This startup offers a molecular modeling and simulation software platform for pharmaceutical and materials science companies. Their tools simplify the setup of complex molecular dynamics simulations, enabling easier analysis of biological and nanomaterial systems.
Funding
Funding not disclosed
Founders
Product
Problem
Pharmaceutical, biotechnology, and nanotechnology companies face challenges in efficiently modeling and simulating complex biological and nanomaterial systems. Existing tools often require specialized expertise and can be cumbersome to use, hindering computer-aided drug discovery and materials design.
Solution
MolCube provides a software platform designed to streamline molecular modeling and simulation workflows. The platform consists of three main modules: MolCube-Builder for model building and input generation, MolCube-Simulator for job submission and management on cloud systems, and MolCube-Analyzer for simulation trajectory analysis. MolCube-Builder is designed to be accessible as a web server or for local/cloud installation, eliminating the need for commercial third-party software. The platform aims to simplify the process of simulating complex biomolecular and material systems, facilitating drug and material discovery.
Target Audience
The primary target audience includes pharmaceutical, biotechnology, and nanotechnology companies involved in molecular modeling and simulation for drug discovery and materials science.
Features
- MolCube-Builder API for complex model building and simulation input generation
- Supports various force fields including CHARMM (classical | Drude), AMBER, Martini 3, LF | LF-fast (with Espaloma Charge), LF = GAFF, OpenFF, and XFF
- Input generation for GROMACS, NAMD, GENESIS, AMBER, OpenMM, and Desmond
- Reads PDB, PDBx/mmCIF, and GROMACS gro formats, with capabilities for missing residue detection and modeling, nonstandard AA/NA reading and modeling, and glycoconjugates reading and modeling
- Ligand reader and modeler with multiple ligand uploading or substituent drawing, ligand force field generation, and ligand alignment with reference PDB
- Solution builder for cubic and truncated octahedron systems
- Membrane builder for bilayer, nanodisc, micelle, vesicle, and hex phase systems, with or without protein, glycolipids, LPS, and PEG-lipids
- High-throughput simulator for solution and membrane systems, enabling multiple protein-ligand simulation setup
- Alchemical Free Energy Simulator (AFES) for solution and membrane systems, supporting BLaDE-MSLD and Amber-TI