Molecular Modeling, Simulation & AI Drug Discovery Software

MolCube has been developing a global-leading computational platform to provide an ultimate solution for modeling and simulation of complex biomolecular and/or material systems that enables drug and material discovery.

Overview

MolCube-Designer

MolCube-Designer is for AI-based model generation, automatically proposing and creating diverse molecular structures such as proteins, ligands, and complexes. It streamlines the design process, expands the scope of exploration, and helps researchers validate hypotheses more efficiently.

MolCube-Builder

MolCube-Builder is for complex model building and simulation input generation. MolCube-Builder does not require any commercial third-party software and will be available as a web server or can be installed locally or in your cloud system. 

MolCube-Simulator

MolCube-Simulator is for job submission to designated cloud systems and job management.

MolCube-Analyzer

MolCube-Analyzer is for simulation trajectory analysis on designated cloud systems.

Tutorial Video Demos

Current Development Status of Cubie

Current Development Status of MolCube-Builder

Available:

  • MolCube-Builder API

    - Install Package: pip install -U <http://deployments.molcube.com/api/molcube-0.4.2-py3-none-any.whl

    - User Guide: https://molcube.github.io/molcube-api

    - API Example:https://github.com/molcube/molcube-api-example

  • Force Fields

    CHARMM (classical | Drude) | AMBER | Martini 3
    LF | LF-fast  (with Espaloma Charge), LF = GAFF | OpenFF | XFF

  • Input Generation

    GROMACS | NAMD | GENESIS | AMBER | OpenMM | Desmond

  • PDB Reader

    - reading PDB | PDBx/mmCIF | GROMACS gro formats

    - missing residue detection & modeling

    - nonstandard AA / NA reading & modeling

    - glycoconjugates reading & modeling (with predefined N-/O-glycans)

    - (covalent) ligand reading & modeling

    - ligand FF reading (CHARMM | AMBER | GROMACS)

    - ligand chemical structure view & edit

    - heme reading & coordination

    - cyclic peptide modeling

    - peptide stapling reading & modeling

    - mutation | protonation

    - disulfide bond | phosphorylation | lipidation

    - pKa-based protonation assignment and ligand FF @ given pH

    - Post-translational Modifications

    - Side chain orientation

    - GPI anchor

  • Bioconjugate Modeler

    - automatic conjugation with predefined libraries of 100+ linker and 100+ payload

    - conjugation with peptide or RNA modelled using PDB Reader

  • Ligand Reader & Modeler

    - multiple ligand uploading or substituent drawing

    - ligand force field generation

    - ligand alignment with the reference PDB Reader project

  • Solution Builder

    - cubic | truncated octahedron

  • Membrane Builder

    - with or without protein

    - bilayer | double bilayer | nanodisc | micelle | vesicle | hex phase

    - glycolipids | LPS | PEG-lipids

  • Multicomponent Assembler

    - solution | membrane

  • Implicit Solvent Modeler

    - Simulation with various GB models (GBn, GBn2, HCT, OBC1, and OBC2)

    - AMBER | OpenMM | NAMD | GENESIS

  • Alchemical Free Energy Simulator (AFES)

    - solution | membrane

    - Absolute binding Free energy: Amber-TI, Gromacs-NETI, OpenMM-FEP

    - Relative binging Free energy: Amber-TI, Gromacs-NETI, BLaDE-MSLD, OpenMM-FEP

    - Mutation free energy: Amber-TI, Gromacs-NETI, BLaDE-MSLD

  • High-Throughput Simulator

    - solution | membrane

    - multiple protein-ligand simulation setup

  • Ligand Docker

    - vina | smina | RxDock | DiffDock

  • Enhanced Sampler

    - Accelerated MD (aMD)

    - Gaussian accelerated MD (GaMD)

    - Steered MD (SMD)

    - Adaptive Biasing Force (ABF)

    - Metadynamics (MTD)

    - Replica Exchange Solute Tempering 2 (REST2)

  • Hybrid ML/MM Builder

    - Simulation with NNPs for ligands and classical FFs for proteins

    - AMBER | OpenMM

  • Constant pH Simulator

    - Simulate dynamic protonation states on user-selected titratable residues

    - AMBER | GROMACS | NAMD

Current Development Status of MolCube-Simulator

Available:

  • Solution / Membrane

    - Job submission and management of solution and membrane MD simulations

    - GROMACS | OpenMM

  • Alchemical Free Energy Simulation

    - Job submission and management of AFEC

    - AMBER | GROMACS | OpenMM | BLaDE

  • Ligand Docker

    - Job submission and management of ligand docking

    - vina | smina | RxDock | DiffDock

Available:

  • Solution / Membrane

    - Trajectory analysis of solution and membrane simulations

    - Result visualization and download

  • Alchemical Free Energy Simulation

    - Post-AFES analysis for binding affinities

Upcoming:

  • Covalent Ligand Docker

  • Polymer Builder

  • Nanomaterial Modeler

  • Weighted Ensemble Sampler

  • QM/MM Interfacer

Upcoming:

Current Development Status of MolCube-Analyzer

Upcoming:

  • Ligand Docker

What is Cubie?

Cubie is an agentic AI assistant for MolCube that transforms natural language instructions into configured projects while providing advice and explanations of MolCube-Apps and configuration options. Powered by Gemini, integrated with RCSB, native visualization, and access to a user's Molcube project database, Cubie is a powerful productivity multiplier for the MolCube ecosystem.

Currently in development and planned for future release.

Current Development Status of MolCube-Designer

Available:

  • Boltz

    - Biomolecules & ligand prediction
    - Ligand binding affinity calculation‍

  • Protenix

    - Biomolecules & ligand prediction

  • Ligand Binding Site (LBS) Finder

  • Protein (Peptide) Design AI

    - RFdiffusion

    - ProteinMPNN

    - BoltzGen

  • Antibody Design AI

    - RFantibody

    - ProteinMPNN

    - Boltz-2 | Protenix | RoseTTAFold

  • ADMET Predictor & Optimizer

    - Candidates drug design via AI-based ADMET prediction and parameter optimization

  • AI QSAR

    - Predicts QSAR by data curation, descriptor calculation and training data set

  • Chem Patent Searcher

Upcoming:

  • Ligand Generation AI

    - REINVENT4

  • Membrane Permeability Predictor

FAQs

  • MolCube is a comprehensive molecular simulation platform that provides researchers with powerful tools for molecular dynamics simulations, analysis, and visualization.

  • MolCube uses advanced computational algorithms to simulate molecular behavior, allowing researchers to model complex biological and chemical systems with high accuracy.

  • MolCube offers user-friendly interfaces, high-performance computing capabilities, comprehensive analysis tools, and seamless integration with existing research workflows.

  • Yes, MolCube implements enterprise-grade security measures to protect your research data and intellectual property, with options for both cloud and on-premises deployment.

  • MolCube offers flexible token-based pricing with various packages to suit different research needs and budgets. Contact us for detailed pricing information.

  • Absolutely! MolCube is designed to integrate seamlessly with existing research workflows and supports multiple molecular dynamics engines including GROMACS, AMBER, and CHARMM.