Our 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-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.

Current Development Status of MolCube-Builder

Available:

  • MolCube-Builder API

  • 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 | conjugated) ligand reading & modeling

    - ligand FF reading (CHARMM | AMBER | GROMACS)

    - ligand chemical structure view & edit

    - heme reading & coordination

    - cyclic peptide modeling

    - peptide stapling

    - mutation | protonation

    - disulfide bond | phosphorylation | lipidation

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

  • 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 | nanodisc | micelle | vesicle | hex phase

    - glycolipids | LPS | PEG-lipids

  • High-Throughput Simulator

    - solution | membrane

    - multiple protein-ligand simulation setup

  • Alchemical Free Energy Simulator (AFES)

    - solution | membrane

    - BlaDE-FEP/MSLD

    - AToM-OpenMM

    - Amber-TI

    - Gromacs-TI

  • Ligand Docker

Upcoming:

  • Alchemical Free Energy Simulator (Residue | NAMD | GENESIS)

  • Ligand Binding Site Predictor

  • Enhanced Sampler

  • CpHMD Simulator

  • Polymer Builder

  • Nanomaterial Modeler