfaces

Run molecular dynamics simulations with leading engines. Configure, launch and monitor trajectories from one unified interface.

LAMMPS

Massively parallel classical MD for materials and biomolecules.

GROMACS

High-performance MD optimized for biomolecular systems.

NAMD

Scalable MD engine designed for large biomolecular assemblies.

CHARMM

Comprehensive package for simulation and analysis of macromolecules.

Amber

Suite of force fields and tools for biomolecular MD simulations.

22+ interfaces and growing

We add new tools regularly. Don't see the engine your research depends on? Let us know and we'll work to bring it onto the platform.

Request an Interface

All the Power.
None of the Complexity.

Open-source tools have always been remarkably capable — often matching or exceeding commercial alternatives. We kept that power and removed the friction. Every interface comes preconfigured and production-ready, so you can launch simulations, monitor progress, and analyze results in a few clicks.

Request a Custom Demo