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CANDDIE Platform - Atomatrix
PLATFORM

CANDDIE Platform Service

Cloud-based drug design SaaS platform launching in 2026.
Revolutionizing drug development with fully automated workflows accessible to everyone.

Next-Generation Cloud-Based
Drug Design Platform

The CANDDIE Platform Service, spanning from AlphaFold-based modeling to BARon/Allopiper, is a fully automated simulation-based CADD platform usable by anyone without complex computational chemistry expertise.

Core Values of CANDDIE Platform

CANDDIE: Computational Automation for New Drug Discovery with Intelligent Experimentation

Accessibility
Intuitive interface usable even by non-CADD specialists
Full Automation
Complete workflow automation requiring no specialized knowledge
Cloud-Based
SaaS platform accessible from anywhere
CANDDIE Platform Features
Integrates multiple in silico modules into packaged workflows for easy experimentation without complex setup
Provides recommended templates and auto-optimized parameter settings for non-experts
Supports flexible parameter adjustment for expert users
Implements precision molecular dynamics (MD) simulations capable of replacing actual experiments with dozens of built-in automated analysis tools
Automatically analyzes and visualizes complex MD data for intuitive utilization
Provides fully automated analysis environment from basic analysis to advanced tools like BARon and Allopiper

CANDDIE Platform Workflow

Automated process in 3 stages and 10 steps from protein input to final analysis

STAGE 1: Drug Design Preparation
1
Protein Selection
PDB file or UniProt ID input
2
Structure Preparation
AlphaFold structure optimization & validation
3
Binding Site Detection
Automatic active site search & definition
STAGE 2: MD + Binding Analysis
4
Equilibration
Automatic system stabilization
5
Ligand-Bound MD
Bound state molecular dynamics
6
Ligand-Free MD
Unbound state molecular dynamics
7
Affinity Calculation
BAR/MBAR-based ΔG prediction
STAGE 3: Analysis & Visualization
8
Binding Pose Structure
3D visualization & 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
Signal Pathway
Allopiper prediction

CANDDIE Platform UI Overview

UI providing intuitive visualization of step-by-step workflow progress

Input Stage
Protein structure and ligand information input
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 production MD simulation on equilibrated systems, generating trajectories for both ligand-bound and ligand-free states.

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

Applicable to Diverse Molecular Types

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

Antibody

Antibody therapeutics

Chemical

Small molecule compounds

Peptide

Peptides

Affibody

Affibodies

Especially Optimized for GPCRs

CANDDIE Platform Service is equipped with algorithms optimized for membrane proteins, especially GPCR targets. It provides GPCR-specialized technologies including optimal biomembrane formation using InflateGro, distance restraints for preserving native structure, and detailed production protocols.

Increase Your Drug Development
Success Rate with CANDDIE Platform Service

⚡

Fast Prediction

Accurately calculates GPCR system binding affinity within approximately 4 days.

🎯

High Accuracy

Provides validated prediction performance with strong correlation (R² > 0.7) to experimental data.

🔬

Scientific Reliability

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

CANDDIE Platform Service raises the baseline for initial design, reducing failure probability in subsequent research stages and making your R&D resource allocation more strategic.

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.