MolNexus Molecular docking desktop software

Windows desktop scientific software · Available now

Prepare, run, and review molecular docking in one workspace.

MolNexus brings receptor and ligand preparation, interaction-box setup, AutoDock Vina execution with selectable Vina and Vinardo scoring, pose review, and complex export into a focused Windows desktop application.

  • Windows 10/11 · 64-bit
  • Vina + Vinardo scoring
  • Embedded Mol* viewer
Try MolNexus free Buy MolNexus — US$499 See the real interface

Version 0.1.1 · Free trial includes two ligand dockings; the full license is a digital Windows download.

Scoring function
MolNexus 0.1.1 development interface showing the validated PDB 1IEP and imatinib Vina redocking control, interaction box, molecular pose, and five ranked poses
Vina selected Validated 1IEP/imatinib control · five retained poses
Authentic v0.1.1 interface captures. Both scoring functions use the same preparation, search, review, and export workflow; displayed outputs are not a cross-method benchmark.

Simple perpetual license

One purchase. One Windows PC at a time.

Install MolNexus on one Windows computer and keep using the purchased version indefinitely. If you replace the computer, move the license after removing MolNexus from the previous PC.

Delivery Digital download

The Windows installer is provided after successful payment.

Updates 12 months included

Keep the last eligible version permanently after that period.

MolNexus 0.1.1

US$ 499

One-time purchase

  • One Windows PC at a time
  • Perpetual use of the purchased version
  • Transferable to a replacement PC
  • 12 months of product updates
  • Downloadable Windows application
Buy MolNexus — US$499
Evaluate before purchasing Try two ligand dockings free

The free MolNexus trial is a Windows download limited to two ligand docking runs. Purchase the perpetual license whenever you are ready to activate the full version.

Free-trial delivery and paid checkout are processed by Lemon Squeezy; it acts as Merchant of Record for the paid order.

One continuous workflow

Move from molecular inputs to reviewable poses without stitching separate interfaces together.

The preparation, configuration, execution, and review stages remain visible in the same project workspace.

  1. 01

    Load the receptor

    Open a local PDB or mmCIF structure, or retrieve a structure by RCSB PDB identifier.

  2. 02

    Prepare the study

    Review receptor clean-up decisions, add one or many ligands, and create docking-ready structures.

  3. 03

    Define the search

    Position the interaction box, choose Vina or Vinardo scoring, and set exhaustiveness, pose count, energy range, and seed.

  4. 04

    Review and export

    Compare affinities and RMSD values, inspect poses in 3D, and export results or protein–ligand complexes.

Complete UI sweep

Follow verified inputs from preparation to saved history.

These authentic captures come from MolNexus 0.1.1 running in Tauri development mode at revision 06429bb. They document a 1IEP/imatinib Vina redocking control and a CDK2 ligand-preflight batch. The scoring preview above shows the corresponding Vinardo selection in the same application workflow.

Redocking control
0.375 Å mode-1 native RMSD
Ligand preflight
2 / 3 / 3 Ready / Review / Rejected
CDK2 batch
2 ligands 10 retained poses
Displayed output
−6.991 best CDK2 score shown, kcal/mol
01

Validated redocking control

Keep the protocol, pose, and result table in one view.

PDB 1IEP, imatinib, the 20 Å cubic search box, Vina settings, the selected molecular pose, and five ranked modes remain visible together for direct review.

MolNexus 0.1.1 showing the validated PDB 1IEP and imatinib Vina redocking control, 20 angstrom interaction box, seed 42, molecular pose, and five ranked modes
Mode 1 scored −13.225 kcal/mol and reproduced the native ligand pose at 0.375 Å RMSD under the frozen protocol.
02

Preparation and preflight

Resolve molecular-input decisions before computation.

MolNexus exposes receptor cleanup choices and classifies every ligand source as Ready, Review, or Rejected before docking can begin, rather than hiding preparation behind a progress bar.

MolNexus 0.1.1 receptor preparation review for the CDK2 structure showing 2,588 atoms, 284 residues, one chain, 303 waters, and explicit cleanup controls
CDK2 receptor review with explicit exclusions recorded before PDBQT generation.
MolNexus 0.1.1 CDK2 ligand preflight showing eight YuelDesign sources classified as two Ready, three Review, and three Rejected before docking
A visible decision boundary: two Ready, three Review, and three Rejected sources before the run is authorized.
03

Protocol control

Keep the batch and every consequential parameter visible.

