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Computer Graphics, Homology Modeling, and Bioinformatics

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Creative Biolabs offers customers different computational protein design (CPD) techniques for protein engineering, including those of computer graphics, homology modeling and bioinformatics.

Computer graphics, homology modeling and bioinformatics are the three major methods of CPD techniques employed for protein engineering. They are aimed at combining physical chemistry models governing amino acids and protein structures with advanced computational algorithms. These methods play an important role for protein structure prediction, protein sequences redesign, new function domain identification and characterization. They can perform sequence similarity searches, multiple sequence alignments, secondary structure prediction, solvent accessibility prediction, automatic protein fold recognition, constructing three-dimensional models to atomic detail and model validation. The rational, structure-based CPD has been applied to a wide variety of proteins and enzymes of scientific and industrial interests.

Computer Graphics, Homology Modeling and Bioinformatics Figure 1. Schematic representation of the homology model of Atractaspis 3FTx. (Yves Terret et al., 2013)

One of the most attractive benefits to engineer protein in silico is the cost efficiency. Since proteins can have their models simulated with the incorporation of different mutations, conventional plasmid construction, protein synthesis and crystallization are not required, thus saving a huge amount of time and effort. What is more, big libraries (i.e., those of millions of ligands) can be screened within a timeframe of days or weeks, providing valuable insight into possible substrate preference and mechanism of action. Subsequently, the dynamics of molecular interaction between a protein and the ligand can also be simulated using appropriate software, though the computational cost can be at times quite high.

However, in silico methods have to be used with caution and interpreted by experienced personnel. Due to the fact that computational prediction/simulation can not be totally conclusive, experimental confirmation is needed to ensure the acceptance of the in silico output.

We can help your protein engineering projects with suitable computation protein design techniques. Given the primary sequence, we can identify critical residues for the structure and function. Followed by that, amino acid substitution for desired properties will be carried out, and corresponding models built computationally (i.e., by homologous modeling). Lastly, designed properties can be confirmed by docking or molecular dynamics modeling methods. If possible and with your approval, we can proceed with the synthesis of proteins/peptides computationally designed, and biochemical/biophysical studies will be used to experimentally confirm the designed properties.

List of References:
1. Yves Terrat, Kartik Sunagar: Atractaspis aterrima Toxins. The First Insight into the Molecular Evolution of Venom in Side-Stabbers. Toxins 2013, 5(11), 1948-1964.

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