Computational Enzyme Discovery & Mining Services

CD Biosynsis offers integrated Computational Enzyme Discovery & Mining Services, providing a powerful in silico pipeline to identify, characterize, and optimize novel biocatalysts with unparalleled speed and precision. We combine high-throughput genomic and metagenomic database mining with advanced Artificial Intelligence and structural bioinformatics to unlock the vast enzyme diversity hidden in nature and data repositories. Our platform is designed to bypass the limitations of traditional wet-lab screening, enabling the rational identification of enzymes with superior activity, stability, and substrate specificity. This comprehensive computational approach accelerates the entire discovery process, delivering highly promising enzyme candidates ready for experimental validation and industrial application.

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The In Silico Engine for Biocatalyst Innovation

Modern biotechnology demands biocatalysts with non-natural properties, such as tolerance to organic solvents or extreme temperatures. Computational discovery is the most efficient way to meet this demand. Our services unify sequence mining (identifying potential enzyme genes), functional prediction (determining what the enzyme does), and structural modeling (understanding how it works). By using computational filtering, we ensure that experimental resources are focused only on the most promising candidates, dramatically increasing the success rate for finding and developing the next generation of industrial enzymes, making the journey from big data to functional protein seamless and rapid.

Integrated Computational Modules

Sequence Mining & Discovery AI-Driven Function Prediction Structural Modeling & Rational Design

Broad Search of Enzyme Space

Identifying Novel Scaffolds and Gene Families

Enzyme Genome & Database Mining Services

High-throughput screening of genomic, transcriptomic, and metagenomic data to identify and annotate potential enzyme genes based on sequence homology and motif analysis.

Metagenomic Sequence Assembly

Assembly and binning of environmental DNA data to reconstruct complete enzyme pathways from uncultured microbial communities.

Evolutionary Profiling

Phylogenetic analysis to target enzyme variants that display unique evolutionary relationships, often correlating with novel function.

AI and Deep Learning Prediction

Inferring Activity and Properties In Silico

AI-Driven Enzyme Discovery and Function Prediction Services

Utilization of deep learning models to predict enzyme function, catalytic efficiency (kcat/Km), and stability (Tm) directly from the primary sequence data.

Substrate Specificity Prediction

AI algorithms trained on vast reaction databases predict the most likely native and non-native substrates for novel enzymes.

Active Site Identification

Machine learning models accurately locate key catalytic residues and potential binding pockets for initial structural hypotheses.

Structural Modeling and Design Guidance

Precision Engineering Based on 3D Blueprint

Enzyme Structural Bioinformatics and Modeling Services

High-resolution homology modeling, molecular docking, and molecular dynamics simulations to visualize substrate binding and predict mutation effects.

Molecular Dynamics Simulation

Simulating the dynamic behavior of the enzyme-substrate complex to understand conformational changes critical for catalysis and stability.

Rational Mutagenesis Guidance

Providing a prioritized list of amino acid substitutions (rational design) to optimize activity or stability based on structural calculations (ΔΔG prediction).

Computational Discovery and Prioritization Pipeline

An efficient, iterative cycle from Big Data to Biocatalyst Lead.

Data Acquisition & Mining

Function & Property Prediction

Structural Validation & Refinement

Delivery

Project Consultation: Define target function and desired properties.

Enzyme Genome & Database Mining Services: Identify thousands of potential candidates from sequence data.

AI-Driven Enzyme Discovery and Function Prediction Services: Use deep learning to predict kcat/Km, stability, and substrate specificity.

Candidate Filtering: Shortlist candidates based on predictive scoring and novelty.

Enzyme Structural Bioinformatics and Modeling Services: Model 3D structure, dock substrate, and identify mutation sites for optimization.

Mutagenesis Plan: Generate a clear, prioritized list of sequences for wet-lab synthesis.

Codon Optimization: Sequence refinement for expression host.
Delivery: Final gene sequences, detailed reports, 3D structure models, and mutation strategy.
Optional: Gene Synthesis and Cloning into expression vector.

Accelerated Discovery Through Computational Synergy

Unmatched Efficiency

Replaces years of wet-lab screening with rapid, high-throughput in silico analysis.

High Predictive Accuracy

AI and structural models provide high-confidence predictions of function, stability, and mutation effects.

Deep Structural Insight

Molecular dynamics and modeling reveal atomic-level details of catalysis for true rational design.

Access to Novelty

Systematically unlocks enzyme diversity from vast environmental metagenomes (the "dark matter").

Client Testimonials on Computational Enzyme Discovery

"The integrated computational service—from mining to structural modeling—provided a perfect set of high-potential candidates that we couldn't have found through traditional methods."

Dr. Samuel Liu, R&D Director

"The AI-Driven prediction of thermal stability was a game-changer. We immediately focused our wet-lab resources on the most robust variants, saving months of screening time."

Ms. Janet Chen, Lead Bioengineer

"The structural bioinformatics report was incredibly detailed, giving us a clear map of which residues to mutate for enhanced substrate specificity, leading to a successful rational design."

Dr. Kenji Tanaka, Principal Scientist

"We used the Enzyme Genome & Database Mining Service to explore novel lipases. The prioritized list contained a truly unique scaffold that showed exceptional activity on a non-native substrate."

Mr. Alex Johnson, Research Manager

"This computational pipeline allowed us to move directly to targeted optimization. The predicted mutations for kcat improvement were validated experimentally with very high fidelity."

Dr. Maria Gomez, Group Leader

FAQs about Computational Enzyme Discovery & Mining Services

Still have questions?

How accurate are the AI-driven predictions?

Our deep learning models, part of the AI-Driven Enzyme Discovery and Function Prediction Services, are trained on extensive, high-quality kinetic and structural datasets, providing high-confidence predictions for properties like kcat/Km and stability, significantly reducing false positives in wet-lab validation.

Can you find enzymes from non-culturable organisms?

Yes. A core component of our service, through the Enzyme Genome & Database Mining Services, is the analysis of metagenomic data, allowing us to discover enzymes from environmental samples without the need to culture the source organism.

How does structural modeling aid enzyme engineering?

The Enzyme Structural Bioinformatics and Modeling Services provides the 3D blueprint necessary for rational design. It helps identify specific residues for mutation to enhance stability or alter substrate binding, guiding highly targeted and effective engineering campaigns.

What is the final deliverable?

The final deliverables include a detailed bioinformatics report, high-confidence enzyme gene sequences (codon-optimized for your host), 3D structural models, and a prioritized strategy for subsequent wet-lab expression and optimization.

How much does Metabolic Engineering services cost?

The cost of Metabolic Engineering services depends on the project scope, complexity of the target compound, the host organism chosen, and the required yield optimization. We provide customized quotes after a detailed discussion of your specific research objectives.

Do your engineered strains meet regulatory standards?

We adhere to high quality control standards in all strain construction and optimization processes. While we do not handle final regulatory approval, our detailed documentation and compliance with best laboratory practices ensure your engineered strains are prepared for necessary regulatory filings (e.g., GRAS, FDA).

What to look for when selecting the best gene editing service?

We provide various gene editing services such as CRISPR-sgRNA library generation, stable transformation cell line generation, gene knockout cell line generation, and gene point mutation cell line generation. Users are free to select the type of service that suits their research.

Does gene editing allow customisability?

Yes, we offer very customised gene editing solutions such as AAV vector capsid directed evolution, mRNA vector gene delivery, library creation, promoter evolution and screening, etc.

What is the process for keeping data private and confidential?

We adhere to the data privacy policy completely, and all customer data and experimental data are kept confidential.