The CDK2 batch is configured with a documented search box, scoring function, exhaustiveness, pose count, energy range, seed, and CPU allocation before execution.

  • Two Ready ligand sources selected
  • Vina, exhaustiveness 16, seed 20260725
  • Search box 24 × 20 × 20 Å
MolNexus 0.1.1 CDK2 docking protocol showing two selected ligands, Vina scoring, 24 by 20 by 20 angstrom search box, exhaustiveness 16, five poses, and seed 20260725
The exact protocol used for the current two-ligand CDK2 batch is visible before execution.
04

Pose review

Move from the result table to molecular evidence in one view.

Select a row to display its docked pose alongside the receptor and its 2D ligand structure while retaining affinities, RMSD values, sequence, box geometry, and the run configuration.

Completed MolNexus 0.1.1 CDK2 docking workspace showing two completed ligands, ten retained poses, the selected molecular pose, affinity values, and RMSD columns
Two of two Ready ligands completed. Ten retained poses remain sortable and inspectable; the best score shown in this interface run was −6.991 kcal/mol.
05

Persistent job history

Reopen, compare, and export completed work.

The completed batch is saved to the local SQLite history with summary metrics, search, multi-row selection, job reopening, PDF and Excel exports, and downloadable docked complexes.

MolNexus 0.1.1 local docking history showing the saved CDK2 job, two ligands, ten poses, best score, creation time, search, reopening, and export controls
This is the job created by the same CDK2 walkthrough, not a populated mockup. It can be reopened or exported without rerunning docking.

About the displayed values: these runs were configured to validate and present the application workflow. Their docking scores and timings are interface evidence, not a performance benchmark or a biological conclusion.

Built around the scientific task

The controls and context needed to run a docking study.

Integrated molecular view

Inspect the receptor, interaction box, sequence, ligands, and docked poses in an embedded Mol* workspace.

Explicit preparation

Prepare supported receptor and ligand inputs through a defined Meeko and AutoDock Vina boundary.

Configurable docking

Choose Vina or Vinardo scoring, set the interaction box and core run parameters, and keep the configuration beside the structure.

Reviewable outputs

Compare modes, affinity, and RMSD; inspect a selected pose; then export results and validated complexes.

Product specifications

Know what you receive before purchasing.

The current commercial package is a locally installed Windows desktop application. Scientific results remain on the user's PC unless the user deliberately exports or shares them.

Application
MolNexus 0.1.1 · Windows desktop software
Operating system
Windows 10 or Windows 11, 64-bit
Delivery
Digital installer provided after purchase
Free trial
Windows download · Two ligand docking runs
License
One Windows PC at a time · Perpetual use
Updates
Updates released during the first 12 months are included
Download and storage
Approximately 87 MB download · 2 GB free disk space recommended
Docking engine
AutoDock Vina 1.2.7
Scoring functions
Vina and Vinardo
3D viewer
Embedded Mol*
Receptor inputs
PDB, CIF/mmCIF, or RCSB PDB identifier
Ligand inputs
SDF, MOL, MOL2, and PDBQT
Outputs
Result tables, CSV data, PDB complexes, and ZIP bundles
Project continuity
Local SQLite docking-job history
Availability
Free trial and perpetual license available through Lemon Squeezy

Scientific use and engine transparency

For research use only.

MolNexus is not intended for clinical diagnosis, medical treatment decisions, patient management, or regulatory use. Users must independently validate scientific inputs, methods, outputs, and conclusions.

MolNexus is an independent commercial desktop application that integrates AutoDock Vina, an open-source molecular docking engine. AutoDock Vina is not owned by or affiliated with BioChemIntelli.

Read Third-Party Notices

Created and developed by Jorge F. Beltrán, PhD, scientific software developer, AI engineer and computational biologist.

MolNexus

A focused desktop path from structures to docked poses.

Review the real interface and specifications, try two ligand dockings free, or purchase the perpetual Windows license.

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