At CD ComputaBio, we provide our clients with superior Computer Aided Drug Design (CADD) solutions. One of our top-tier specialties lies in our protein modeling services. Understanding and modeling the three-dimensional structure of proteins is a crucial aspect in current computational biology and drug discovery processes. At CD ComputaBio, we possess an extensive track record of fulfilling our clients' requirements in the field of protein modeling.
Introduction of Protein Modeling Service
Protein modeling is a critical component of drug discovery that utilizes computational techniques to predict and analyze the structure and function of proteins. By simulating the three-dimensional structure of proteins and their interactions with ligands, protein modeling plays a crucial role in rational drug design, lead optimization, and understanding biological processes at the molecular level.
Figure 1. Protein Modeling.( Liu F,et al. 2022)
Our Service
Membrane Protein Modeling Service
Membrane proteins play various essential roles, which include signal transduction, transporting molecules across the membrane, cell adhesion, and more. Our membrane protein modeling service techniques utilize both homology modeling and ab initio modeling (when crystal structures are unavailable).
Receptor Protein Modeling Services
Receptor proteins play a pivotal role in signal transduction pathways. By understanding the manner in which these proteins interact with ligands, we can gain important insight into drug design and development. Our service provides accurate receptor protein modeling based on experimentally solved receptor-ligand complexes.
Antibody Protein Modeling Service
At CD ComputaBio, we recognize the role of antibodies in the field of therapeutic development and diagnostics. Our antibody protein modeling service contributes an accurate understanding of the structure-function relationship of antibodies. Our service includes both the sequence and structural alignment of the variable and constant regions, heavy and light chains, and the H3 loop, essential in antibody-antigen binding.
G Protein-coupled Receptor Modeling Service
G protein-coupled receptors (GPCRs) are an integral part of signal transduction pathways. As the target of a large proportion of drugs currently on the market, accurate structural representation of GPCRs is essential in drug discovery. Our GPCR modeling service generate detailed models of GPCRs that allow clients to study dynamic events like ligand binding, receptor activation, G protein coupling, and others.
The Process of Protein Modeling Service
Project Initiation - We work closely with our clients to understand their specific requirements, project goals, and timelines, ensuring a customized approach to meet their needs effectively.
Data Collection and Preparation - We gather relevant biological data, including protein sequences, crystal structures, and ligand information, preparing the input data for modeling and simulation studies.
Modeling and Simulation - Our team employs advanced computational methods, such as homology modeling, molecular dynamics simulations, and quantum mechanical calculations, to generate detailed models of protein structures and interactions.
Analysis and Interpretation - We carefully analyze the results of our simulations, extracting key insights and actionable information to guide further experimental studies and decision-making in the drug discovery process.
Reporting and Communication - We provide comprehensive reports summarizing our findings, methodologies, and recommendations, ensuring transparency and clear communication with our clients throughout the project.
Approach to Protein Modeling Service
Homology Modeling
Leveraging known protein structures as templates, we predict the structure of target proteins with high accuracy, enabling the study of protein-ligand interactions and molecular mechanisms.
Molecular Docking
Through molecular docking simulations, we explore the binding modes of ligands to target proteins, guiding the design of potent and selective drug candidates with optimal binding affinities.
Quantum Mechanical
We employ quantum mechanical calculations to study the electronic properties and energetics of protein-ligand complexes, providing detailed insights into molecular recognition and binding mechanisms.
Advantages of Our Services
We tailor our services to meet the specific requirements and objectives of each client, ensuring personalized support.
We leverage cutting-edge algorithms and software tools to ensure accurate and reliable pharmacophore modeling.
Our services offer cost-effective solutions for drug discovery, maximizing value for our clients' research endeavors.
CD ComputaBio has been at the forefront of providing predictive modeling strategies in the drug discovery pipeline. Leveraging our expertise in computational biology and bioinformatics, we provide advanced solutions that enhance our client's project success rate. Our team of experienced computational biologists, combined with our robust technological infrastructure, allows us to serve varied project requirements effectively and efficiently.
Reference:
- Liu F, Tian M. Study on the mechanism of Qiju Dihuang pill in the treatment of ophthalmic diseases based on systems pharmacology. Medicine, 2022, 101(31): e30033.
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