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CANDDIE Platform - Atomatrix
PLATFORM

CANDDIE Platform Service

A cloud-based drug design SaaS platform scheduled for launch in 2026.
Driving innovation in drug development with fully automated workflows accessible to everyone.

Next-Generation Drug Design Platform
Based on the Cloud

The CANDDIE Platform Service, encompassing Alphafold-based modeling, BARon, and Allopiper, is a fully automated simulation-based Computer-Aided Drug Design (CADD) platform that anyone can use, regardless of complex computational chemistry expertise.

Core Value of the CANDDIE Platform

CANDDIE: Computational Automation for New Drug Discovery with Intelligent Experimentation

Accessibility
Intuitive interface usable by CADD non-experts
Full Automation
Entire workflow automated, eliminating the need for specialized knowledge
Cloud-Based
SaaS platform accessible anywhere

CANDDIE Platform Workflow

Automated process composed of 3 stages and 10 steps, from protein input to final analysis

STAGE 1: Drug Design Preparation
1
Protein Selection
Input PDB file or UniProt ID
2
Structure Ready
AlphaFold structure optimization and validation
3
Find Binding Site
Automatic active site detection and definition
STAGE 2: MD + Binding Analysis
4
Equilibration
Automatic system stabilization execution
5
Ligand Bound MD
Bound state Molecular Dynamics
6
Ligand X Structure MD
Unbound state Molecular Dynamics
7
Binding Affinity Calculation
BAR/MBAR-based ΔG prediction
STAGE 3: Analysis Result Visualization
8
Binding Pose Structure
3D visualization and structural analysis
9
BARon
Detailed binding affinity analysis
10
Allopiper
Signal transduction pathway prediction

Final Output Results

Binding Affinity
Quantitative ΔG value
Interaction Map
Key binding residues
Structural Stability
RMSD/RMSF analysis
Signaling Pathway
Allopiper prediction

CANDDIE Platform UI Overview

Provides an intuitive UI for users to clearly track the results of each step in the platform workflow

Input Stage
Input protein structure and ligand information
Step 1: Protein Preparation
Protein structure preparation and optimization
Step 2: SitePrep
Binding site detection and preparation
Step 3: SimRunner-EQ
System equilibration simulation
Step 4: SimRunner-PR
Production MD simulation and binding affinity calculation

Automatically executes the production MD simulation on the equilibrated system, generating trajectories for the bound and unbound states of the ligand.

  • → Parallel simulation of bound/unbound states
  • → Calculation of binding free energy (ΔG) using BAR/MBAR algorithms
  • → Automatic trajectory data storage and preparation for analysis

Applicable to Various Molecular Types

The CANDDIE Platform Service supports binding affinity prediction for various therapeutic modalities.

Antibody

Antibody Therapeutics

Chemical

Small Molecule Compounds

Peptide

Peptides

Affibody

Affibodies

Optimized Specifically for GPCRs

The CANDDIE Platform Service is equipped with optimized algorithms for membrane proteins, especially GPCR targets. It provides GPCR-specific technologies such as optimal biomembrane formation using InflateGro, distance restraints to preserve the native structure, and segmented production runs.

Increase Your Drug Development Success Rate
with the CANDDIE Platform Service

⚡

Rapid Prediction

Accurately calculates the binding affinity of GPCR systems in approximately 4 days or less.

🎯

High Accuracy

Provides validated prediction performance through a high correlation coefficient (R2 > 0.7) with experimental data.

🔬

Scientific Reliability

Validated through over 10 years of GPCR research and numerous SCI-level publications.

The CANDDIE Platform Service raises the initial design standard, lowering the probability of failure in subsequent research stages, and enabling companies to allocate R&D resources more strategically.

CANDDIE Reference Papers

QM
Oxidative denitrogenation of liquid fuel over W2N@carbon catalyst derived from a phosphotungstinic acid encapsulated metal-azolate framework
Appl. Catal. B: Environ., 2021 | IF 22
Research involving Kim et al.
 CADD
Identification of ACK1 Inhibitors as Anticancer Agents by using Computer-Aided Drug Designing
J. Mol. Struct., 2021 | IF 4.7
Research involving Kim et al.
 MD
IOX1 activity as sepsis therapy and an antibiotic against multidrug-resistant bacteria
Sci. Rep., 2021 | IF 3.9
Research involving Kim et al.
 QM
Optimization of Three State Conical Intersections by Adaptive Penalty Function Algorithm in Connection with the MRSF-TDDFT Method
J. Phys. Chem. A, 2021 | IF 3
Baek et al.
 QM
How neutral nitrogen-containing compounds are oxidized in oxidative-denitrogenation of liquid fuel with TiO2@carbon
Phys. Chem. Chem. Phys., 2021 | IF 2.9
Baek et al.
 CADD
In Silico Study Identified Methotrexate Analog as Potential Inhibitor of Drug Resistant Human Dihydrofolate Reductase for Cancer Therapeutics
Molecules, 2020 | IF 4.6
Research involving Kim et al.
 QM
Entangled iodine and hydrogen peroxide formation in ice
Phys. Chem. Chem. Phys., 2020 | IF 2.9
Baek et al.
 CADD
Computational Simulations Identify Pyrrolidine-2,3-Dione Derivatives as Novel Inhibitors of Cdk5/p25 Complex to Attenuate Alzheimer's Pathology
J. Clin. Med., 2019 | IF 2.9
Kim et al.
 GPCR
How do branched detergents stabilize GPCRs in micelles?
Biochemistry, 2020 | IF 2.6
Lee et al.
 GPCR
Activation Microswitches in Adenosine Receptor A2A Function as Rheostats in the Cell Membrane
Biochemistry, 2020 | IF 2.6
Research involving Lee et al.
 Kinase
Kaempferol targeting on the fibroblast growth factor receptor 3-ribosomal S6 kinase 2 signaling axis prevents the development of rheumatoid arthritis
Cell Death & Disease, 2018 | IF 9.6
Research involving Lee et al.
 MD
One-Dimensional Projection of Collective Variables for Effective Sampling of Complex Chemical Reaction Coordinates
J. Chem. Theory Comput., 2018 | IF 5.5
Baek et al.
 GPCR
Identifying functional hotspot residues for biased ligand design in GPCRs
Mol. Pharmacol., 2018 | IF 3.0
Research involving Lee et al.
 Kinase
Bitopic inhibition of ATP and substrate binding in Ser/Thr kinases through a conserved allosteric mechanism
Biochemistry, 2018 | IF 2.6
Research involving Lee et al.
 MD
Sampling long timescale protein motions: OSRW simulation of active site loop conformational free energies in formyl-CoA:Oxalate CoA transferase
J. Am. Chem. Soc., 2010 | IF 15.6
Lee et al.