Enzyme Active Site Prediction & Analysis Service

Enzyme Active Site Prediction & Analysis is a critical computational service focused on identifying the specific pocket or region within a protein structure where the catalytic reaction occurs and substrate binding takes place. By utilizing advanced geometric and physico-chemical algorithms, we accurately map the active site, identify key catalytic residues, and characterize the pocket's volume, shape, and polarity. This deep structural insight is essential for rational drug design, targeted enzyme engineering, and understanding the precise molecular mechanism of an enzyme's function.

CD Biosynsis offers a dedicated CRO service for Active Site Prediction and Analysis, leveraging high-resolution protein structures (PDB, Cryo-EM, or AlphaFold models). Our platform integrates ligand-binding simulation, molecular dynamics (MD) analysis, and evolutionary conservation scoring to provide the most reliable identification of functional regions. We deliver comprehensive data on the active site environment, including potential protonation states, water networks, and druggability scores. This detailed analysis transforms raw structural data into actionable targets for mutation studies, inhibitor design, and biocatalyst optimization.

Highlights

Our platform provides comprehensive characterization of the active site, ensuring high confidence in downstream experimental design.

• Accurate Pocket Identification: Utilize geometric and energy-based algorithms to precisely delineate the boundaries of the catalytic and binding pockets.
• Catalytic Residue Prediction: Identify the specific amino acid residues crucial for substrate binding, proton transfer, and transition state stabilization.
• Druggability and Allosteric Site Scoring: Assess the potential of a pocket to bind small molecules and identify secondary, allosteric regulatory sites.
• Dynamic Analysis: Employ Molecular Dynamics to study how the active site changes shape upon substrate entry or during catalysis (induced fit).

Applications

Active site analysis is a foundational step for targeted intervention and engineering across biotechnology and medicine:

Rational Drug Design

Targeted design of inhibitors or modulators that fit precisely into the enzyme's active site or predicted allosteric pockets.

Directed Evolution Guidance

Selecting key residues surrounding the active site for focused site-directed mutagenesis to alter substrate specificity or efficiency.

Functional Annotation of Novel Enzymes

Inferring the likely substrate class (e.g., protease, kinase) of an uncharacterized enzyme based on active site topology and residue composition.

Mechanistic Insight for Biocatalysis

Detailed analysis of protonation states and binding geometry to understand and optimize reaction mechanisms for industrial use.

Platform

Our Active Site Prediction platform integrates structural bioinformatics, molecular modeling, and simulation tools.

Geometric Pocket Detection

Algorithms that search the protein surface for concave regions using spherical probes, regardless of bound ligand status (apo-structure analysis).

Evolutionary Conservation Scoring

Using phylogenetic analysis to identify highly conserved surface residues, which often indicate functional or catalytic importance.

Ligand Docking and Simulation

Utilizing known or proposed substrates to guide the prediction of the binding pose and confirm the location of the active site.

Electrostatic and pKa Analysis

Calculation of the electrostatic potential surface and prediction of the pKa values of key active site residues under physiological conditions.

Pocket Volume and Flexibility Metrics

Quantitative assessment of the pocket size, shape, and inherent flexibility (via MD) to determine substrate promiscuity and selectivity.

Workflow

Our Active Site Prediction and Analysis service follows a multi-faceted approach, combining structural and evolutionary data for high-confidence results:

• Structural Input and Preparation: Receive the 3D protein structure. Clean, optimize, and refine the model (including adding hydrogens and assigning correct formal charges).
• Initial Pocket Identification: Employ multiple geometric and energy-based algorithms to identify all potential surface cavities.
• Functional Filtering and Scoring: Filter the identified pockets using conservation scores, evolutionary data, and comparison to known catalytic mechanisms to select the most probable active site.
• Detailed Active Site Characterization: Analyze the confirmed site for volume, shape, polarity, key residue pKa, and potential water networks. Perform substrate docking if required.
• Reporting and Visualization: Deliver a comprehensive report including 3D coordinates of the predicted active site residues, druggability score, and high-resolution visualizations for targeted experimental design.

CD Biosynsis guarantees a high level of detail and accuracy, providing direct guidance for your enzyme engineering or drug discovery projects. Every project includes:

• Confirmed Active Site Coordinates: PDB file excerpts marking the key catalytic and binding residues.
• Druggability Score: A quantitative metric assessing the likelihood of the pocket binding a small-molecule ligand.
• Mutagenesis Target List: A prioritized list of residues suitable for targeted mutation to alter function or specificity.
• Detailed Mechanistic Hypotheses: Suggested roles for key active site residues in the catalytic mechanism.