Molecular Docking Services

High-throughput screening, precise scoring, and expert analysis. We empower pharmaceutical companies, biotechs, and academic institutions to accelerate lead discovery and optimization.

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# B7-H3 (CD276) # GPRC5D # KRAS (G12D/G12V) # Protein-Ligand Interaction # PPI Analysis # Binding Free Energy # GIPR # GLP-1 RA # PD-L1 # GCG-R # GLP-1 # BTK # B7-H3 (CD276) # GPRC5D # KRAS (G12D/G12V) # Protein-Ligand Interaction # PPI Analysis # Binding Free Energy # GIPR # GLP-1 RA # PD-L1 # GCG-R # GLP-1 # BTK

What Is Molecular Docking?

Molecular docking is a pivotal computational technique that predicts the preferred orientation of a ligand to a receptor when bound to each other to form a stable complex. It serves as the cornerstone of structure-based drug design (SBDD).

Receptor-Ligand Interaction: Accurately predicting the binding mode and active site interactions.
Binding Affinity Assessment: Estimating the strength of the association to rank potential drug candidates.

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Application Fields

Core Application Scenarios

Comprehensive solutions covering the full spectrum of drug discovery from macromolecules to small molecules.

Small Molecule Design

Rapid hit identification for challenging targets.

AI-enhanced virtual screening for covalent inhibitors & active hits.
Modeling for PROTACs and molecular glues.
Identifying cryptic pockets for allosteric modulators & PPI Inhibitors.

Enzyme Engineering

Optimizing biocatalysts & therapeutic Enzymes.

Create novel enzymes for specific industrial needs.
Improve the activity, stability, and specificity of existing enzymes.
Prediction of evolutionarily favourable mutations.

Antibody Discovery

AI conjures up potential new antibody drugs.

Precise epitope mapping of binding interfaces.
De novo design and humanization of antibodies.
AI based affinity maturation to optimize potency.

RNA Therapeutics

Targeting the "undruggable" genome.

Small molecule docking to RNA.
Riboswitch & Aptamer modeling.
G-quadruplex interaction analysis and characterization.

Protein Design

AI engine for de novo protein design.

150+ targets explored.
AI-generated purpose-built miniproteins.
Systematically refining designs into novel molecules.

Peptide & Macrocycles

Designing larger molecules for complex targets.

Stapled peptide design.
Cyclic peptide conformational sampling.
Permeability & bioavailability optimization.

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Our Molecular Docking Services

We offer a comprehensive suite of docking simulations, from standard small molecules to complex biologics, empowering your drug discovery with precision and speed.

Protein-Small Molecule Docking

The gold standard for structure-based drug design. We accurately predict the binding mode of small molecule inhibitors within the target binding pocket.

High-Throughput Virtual Screening (HTVS) of massive libraries.
Induced-fit docking to account for receptor flexibility.
Covalent docking for irreversible inhibitors.

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Protein-Protein Docking

Essential for biologics design and understanding signal transduction. We model macromolecular assemblies to reveal interaction interfaces and stability.

Ab initio and template-based complex modeling.
Hot-spot residue analysis and mutation prediction.
Protein-Protein Interaction (PPI) inhibitor design.

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Protein-Peptide Docking

Designing peptide therapeutics requires handling high flexibility. Our specialized protocols model peptide folding and binding simultaneously.

Flexible peptide docking (Global & Local).
Cyclic peptide and stapled peptide modeling.
Peptidomimetic design and optimization.

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Protein-RNA Docking

RNA is a challenging but high-value target. We simulate interactions involving riboswitches, aptamers, and RNA-binding proteins (RBPs).

Protein-RNA complex structure prediction.
Aptamer screening and specificity analysis.
Small molecule docking to RNA targets.

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Antibody-Antigen Docking

Critical for vaccine development and immunotherapy. We characterize the immune interface to optimize antibody affinity and specificity.

Epitope mapping & Paratope prediction.
Affinity maturation via computational design.
Bispecific antibody interface modeling.

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Nucleic Acid Binding

Targeting the genome directly. We analyze the interaction of small molecules, proteins, and peptides with DNA and RNA structures.

Small molecule-DNA intercalation & groove binding.
Transcription Factor (TF) binding site analysis.
Gene editing guide RNA off-target prediction.

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Powered by Proprietary Technology

Advanced computational engines and proprietary algorithms designed to overcome the limitations of traditional docking methods.

BioAI-Dock Deep Learning Engine

Our proprietary hybrid engine combines physics-based scoring with deep neural networks. It learns from millions of protein-ligand crystal structures to predict binding affinity with higher accuracy than traditional force fields, significantly reducing false positives.

TurboAI-Screen High-Throughput System

An ultra-fast virtual screening architecture optimized for our GPU clusters. TurboAI-Screen allows for the concurrent docking of billions of compounds from the Zinc and disease databases, completing campaigns in days rather than months without compromising sampling precision.

FlexAI-Fit Dynamic Sampling

Addresses the "rigid receptor" problem by integrating molecular dynamics snapshots into the docking process. FlexAI-Fit accounts for induced-fit effects and side-chain rotamers, crucial for cryptic pockets and protein-protein interaction (PPI) inhibition targets.

FragAI-Grow Fragment Evolution

A proprietary algorithm for fragment-based drug design (FBDD). It automatically identifies seed fragments within the binding pocket and "grows" them into drug-like molecules using a vast library of synthetically feasible chemical building blocks.

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Seamless Collaboration Process

From initial consultation to final data delivery, our streamlined workflow ensures transparency, efficiency, and scientific rigor.

1. Consultation

We analyze your target and goals to define the scope and select the optimal docking strategy.

2. Strategy Design

Our scientists curate libraries, prepare protein structures, and set up custom docking protocols.

3. Execution

High-performance computing clusters run the simulations, followed by expert manual inspection.

4. Delivery

You receive a comprehensive report, raw data files, and 3D visualization sessions.

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Trusted by Researchers Worldwide

“The BioAI-Dock engine significantly accelerated our lead discovery timeline. We identified three potent hits from a library of millions in just two weeks. The accuracy of the binding mode prediction was confirmed by our crystal structures.”

— Dr. Sarah Jenkins

Principal Scientist

“CD ComputaBio's expertise in handling flexible peptide docking was crucial for our project. Their report was incredibly detailed, providing not just the data but the mechanistic insights we needed to publish our findings.”

— Prof. Michael Chen

Professor of Chemistry

“Professional, fast, and secure. We needed to outsource covalent docking for a challenging target, and their team handled the warhead reactivity analysis perfectly. Highly recommended for biotech startups seeking efficiency and expertise.”

— Elena Rodriguez

CSO

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Supported Disease Research Areas

Oncology Anti-Infectives Neurology (Alzheimer's/Parkinson's) Metabolic Diseases Autoimmune Disorders Cardiovascular Diseases Rare Diseases & Orphan Drugs Epigenetics Pain & Inflammation

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