Knowledge-Based Protein Design Services

Creative BioMart's extensive experience in predicting protein sequences and protein design that fold into specific native 3D structures enables us to provide knowledge-based protein design services to accelerate your projects. This service can help us guide the formation of desired 3D structures by using knowledge-based methods to engineer favorable interactions (local secondary structure and long-range tertiary interactions) into the design of linear amino groups, in the design of drugs, herbicides or pesticides, antigens in vaccine design and new molecules in protein engineering are of great value.

A key problem in protein design is to determine the rules for predicting amino acid sequences that will stably fold into a specific target three-dimensional structure. Prediction of protein tertiary structure can be performed using knowledge-based methods. This depends on the identification of similarities in secondary structure, motifs, domains or ligand interactions between the protein to be modeled and a protein of known three-dimensional structure. Knowledge-based approaches provide a shortcut to rational protein design by predicting site-specific potential, learning from protein structure and sequence databases. This technique has been demonstrated to help in both reducing the combinatorial complexity of searching sequence space and refining the scoring functions. In addition, it has been used to design a variety of constructs: such as transmembrane-bound peptides, surface tissue peptide superstructures, and protein crystals.

Fig 1. Schematic representation of the protein sequence-structure-function problem. (Poole A M, et al., 2006)

Knowledge based on protein secondary and tertiary structure is a key element of almost all protein design algorithms. Focused on knowledge-based protein research, Creative BioMart provides critical information on the global topology of amino acid interactions in native proteins, enabling modification of existing protein functions, redesign of native protein folds, and complete design of non-native protein folds. As with sequence-based information, knowledge-based methods influence the design process by correcting defects in interatomic energy functions and limiting the complexity of the search sequence space. Features of knowledge-based protein design include:

• Rotational molecular library deduced from known protein structures.
• Binary pattern.
• Calculate the buried depth area of residues or residue pairs and establish an implicit solvation model.
• Secondary structure tendencies.
• The protein database is a library of small fragments of protein sequences related to the main chain structure.

Creative BioMart has successfully applied a knowledge-based approach to tune the parameters of the energy function to achieve optimal correlation between the computational and experimentally observed properties of the designed sequence. Our complete redesign of the following proteins is popular with customers around the world:

• Knowledge-Based Secondary Structure Self-Assembly Design
• Knowledge-Based Single-Chain Protein Design
• Knowledge-Based Preorganized Structure Design
• Knowledge-Based Novel Protein Folds Design
• Knowledge-Based Membrane Protein Design

If you have any special requirements about our knowledge-based protein design services, please feel free to contact us. We are looking forward to working together with your attractive projects.

• In-Silico Pharmacology Services
• Computational Therapeutic Protein Design Services
• Protein Structure Prediction and Assessment Services
• Rotamer Libraries for Molecular Modeling and Design of Proteins