Structure-based Target Prediction

At CD ComputaBio, we leverage advanced AI methodologies to provide comprehensive structure-based target prediction services. These services are indispensable for drug discovery and development, enabling researchers to identify potential drug targets with high precision and efficiency. By utilizing structural information and bioinformatics tools, we ensure that our clients can streamline their research processes, reduce costs, and improve their chances of success in bringing new therapeutics to market.

Our Services

At CD ComputaBio, we utilize advanced AI techniques to deliver thorough structure-based target prediction services. These services are essential for drug discovery and development, allowing researchers to identify potential drug targets with high accuracy and efficiency.

Structure alignment and homology modeling

Structure Alignment and Homology Modeling

Our team uses structure alignment and homology modeling to analyze evolutionary relationships and predict unknown protein structures.

Sequence Alignment - To identify conserved regions across related structures.
3D Structure Prediction - Generate high-quality 3D models using templates from protein databases.

Predicting binding sites on target proteins

Binding Site Prediction

Predicting binding sites on target proteins is crucial for understanding potential interactions. Our service provides:

Computational Algorithms - Utilizing various algorithms to identify and characterize binding pockets.
Visualization Tools - Providing interactive models for easy interpretation.

Flexible docking

Protein-Ligand Docking Simulation

Our protein-ligand docking simulation service allows for the visualization of how small molecules interact with target proteins.

Flexible Docking - Account for the dynamic nature of proteins during ligand binding.
Virtual Screening - Rapidly evaluate large compound libraries to identify potential lead compounds.

Molecular dynamics

Molecular Dynamics Simulations

We offer detailed molecular dynamics simulations to study the behavior of proteins and their interactions with ligands over time. Our approach includes:

Enhanced Sampling - Use advanced techniques to explore protein conformational spaces.
Free Energy Calculations - Determining the binding affinities of ligands to proteins.

Analysis Methods

Reinforcement Learning (RL)

Q-Learning
Deep Q-Networks (DQN)
Policy Gradients
Actor-Critic Methods
Long Short-Term Memory (LSTM)

Tokenization

Part-of-Speech Tagging
Named Entity Recognition
Sentiment Analysis
Machine Translation
Computer Vision

Machine Learning (ML)

Supervised Learning
Unsupervised Learning
Reinforcement Learning
Semi-Supervised Learning
Transfer Learning

Sample Requirements

Chemical Structure Protein Data

Format - PDB (Protein Data Bank) format.
Quality - Ensure that proteins are crystallized or have NMR data when available.
Conformation - Provide multiple conformations if available to account for flexibility.

Ligand Information

SMILES or 3D Structures - Provide the chemical structure in SMILES format or as 3D files (preferably MOL2 or PDB).
Characterization - Include information on the ligand's functional groups and previous biological activity data, if applicable.

Our Capabilities

Replica Exchange Molecular Dynamics (REMD)

Lipid Molecular Dynamics

Membrane Protein Molecular Dynamics

Our Advantages

Timely updates throughout the project.
Rapid turnaround of results without compromising quality.
Leading-edge methodologies in AI and machine learning.
Continuous updates on advancements in structural biology.

At CD ComputaBio, we specialize in providing advanced SBTP services that accelerate the drug discovery process by offering insights into molecular interactions and affinities. Our target identification service involves utilizing cutting-edge algorithms to predict potential biomolecular targets for your compounds. We analyze existing structural data from databases to establish a shortlist of targets that may interact with your molecule of interest. If you are interested in our services or have any questions, please feel free to contact us.

Services

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