Protein Structure Modeling Service
Protein structure modeling is a group of computational method used to describe the three-dimensional structure of a protein or protein complex. CD ComputaBio offers a wide range of protein structure modeling services to address the lack of protein crystal structures during drug discovery. Our structure modeling services cover a wide range of protein types.
Introduction to Protein Structure Modeling
Protein structure modeling is a crucial method in modern molecular biology, aiming to predict the 3D structure of proteins based on their amino acid sequences. Template-based protein modeling methods include threading modeling and comparative modeling. This protein structure modeling method relies on detectable similarity between a large portion of the modeled sequence and at least one known structure. Proteins from the same family are more conserved in their amino acid sequence. Therefore, if similarities between two proteins in the same family can be detected at the sequence level, it is often possible to assume that the structures are similar and model accordingly.
Fig 1. Protein complex structure prediction and evaluation pipeline. (Chen X, et al., 2024)
Computational Tools for Protein Structure Modeling
| Tool |
Description |
| CPH-MODELS |
CPHmodels-3.0 is a web server for predicting protein three-dimensional structures using single-template homology modeling. |
| SWISSMODEL |
SWISSMODEL is a fully automated protein structure homology modeling server accessible via the Expasy web server. The server aims to make protein modeling accessible to all life science researchers worldwide. |
| ESyPred3D |
ESyPred3D is an automated homology modeling program that obtains alignments by combining, weighting, and filtering the results of multiple alignment programs. |
| MODELLER |
MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of the sequence to be modeled with known related structures, and MODELLER automatically calculates a model that includes all non-hydrogen atoms. |
Our Services
CD ComputaBio uses computational modeling to predict 3D structure of proteins. We have extensive experience in modeling various proteins. The generated structures are evaluated and can be used for a variety of purposes, such as predicting ligand binding sites. Our services are listed below but are not limited to:
Methods of Protein Structure Modeling
- Homology Modeling
Homology modeling involves using known protein structures (templates) as references to build models for target proteins with similar sequences. CD ComputaBio has a rich protein database, and for proteins with unknown structures, we can search the database for sequences and find proteins with high homology as templates for structure prediction.
- Fold Recognition
Fold recognition is a powerful and versatile method for predicting protein structure, especially for sequences with low similarity to known structures. CD ComputaBio leverages the rich structural data in databases and employs sophisticated alignment and scoring algorithms to provide valuable insights into protein structure and function.
Process of Protein Structure Modeling
- 1Sequence Identification - to search for proteins with known 3D structures that are related to the target sequence
- 2Sequence Alignment - to pick those structures that will be used as templates and align their sequences with the target sequence
- 3Model Building - to build the model for the target sequence given its alignment with the template structures
- 4Model Refinement - to evaluate the model, using a variety of criteria.
CD ComputaBio focuses on protein structure modeling services, using a variety of modeling methods and rich knowledge to provide protein structure modeling solutions. If you are interested in our services or have any questions, please feel free to contact us.
Reference:
- Chen X, Liu J, Park N, et al. A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models[J]. Biomolecules, 2024, 14(5): 574.
* For Research Use Only.
