Overview
CD ComputaBio is a pioneering company in the fields of computational and structural biology. We specialize in
computer-aided drug design and De Novo Protein Design, key technologies that help accelerate drug discovery and
design. One of our sought-after services is Protein Conformation Prediction which is a cornerstone of structural
biology and plays a critical role in understanding the properties, functions, and interactions of proteins.
Background
Protein conformation prediction is a fundamental aspect of bioinformatics, aimed at predicting the spatial structure
of a protein from its amino acid sequence. This service is indispensable in research for predicting protein-ligand
interactions, drug design, and studying protein-protein interactions.
Our Algorithm
Structure-Based Virtual Screening
Harnessing the predictive power of Protein Conformation Prediction, our structure-based virtual screening
services enable swift and comprehensive identification of potential drug candidates. By scrutinizing the
conformational space of target proteins, we facilitate the efficient screening of diverse compound libraries,
pinpointing molecules with the highest likelihood of binding and therapeutic relevance.
Ligand-Binding Affinity Prediction
Understanding the nuances of protein-ligand interactions is pivotal in drug design. Our expertise in accurately
predicting ligand-binding affinities empowers our partners to prioritize and optimize their lead compounds with
unparalleled precision. Through in-depth analysis of conformational dynamics and molecular interactions, we
enable informed decision-making in the pursuit of potent and selective drugs.
Protein Engineering and Design
Our services encompass the design and modification of proteins for specific applications, underpinned by a
profound understanding of protein structure and dynamics. Whether it involves optimizing enzyme activity,
designing novel biologics, or engineering proteins with tailored functionalities, our computational approach
facilitates groundbreaking advancements in diverse fields.
Our Service
|
Service
|
Descriptions |
| Ab Initio Modeling |
We focus on predicting protein folding without the need for homologous sequences. |
| Homology Modeling |
Using previously solved structures to predict the fold of the target protein. |
| Threading or Fold Recognition |
We compare the primary sequence of the unknown structure directly with the known structures. |
| Protein Conformation Prediction |
We utilize state-of-the-art algorithms to predict the 3D structures of proteins, enabling precise modeling for
various applications in drug design, protein engineering, and structural biology. |
| Dynamic Simulations |
Our services extend to molecular dynamics simulations, offering in-depth analysis of protein behaviors and
interactions to guide drug design and development. |
| Structure Validation |
We offer thorough validation of predicted protein structures, providing crucial insights into their stability
and accuracy. |
BioEmu-based Protein Conformation Prediction
CD ComputaBio has utinized a new open-source artificial intelligence (AI) tool, BioEmu, to enable accurate prediction of protein dynamic conformations. BioEmu (short for Biomolecular Emulator) is a deep learning model developed by Microsoft Research (AI for Science).
Key Capabilities
BioEmu emulates the equilibrium ensemble of protein structures — i.e. the set of conformations (shapes) that a protein naturally samples under physiological conditions
- Generate thousands of statistically independent protein conformations per hour on a single GPU.
- Use a large dataset combining static protein structures, molecular dynamics (MD) simulation data (over 200 milliseconds of total MD simulation) and protein stability experimental measurements to train model.
-
Capture functional motions such as:
- cryptic (hidden) pocket formation
- local or partial unfolding of regions
- large-scale domain rearrangements
- Predict relative free energies among conformations with ≈ 1 kcal/mol accuracy compared to experimental/MD data.
Sample Requirements
To utilize our protein conformation prediction services, clients are required to provide the amino acid sequence of
the protein of interest. Additionally, any relevant information on ligands, cofactors, or specific functional domains
would be beneficial to enhance the accuracy of the predictions.
Results Delivery
Upon completion of the protein conformation prediction process, clients receive detailed reports containing the
predicted 3D structures, along with comprehensive analyses outlining the stability, interactions, and potential
binding sites. We ensure timely delivery of results, enabling clients to efficiently integrate our findings into their
research and development processes.
Our Advantages
Cutting-edge Technology
We leverage the latest advancements in computational algorithms and bioinformatics, ensuring that our
predictions are at the forefront of accuracy and reliability.
Interdisciplinary Expertise
Our team comprises experts with diverse backgrounds in computational biology, bioinformatics, and drug
discovery, allowing us to offer comprehensive insights and solutions across various domains of research and
development.
Customization
We understand that every project is unique, and thus, we tailor our services to meet the specific needs of each
client, providing personalized solutions that align with their research goals.
CD ComputaBio is committed to providing efficient and reliable services to facilitate protein research. Our Protein
Conformation Prediction Service is a significant part of our endeavor to forward biotechnological advancements and
accelerate drug discovery and design. The bespoke combination of leading-edge computational tools, professional
knowledge, and unparalleled customer service offers our clients an unmatched experience and meaningful insights.
For research use only. Not intended for any clinical use.
